Table of contents for issues of IEEE\slash ACM Transactions on Computational Biology and Bioinformatics

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Volume 1, Number 1, January, 2004
Volume 1, Number 2, April, 2004
Volume 1, Number 3, July, 2004
Volume 1, Number 4, October, 2004
Volume 2, Number 1, January, 2005
Volume 2, Number 2, April, 2005
Volume 2, Number 3, July, 2005
Volume 2, Number 4, October, 2005
Volume 3, Number 1, January, 2006
Volume 3, Number 2, April, 2006
Volume 3, Number 3, July, 2006
Volume 3, Number 4, October, 2006
Volume 4, Number 1, January, 2007
Volume 4, Number 2, April, 2007
Volume 4, Number 3, July, 2007
Volume 4, Number 4, October, 2007
Volume 5, Number 1, January, 2008
Volume 5, Number 2, April, 2008
Volume 5, Number 3, July, 2008
Volume 5, Number 4, October, 2008
Volume 6, Number 1, January, 2009
Volume 6, Number 2, April, 2009
Volume 6, Number 3, July, 2009
Volume 6, Number 4, October, 2009
Volume 7, Number 1, January, 2010
Volume 7, Number 2, April, 2010
Volume 7, Number 3, July, 2010
Volume 7, Number 4, October, 2010
Volume 8, Number 1, January, 2011
Volume 8, Number 2, March, 2011
Volume 8, Number 3, May / June, 2011
Volume 8, Number 4, July, 2011
Volume 8, Number 5, September, 2011
Volume 8, Number 6, November, 2011
Volume 9, Number 1, January, 2012
Volume 9, Number 2, March, 2012
Volume 9, Number 3, May, 2012
Volume 9, Number 4, July, 2012
Volume 9, Number 5, September, 2012
Volume 9, Number 6, November, 2012
Volume 10, Number 1, January, 2013
Volume 10, Number 2, March, 2013
Volume 10, Number 3, May, 2013
Volume 10, Number 4, July, 2013
Volume 10, Number 5, September, 2013
Volume 10, Number 6, November, 2013
Volume 11, Number 1, January, 2014
Volume 11, Number 2, March, 2014
Volume 11, Number 3, May, 2014
Volume 11, Number 4, July, 2014
Volume 11, Number 5, September, 2014
Volume 11, Number 6, November, 2014
Volume 12, Number 1, January, 2015
Volume 12, Number 2, March, 2015
Volume 12, Number 3, May, 2015
Volume 12, Number 4, July, 2015
Volume 12, Number 5, September, 2015
Volume 12, Number 6, November, 2015
Volume 13, Number 1, January, 2016
Volume 13, Number 2, March, 2016
Volume 13, Number 3, May, 2016
Volume 13, Number 4, 2016
Volume 13, Number 5, September, 2016
Volume 13, Number 6, November, 2016
Volume 14, Number 1, January, 2017
Volume 14, Number 2, March, 2017
Volume 14, Number 3, May, 2017
Volume 14, Number 4, July, 2017
Volume 14, Number 5, September, 2017
Volume 14, Number 6, November, 2017
Volume 15, Number 1, January, 2018
Volume 15, Number 2, March, 2018
Volume 15, Number 3, May, 2018
Volume 15, Number 4, July, 2018
Volume 15, Number 5, September, 2018
Volume 15, Number 6, November, 2018
Volume 16, Number 1, January, 2019
Volume 16, Number 2, March, 2019
Volume 16, Number 3, May, 2019
Volume 16, Number 4, July, 2019
Volume 16, Number 5, September, 2019
Volume 16, Number 6, November, 2019
Volume 17, Number 1, January, 2020
Volume 17, Number 2, March, 2020
Volume 17, Number 3, May, 2020
Volume 17, Number 5, September, 2020
Volume 17, Number 6, November, 2020
Volume 18, Number 1, January, 2021
Volume 18, Number 2, March, 2021
Volume 18, Number 3, May / June, 2021
Volume 18, Number 4, July / August, 2021
Volume 18, Number 5, September / October, 2021
Volume 18, Number 6, November / December, 2021
Volume 19, Number 1, January, 2022
Volume 19, Number 2, March, 2022
Volume 19, Number 3, May, 2022
Volume 19, Number 4, July, 2022
Volume 19, Number 5, 2022
Volume 19, Number 6, 2022
Volume 20, Number 1, 2023
Volume 20, Number 2, March, 2023
Volume 20, Number 3, May, 2023
Volume 20, Number 4, July, 2023
Volume 20, Number 5, 2023
Volume 20, Number 6, 2023
Volume 21, Number 1, 2024
Volume 21, Number 2, March, 2024
Volume 21, Number 3, May, 2024
Volume 21, Number 4, July, 2024
Volume 21, Number 5, September / October, 2024


IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 1, Number 1, January, 2004

            Michael R. Williams   Welcome Message  . . . . . . . . . . . . 1--1
                   Dan Gusfield   Introduction to the IEEE/ACM
                                  Transactions on Computational Biology
                                  and Bioinformatics . . . . . . . . . . . 2--3
            Michael R. Williams   Introduction of New Associate Editors    4--12
        Bernard M. E. Moret and   
               Luay Nakhleh and   
               Tandy Warnow and   
           C. Randal Linder and   
                Anna Tholse and   
            Anneke Padolina and   
                  Jerry Sun and   
                     Ruth Timme   Phylogenetic Networks: Modeling,
                                  Reconstructibility, and Accuracy . . . . 13--23
            Sara C. Madeira and   
            Arlindo L. Oliveira   Biclustering Algorithms for Biological
                                  Data Analysis: a Survey  . . . . . . . . 24--45
            Franco P. Preparata   Sequencing-by-Hybridization Revisited:
                                  The Analog-Spectrum Proposal . . . . . . 46--52
    Matthias Höchsmann and   
            Björn Voss and   
               Robert Giegerich   Pure Multiple RNA Secondary Structure
                                  Alignments: a Progressive Profile
                                  Approach . . . . . . . . . . . . . . . . 53--62

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 1, Number 2, April, 2004

                      Anonymous   Introduction of New Associate Editor . . 65--65
           Christina Witwer and   
            Ivo L. Hofacker and   
               Peter F. Stadler   Prediction of Consensus RNA Secondary
                                  Structures Including Pseudoknots . . . . 66--77
               Vineet Bafna and   
                   Vikas Bansal   The Number of Recombination Events in a
                                  Sample History: Conflict Graph and Lower
                                  Bounds . . . . . . . . . . . . . . . . . 78--90
           Benjamin Raphael and   
              Lung-Tien Liu and   
                George Varghese   A Uniform Projection Method for Motif
                                  Discovery in DNA Sequences . . . . . . . 91--94

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 1, Number 3, July, 2004

                   Dan Gusfield   Introduction of New Associate Editors    97--97
            Stefanie Scheid and   
                   Rainer Spang   A Stochastic Downhill Search Algorithm
                                  for Estimating the Local False Discovery
                                  Rate . . . . . . . . . . . . . . . . . . 98--108
        Andreas W. M. Dress and   
                Daniel H. Huson   Constructing Splits Graphs . . . . . . . 109--115
            Michael Cameron and   
           Hugh E. Williams and   
                   Adam Cannane   Improved Gapped Alignment in BLAST . . . 116--129
            Steven N. Evans and   
                   Tandy Warnow   Unidentifiable Divergence Times in
                                  Rates-across-Sites Models  . . . . . . . 130--134

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 1, Number 4, October, 2004

               Junhyong Kim and   
                  Inge Jonassen   Guest Editorial: WABI Special Section
                                  Part 1 . . . . . . . . . . . . . . . . . 137--138
                  Miklos Csuros   Maximum-Scoring Segment Sets . . . . . . 139--150
            Daniel H. Huson and   
            Tobias Dezulian and   
             Tobias Klopper and   
                  Mike A. Steel   Phylogenetic Super-Networks from Partial
                                  Trees  . . . . . . . . . . . . . . . . . 151--158
               Hideo Bannai and   
               Heikki Hyyro and   
            Ayumi Shinohara and   
            Masayuki Takeda and   
                Kenta Nakai and   
                  Satoru Miyano   An $ O(N^2) $ Algorithm for Discovering
                                  Optimal Boolean Pattern Pairs  . . . . . 159--170
                     Jens Gramm   A Polynomial-Time Algorithm for the
                                  Matching of Crossing Contact-Map
                                  Patterns . . . . . . . . . . . . . . . . 171--180
                 Jieping Ye and   
                     Tao Li and   
                  Tao Xiong and   
                  Ravi Janardan   Using Uncorrelated Discriminant Analysis
                                  for Tissue Classification with Gene
                                  Expression Data  . . . . . . . . . . . . 181--190
                      Anonymous   Annual Index . . . . . . . . . . . . . . 191--192


IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 2, Number 1, January, 2005

               Junhyong Kim and   
                  Inge Jonassen   Guest Editorial: WABI Special Section.
                                  Part II  . . . . . . . . . . . . . . . . 1--2
              Julien Allali and   
             Marie-France Sagot   A New Distance for High Level RNA
                                  Secondary Structure Comparison . . . . . 3--14
             Denis Bertrand and   
                Olivier Gascuel   Topological Rearrangements and Local
                                  Search Method for Tandem Duplication
                                  Trees  . . . . . . . . . . . . . . . . . 15--28
                Daniel G. Brown   Optimizing Multiple Seeds for Protein
                                  Homology Search  . . . . . . . . . . . . 29--38
                   Dan Gusfield   Editorial-State of the Transaction . . . 39--39
              Nadia Pisanti and   
          Maxime Crochemore and   
             Roberto Grossi and   
             Marie-France Sagot   Bases of Motifs for Generating Repeated
                                  Patterns with Wild Cards . . . . . . . . 40--50
           Gregory Kucherov and   
                Laurent Noe and   
               Mikhail Roytberg   Multiseed Lossless Filtration  . . . . . 51--61
                   Ying Liu and   
        Shamkant B. Navathe and   
               Jorge Civera and   
                Venu Dasigi and   
                 Ashwin Ram and   
            Brian J. Ciliax and   
                 Ray Dingledine   Text Mining Biomedical Literature for
                                  Discovering Gene-to-Gene Relationships:
                                  a Comparative Study of Algorithms  . . . 62--76
                       IEEE and   
ACM Transactions on Computational Biology and   
           Bioinformatics staff   2004 Reviewers List  . . . . . . . . . . 77--77

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 2, Number 2, April, 2005

            Charles X. Ling and   
     William Stafford Noble and   
                     Qiang Yang   Guest Editors' Introduction to the
                                  Special Issue: Machine Learning for
                                  Bioinformatics---Part 1  . . . . . . . . 81--82
                  Wai-Ho Au and   
           Keith C. C. Chan and   
          Andrew K. C. Wong and   
                      Yang Wang   Attribute Clustering for Grouping,
                                  Selection, and Classification of Gene
                                  Expression Data  . . . . . . . . . . . . 83--101
             Pravesh Biyani and   
                 Xiaolin Wu and   
                  Abhijit Sinha   Joint Classification and Pairing of
                                  Human Chromosomes  . . . . . . . . . . . 102--109
          Cesare Furlanello and   
             Maria Serafini and   
             Stefano Merler and   
                Giuseppe Jurman   Semisupervised Learning for Molecular
                                  Profiling  . . . . . . . . . . . . . . . 110--118
              Hiroshi Mamitsuka   Essential Latent Knowledge for
                                  Protein-Protein Interactions: Analysis
                                  by an Unsupervised Learning Approach . . 119--130
        Jagath C. Rajapakse and   
                      Loi Sy Ho   Markov Encoding for Detecting Signals in
                                  Genomic Sequences  . . . . . . . . . . . 131--142
               Simon Rogers and   
              Mark Girolami and   
             Colin Campbell and   
               Rainer Breitling   The Latent Process Decomposition of cDNA
                                  Microarray Data Sets . . . . . . . . . . 143--156
                       Jinbo Xu   Fold Recognition by Predicted Alignment
                                  Accuracy . . . . . . . . . . . . . . . . 157--165
                    Li Shen and   
                  Eng Chong Tan   Dimension Reduction-Based Penalized
                                  Logistic Regression for Cancer
                                  Classification Using Microarray Data . . 166--175

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 2, Number 3, July, 2005

                 C. X. Ling and   
                W. S. Noble and   
                        Q. Yang   Guest Editor's Introduction to the
                                  Special Issue: Machine Learning for
                                  Bioinformatics---Part 2  . . . . . . . . 177--178
          Alexander Schliep and   
              Ivan G. Costa and   
        Christine Steinhoff and   
            Alexander Schonhuth   Analyzing Gene Expression Time-Courses   179--193
             Anshul Kundaje and   
          Manuel Middendorf and   
                   Feng Gao and   
              Chris Wiggins and   
               Christina Leslie   Combining Sequence and Time Series
                                  Expression Data to Learn Transcriptional
                                  Modules  . . . . . . . . . . . . . . . . 194--202
               Samuel Kaski and   
              Janne Nikkila and   
            Janne Sinkkonen and   
                  Leo Lahti and   
       Juha E. A. Knuuttila and   
                Christophe Roos   Associative Clustering for Exploring
                                  Dependencies between Functional Genomics
                                  Data Sets  . . . . . . . . . . . . . . . 203--216
              Jingfen Zhang and   
                    Wen Gao and   
                 Jinjin Cai and   
                   Simin He and   
                  Rong Zeng and   
                  Runsheng Chen   Predicting Molecular Formulas of
                                  Fragment Ions with Isotope Patterns in
                                  Tandem Mass Spectra  . . . . . . . . . . 217--230
            Edward Keedwell and   
                 Ajit Narayanan   Discovering Gene Networks with a
                                  Neural-Genetic Hybrid  . . . . . . . . . 231--242
               John Hawkins and   
                   Mikael Boden   The Applicability of Recurrent Neural
                                  Networks for Biological Sequence
                                  Analysis . . . . . . . . . . . . . . . . 243--253
            Mika Gustafsson and   
          Michael Hornquist and   
                  Anna Lombardi   Constructing and Analyzing a Large-Scale
                                  Gene-to-Gene Regulatory
                                  Network-Lasso-Constrained Inference and
                                  Biological Validation  . . . . . . . . . 254--261
               Cigdem Demir and   
        S. Humayun Gultekin and   
                   Bulent Yener   Learning the Topological Properties of
                                  Brain Tumors . . . . . . . . . . . . . . 262--270
                      Anonymous   Call for Papers for Special Issue on
                                  Computational Intelligence Approaches in
                                  Computational Biology and Bioinformatics 271--271

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 2, Number 4, October, 2005

        Trevor M. Cickovski and   
            Chengbang Huang and   
           Rajiv Chaturvedi and   
              Tilmann Glimm and   
     H. George E. Hentschel and   
              Mark S. Alber and   
           James A. Glazier and   
           Stuart A. Newman and   
             Jesus A. Izaguirre   A Framework for Three-Dimensional
                                  Simulation of Morphogenesis  . . . . . . 273--288
           Riccardo Boscolo and   
             Chiara Sabatti and   
              James C. Liao and   
          Vwani P. Roychowdhury   A Generalized Framework for Network
                                  Component Analysis . . . . . . . . . . . 289--301
                   Xin Chen and   
                  Jie Zheng and   
                   Zheng Fu and   
                   Peng Nan and   
                 Yang Zhong and   
            Stefano Lonardi and   
                      Tao Jiang   Assignment of Orthologous Genes via
                                  Genome Rearrangement . . . . . . . . . . 302--315
          Heather L. Turner and   
           Trevor C. Bailey and   
       Wojtek J. Krzanowski and   
            Cheryl A. Hemingway   Biclustering Models for Structured
                                  Microarray Data  . . . . . . . . . . . . 316--329
            Jose L. Sevilla and   
              Victor Segura and   
             Adam Podhorski and   
        Elizabeth Guruceaga and   
               Jose M. Mato and   
      Luis A. Martinez-Cruz and   
       Fernando J. Corrales and   
                    Angel Rubio   Correlation between Gene Expression and
                                  GO Semantic Similarity . . . . . . . . . 330--338
               Sungroh Yoon and   
          Christine Nardini and   
                Luca Benini and   
            Giovanni De Micheli   Discovering Coherent Biclusters from
                                  Gene Expression Data Using
                                  Zero-Suppressed Binary Decision Diagrams 339--354
           Vincent S. Tseng and   
                  Ching-Pin Kao   Efficiently Mining Gene Expression Data
                                  via a Novel Parameterless Clustering
                                  Method . . . . . . . . . . . . . . . . . 355--365
              Shaojie Zhang and   
                 Brian Haas and   
              Eleazar Eskin and   
                   Vineet Bafna   Searching Genomes for Noncoding RNA
                                  Using FastR  . . . . . . . . . . . . . . 366--379
                      Anonymous   2005 Annual Index  . . . . . . . . . . . 380--384


IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 3, Number 1, January, 2006

                   Dan Gusfield   State of the Journal . . . . . . . . . . 1--1
             John A. Berger and   
          Sampsa Hautaniemi and   
            Sanjit K. Mitra and   
                  Jaakko Astola   Jointly Analyzing Gene Expression and
                                  Copy Number Data in Breast Cancer Using
                                  Data Reduction Models  . . . . . . . . . 2--16
           Rafael Sebastian and   
           Maria-Elena Diaz and   
            Guillermo Ayala and   
           Kresimir Letinic and   
         Jose Moncho-Bogani and   
                   Derek Toomre   Spatio-Temporal Analysis of Constitutive
                                  Exocytosis in Epithelial Cells . . . . . 17--32
            Eli Hershkovitz and   
           Guillermo Sapiro and   
           Allen Tannenbaum and   
            Loren Dean Williams   Statistical Analysis of RNA Backbone . . 33--46
                 Zaher Dawy and   
            Bernhard Goebel and   
          Joachim Hagenauer and   
        Christophe Andreoli and   
           Thomas Meitinger and   
               Jakob C. Mueller   Gene Mapping and Marker Clustering Using
                                  Shannon's Mutual Information . . . . . . 47--56
                  John Goutsias   A Hidden Markov Model for
                                  Transcriptional Regulation in Single
                                  Cells  . . . . . . . . . . . . . . . . . 57--71
                 Luis Rueda and   
              Vidya Vidyadharan   A Hill-Climbing Approach for Automatic
                                  Gridding of cDNA Microarray Images . . . 72--83
             Charles Semple and   
                     Mike Steel   Unicyclic Networks: Compatibility and
                                  Enumeration  . . . . . . . . . . . . . . 84--91
                 Sebastien Roch   A Short Proof that Phylogenetic Tree
                                  Reconstruction by Maximum Likelihood Is
                                  Hard . . . . . . . . . . . . . . . . . . 92--94
                      Anonymous   2005 Reviewers List  . . . . . . . . . . 95--96

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 3, Number 2, April, 2006

                   Dan Gusfield   Introduction of New Associate Editors    97--97
                    Wei Chu and   
          Zoubin Ghahramani and   
      Alexei Podtelezhnikov and   
                  David L. Wild   Bayesian Segmental Models with Multiple
                                  Sequence Alignment Profiles for Protein
                                  Secondary Structure and Contact Map
                                  Prediction . . . . . . . . . . . . . . . 98--113
         Samuel A. Danziger and   
        S. Joshua Swamidass and   
                   Jue Zeng and   
         Lawrence R. Dearth and   
                   Qiang Lu and   
           Jonathan H. Chen and   
              Jianlin Cheng and   
              Vinh P. Hoang and   
               Hiroto Saigo and   
                    Ray Luo and   
               Pierre Baldi and   
        Rainer K. Brachmann and   
             Richard H. Lathrop   Functional Census of Mutation Sequence
                                  Spaces: The Example of p53 Cancer Rescue
                                  Mutants  . . . . . . . . . . . . . . . . 114--125
      Alexandra M. Carvalho and   
             Ana T. Freitas and   
        Arlindo L. Oliveira and   
             Marie-France Sagot   An Efficient Algorithm for the
                                  Identification of Structured Motifs in
                                  DNA Promoter Sequences . . . . . . . . . 126--140
            Daniel G. Brown and   
                Ian M. Harrower   Integer Programming Approaches to
                                  Haplotype Inference by Pure Parsimony    141--154
               Marc T. Vass and   
        Clifford A. Shaffer and   
         Naren Ramakrishnan and   
            Layne T. Watson and   
                  John J. Tyson   The JigCell Model Builder: a Spreadsheet
                                  Interface for Creating Biochemical
                                  Reaction Network Models  . . . . . . . . 155--164
                Duhong Chen and   
          Oliver Eulenstein and   
       David Fernandez-Baca and   
              Michael Sanderson   Minimum-Flip Supertrees: Complexity and
                                  Algorithms . . . . . . . . . . . . . . . 165--173
              Petteri Sevon and   
             Hannu Toivonen and   
                Vesa Ollikainen   TreeDT: Tree Pattern Mining for Gene
                                  Mapping  . . . . . . . . . . . . . . . . 174--185
                    Yun S. Song   A Concise Necessary and Sufficient
                                  Condition for the Existence of a
                                  Galled-Tree  . . . . . . . . . . . . . . 186--191

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 3, Number 3, July, 2006

               Petros Daras and   
         Dimitrios Zarpalas and   
      Apostolos Axenopoulos and   
         Dimitrios Tzovaras and   
   Michael Gerassimos Strintzis   Three-Dimensional Shape-Structure
                                  Comparison Method for Protein
                                  Classification . . . . . . . . . . . . . 193--207
                Weichuan Yu and   
                  Xiaoye Li and   
                Junfeng Liu and   
                  Baolin Wu and   
        Kenneth R. Williams and   
                    Hongyu Zhao   Multiple Peak Alignment in Sequential
                                  Data Analysis: a Scale-Space-Based
                                  Approach . . . . . . . . . . . . . . . . 208--219
                 Osman Abul and   
                Reda Alhajj and   
                    Faruk Polat   A Powerful Approach for Effective
                                  Finding of Significantly Differentially
                                  Expressed Genes  . . . . . . . . . . . . 220--231
    Radhakrishnan Nagarajan and   
               Meenakshi Upreti   Correlation Statistics for cDNA
                                  Microarray Image Analysis  . . . . . . . 232--238
                Yun S. Song and   
                Rune Lyngso and   
                     Jotun Hein   Counting All Possible Ancestral
                                  Configurations of Sample Sequences in
                                  Population Genetics  . . . . . . . . . . 239--251
              Matti Pirinen and   
                 Dario Gasbarra   Finding Consistent Gene Transmission
                                  Patterns on Large and Complex Pedigrees  252--262
             Mihail Popescu and   
            James M. Keller and   
              Joyce A. Mitchell   Fuzzy Measures on the Gene Ontology for
                                  Gene Product Similarity  . . . . . . . . 263--274
             Matthias Bernt and   
              Daniel Merkle and   
              Martin Middendorf   Genome Rearrangement Based on Reversals
                                  that Preserve Conserved Intervals  . . . 275--288
              Vincent Berry and   
        François Nicolas   Improved Parameterized Complexity of the
                                  Maximum Agreement Subtree and Maximum
                                  Compatible Tree Problems . . . . . . . . 289--302
               Roded Sharan and   
      Bjarni V. Halldorsson and   
                  Sorin Istrail   Islands of Tractability for Parsimony
                                  Haplotyping  . . . . . . . . . . . . . . 303--311
              Chaolin Zhang and   
                 Xuesong Lu and   
                  Xuegong Zhang   Significance of Gene Ranking for
                                  Classification of Microarray Samples . . 312--320

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 3, Number 4, October, 2006

                   Rita Casadio   Guest Editor's Introduction to the
                                  Special Issue on Computational Biology
                                  and Bioinformatics -- Part 1 . . . . . . 321--322
                  Sagi Snir and   
                     Satish Rao   Using Max Cut to Enhance Rooted Trees
                                  Consistency  . . . . . . . . . . . . . . 323--333
      Ganeshkumar Ganapathy and   
            Barbara Goodson and   
              Robert Jansen and   
                 Hai-son Le and   
        Vijaya Ramachandran and   
                   Tandy Warnow   Pattern Identification in Biogeography   334--346
             Sebastian Wernicke   Efficient Detection of Network Motifs    347--359
            Vincent Lacroix and   
      Cristina G. Fernandes and   
             Marie-France Sagot   Motif Search in Graphs: Application to
                                  Metabolic Networks . . . . . . . . . . . 360--368
                Isaac Elias and   
                 Tzvika Hartman   A $ 1.375 $-Approximation Algorithm for
                                  Sorting by Transpositions  . . . . . . . 369--379
                Anthony Labarre   New Bounds and Tractable Instances for
                                  the Transposition Distance . . . . . . . 380--394
            Michael Sammeth and   
                     Jens Stoye   Comparing Tandem Repeats with
                                  Duplications and Excisions of Variable
                                  Degree . . . . . . . . . . . . . . . . . 395--407
               Yonatan Bilu and   
          Pankaj K. Agarwal and   
                 Rachel Kolodny   Faster Algorithms for Optimal Multiple
                                  Sequence Alignment Based on Pairwise
                                  Comparisons  . . . . . . . . . . . . . . 408--422
               Yinglei Song and   
                Chunmei Liu and   
              Xiuzhen Huang and   
        Russell L. Malmberg and   
                    Ying Xu and   
                     Liming Cai   Efficient Parameterized Algorithms for
                                  Biopolymer Structure-Sequence Alignment  423--432
                      Anonymous   Annual Index . . . . . . . . . . . . . . ??


IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 4, Number 1, January, 2007

                   Dan Gusfield   State of the Journal . . . . . . . . . . 1--1
                   Dan Gusfield   Associate Editor Appreciation and
                                  Welcome  . . . . . . . . . . . . . . . . 2--2
                   Rita Casadio   Guest Editor's Introduction to the
                                  Special Section on Computational Biology
                                  and Bioinformatics (WABI) -- Part 2  . . 3--3
     Severine Bérard and   
              Anne Bergeron and   
              Cedric Chauve and   
                Christophe Paul   Perfect Sorting by Reversals Is Not
                                  Always Difficult . . . . . . . . . . . . 4--16
             Akshay Vashist and   
      Casimir A. Kulikowski and   
                   Ilya Muchnik   Ortholog Clustering on a Multipartite
                                  Graph  . . . . . . . . . . . . . . . . . 17--27
               Keren Lasker and   
                Oranit Dror and   
              Maxim Shatsky and   
              Ruth Nussinov and   
                Haim J. Wolfson   EMatch: Discovery of High Resolution
                                  Structural Homologues of Protein Domains
                                  in Intermediate Resolution Cryo-EM Maps  28--39
                  Lipo Wang and   
                   Feng Chu and   
                        Wei Xie   Accurate Cancer Classification Using
                                  Expressions of Very Few Genes  . . . . . 40--53
                  Degui Zhi and   
                  Uri Keich and   
              Pavel Pevzner and   
              Steffen Heber and   
                     Haixu Tang   Correcting Base-Assignment Errors in
                                  Repeat Regions of Shotgun Assembly . . . 54--64
                     Rui Xu and   
Georgios C. Anagnostopoulos and   
               Donald C. Wunsch   Multiclass Cancer Classification Using
                                  Semisupervised Ellipsoid ARTMAP and
                                  Particle Swarm Optimization with Gene
                                  Expression Data  . . . . . . . . . . . . 65--77
            Chengbang Huang and   
              Faruck Morcos and   
            Simon P. Kanaan and   
              Stefan Wuchty and   
              Danny Z. Chen and   
             Jesus A. Izaguirre   Predicting Protein-Protein Interactions
                                  from Protein Domains Using a Set Cover
                                  Approach . . . . . . . . . . . . . . . . 78--87
              Jong Hyun Kim and   
        Michael S. Waterman and   
                      Lei M. Li   Accuracy Assessment of Diploid Consensus
                                  Sequences  . . . . . . . . . . . . . . . 88--97
           Max A. Alekseyev and   
               Pavel A. Pevzner   Colored de Bruijn Graphs and the Genome
                                  Halving Problem  . . . . . . . . . . . . 98--107
                Elchanan Mossel   Distorted Metrics on Trees and
                                  Phylogenetic Forests . . . . . . . . . . 108--116
         Kimberly A. Aeling and   
        Nicholas R. Steffen and   
            Matthew Johnson and   
         G. Wesley Hatfield and   
         Richard H. Lathrop and   
               Donald F. Senear   DNA Deformation Energy as an Indirect
                                  Recognition Mechanism in Protein-DNA
                                  Interactions . . . . . . . . . . . . . . 117--125
                  Jing Yang and   
             Sarawan Wongsa and   
    Visakan Kadirkamanathan and   
        Stephen A. Billings and   
              Phillip C. Wright   Metabolic Flux Estimation --- a
                                  Self-Adaptive Evolutionary Algorithm
                                  with Singular Value Decomposition  . . . 126--138
                    Gang Wu and   
               Jia-Huai You and   
                     Guohui Lin   Quartet-Based Phylogeny Reconstruction
                                  with Answer Set Programming  . . . . . . 139--152
             Gesine Reinert and   
            Michael S. Waterman   On the Length of the Longest Exact
                                  Position Match in a Random Sequence  . . 153--156
                  Wai-Ho Au and   
           Keith C. C. Chan and   
          Andrew K. C. Wong and   
                      Yang Wang   Correction to ``Attribute Clustering for
                                  Grouping, Selection, and Classification
                                  of Gene Expression Data''  . . . . . . . 157--157
                       IEEE and   
ACM Transactions on Computational Biology and   
           Bioinformatics staff   2006 Reviewers List  . . . . . . . . . . 158--160

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 4, Number 2, April, 2007

        Jagath C. Rajapakse and   
             Yan-Qing Zhang and   
                  Gary B. Fogel   Guest Editors' Introduction to the
                                  Special Section: Computational
                                  Intelligence Approaches in Computational
                                  Biology and Bioinformatics . . . . . . . 161--162
               Haiying Wang and   
                Huiru Zheng and   
               Francisco Azuaje   Poisson-Based Self-Organizing Feature
                                  Maps and Hierarchical Clustering for
                                  Serial Analysis of Gene Expression Data  163--175
             Ozy Sjahputera and   
            James M. Keller and   
              J. Wade Davis and   
          Kristen H. Taylor and   
       Farahnaz Rahmatpanah and   
                Huidong Shi and   
          Derek T. Anderson and   
          Samuel N. Blisard and   
             Robert H. Luke and   
             Mihail Popescu and   
           Gerald C. Arthur and   
            Charles W. Caldwell   Relational Analysis of CpG Islands
                                  Methylation and Gene Expression in Human
                                  Lymphomas Using Possibilistic C-Means
                                  Clustering and Modified Cluster Fuzzy
                                  Density  . . . . . . . . . . . . . . . . 176--189
                  Yijuan Lu and   
                    Qi Tian and   
                   Feng Liu and   
            Maribel Sanchez and   
                    Yufeng Wang   Interactive Semisupervised Learning for
                                  Microarray Analysis  . . . . . . . . . . 190--203
                Boaz Lerner and   
            Josepha Yeshaya and   
                   Lev Koushnir   On the Classification of a Small
                                  Imbalanced Cytogenetic Image Database    204--215
             Christian Igel and   
         Tobias Glasmachers and   
              Britta Mersch and   
               Nico Pfeifer and   
                 Peter Meinicke   Gradient-Based Optimization of
                                  Kernel-Target Alignment for Sequence
                                  Kernels Applied to Bacterial Gene Start
                                  Detection  . . . . . . . . . . . . . . . 216--226
                 Hasan Ogul and   
           Erkan U. Mumcuo\uglu   Subcellular Localization Prediction with
                                  New Protein Encoding Schemes . . . . . . 227--232
                 Wenyuan Li and   
                   Ying Liu and   
           Hung-Chung Huang and   
              Yanxiong Peng and   
               Yongjing Lin and   
               Wee-Keong Ng and   
                  Kok-Leong Ong   Dynamical Systems for Discovering
                                  Protein Complexes and Functional Modules
                                  from Biological Networks . . . . . . . . 233--250
                 Xiaohua Hu and   
                   Daniel D. Wu   Data Mining and Predictive Modeling of
                                  Biomolecular Network from Biomedical
                                  Literature Databases . . . . . . . . . . 251--263
              Ferrante Neri and   
              Jari Toivanen and   
 Giuseppe Leonardo Cascella and   
                   Yew-Soon Ong   An Adaptive Multimeme Algorithm for
                                  Designing HIV Multidrug Therapies  . . . 264--278
                Julia Handl and   
            Douglas B. Kell and   
                 Joshua Knowles   Multiobjective Optimization in
                                  Bioinformatics and Computational Biology 279--292
              Gianluca Bontempi   A Blocking Strategy to Improve Gene
                                  Selection for Classification of Gene
                                  Expression Data  . . . . . . . . . . . . 293--300
              Yoan Diekmann and   
         Marie-France Sagot and   
                   Eric Tannier   Evolution under Reversals: Parsimony and
                                  Conservation of Common Intervals . . . . 301--309
               Nils Weskamp and   
           Eyke Hullermeier and   
                Daniel Kuhn and   
                  Gerhard Klebe   Multiple Graph Alignment for the
                                  Structural Analysis of Protein Active
                                  Sites  . . . . . . . . . . . . . . . . . 310--320

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 4, Number 3, July, 2007

                   Dan Gusfield   Associate Editor Appreciation and
                                  Welcome  . . . . . . . . . . . . . . . . 321--321
       Krzysztof Fujarewicz and   
               Marek Kimmel and   
           Tomasz Lipniacki and   
              Andrzej Swierniak   Adjoint Systems for Models of Cell
                                  Signaling Pathways and their Application
                                  to Parameter Fitting . . . . . . . . . . 322--335
                  Xiang Wan and   
                     Guohui Lin   CISA: Combined NMR Resonance
                                  Connectivity Information Determination
                                  and Sequential Assignment  . . . . . . . 336--348
            Michael Cameron and   
                  Hugh Williams   Comparing Compressed Sequences for
                                  Faster Nucleotide BLAST Searches . . . . 349--364
                Yuchun Tang and   
             Yan-Qing Zhang and   
                     Zhen Huang   Development of Two-Stage SVM-RFE Gene
                                  Selection Strategy for Microarray
                                  Expression Data Analysis . . . . . . . . 365--381
                   Lydia Ng and   
               Sayan Pathak and   
              Chihchau Kuan and   
                  Chris Lau and   
              Hong-wei Dong and   
                Andrew Sodt and   
                 Chinh Dang and   
               Brian Avants and   
            Paul Yushkevich and   
                  James Gee and   
               David Haynor and   
                    Ed Lein and   
                Allan Jones and   
                 Mike Hawrylycz   Neuroinformatics for Genome-Wide $3$-D
                                  Gene Expression Mapping in the Mouse
                                  Brain  . . . . . . . . . . . . . . . . . 382--393
            C. Thach Nguyen and   
          Nguyen Bao Nguyen and   
              Wing-Kin Sung and   
                   Louxin Zhang   Reconstructing Recombination Network
                                  from Sequence Data: The Small Parsimony
                                  Problem  . . . . . . . . . . . . . . . . 394--402
              Michael Lones and   
                   Andy Tyrrell   Regulatory Motif Discovery Using a
                                  Population Clustering Evolutionary
                                  Algorithm  . . . . . . . . . . . . . . . 403--414
                Andy M. Yip and   
              Michael K. Ng and   
               Edmond H. Wu and   
                   Tony F. Chan   Strategies for Identifying Statistically
                                  Significant Dense Regions in Microarray
                                  Data . . . . . . . . . . . . . . . . . . 415--429
            Kuo-ching Liang and   
              Xiaodong Wang and   
           Dimitris Anastassiou   Bayesian Basecalling for DNA Sequence
                                  Analysis Using Hidden Markov Models  . . 430--440
              Trias Thireou and   
                  Martin Reczko   Bidirectional Long Short-Term Memory
                                  Networks for Predicting the Subcellular
                                  Localization of Eukaryotic Proteins  . . 441--446
             Gergely Korodi and   
                     Ioan Tabus   Compression of Annotated Nucleotide
                                  Sequences  . . . . . . . . . . . . . . . 447--457
           Magnus Bordewich and   
                 Charles Semple   Computing the Hybridization Number of
                                  Two Phylogenetic Trees Is
                                  Fixed-Parameter Tractable  . . . . . . . 458--466
                   D. Huang and   
                     Tommy Chow   Effective Gene Selection Method With
                                  Small Sample Sets Using Gradient-Based
                                  and Point Injection Techniques . . . . . 467--475
                David Hecht and   
                     Gary Fogel   High-Throughput Ligand Screening via
                                  Preclustering and Evolved Neural
                                  Networks . . . . . . . . . . . . . . . . 476--484
              Runxuan Zhang and   
            Guang-Bin Huang and   
            N. Sundararajan and   
               P. Saratchandran   Multicategory Classification Using An
                                  Extreme Learning Machine for Microarray
                                  Gene Expression Cancer Diagnosis . . . . 485--495
                   Louxin Zhang   Superiority of Spaced Seeds for Homology
                                  Search . . . . . . . . . . . . . . . . . 496--505
               Frederick Matsen   Optimization Over a Class of Tree Shape
                                  Statistics . . . . . . . . . . . . . . . 506--512

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 4, Number 4, October, 2007

      Ion I. Mãndoiu and   
                     Yi Pan and   
           Alexander Zelikovsky   Guest Editors' Introduction to the
                                  Special Section on Bioinformatics
                                  Research and Applications  . . . . . . . 513--514
             Chunfang Zheng and   
                   Qian Zhu and   
                  David Sankoff   Removing Noise and Ambiguities from
                                  Comparative Maps in Rearrangement
                                  Analysis . . . . . . . . . . . . . . . . 515--522
             Guillaume Blin and   
              Cedric Chauve and   
           Guillaume Fertin and   
                Romeo Rizzi and   
              Stephane Vialette   Comparing Genomes with Duplications: a
                                  Computational Complexity Point of View   523--534
            Paola Bonizzoni and   
      Gianluca Della Vedova and   
             Riccardo Dondi and   
           Guillaume Fertin and   
            Raffaella Rizzi and   
              Stephane Vialette   Exemplar Longest Common Subsequence  . . 535--543
               Jaime Davila and   
                Sudha Balla and   
        Sanguthevar Rajasekaran   Fast and Practical Algorithms for
                                  Planted $ (l, d) $ Motif Search  . . . . 544--552
           Adrian Schneider and   
              Gaston Gonnet and   
                Gina Cannarozzi   SynPAM---A Distance Measure Based on
                                  Synonymous Codon Substitutions . . . . . 553--560
            Srinath Sridhar and   
            Kedar Dhamdhere and   
               Guy Blelloch and   
              Eran Halperin and   
                    R. Ravi and   
               Russell Schwartz   Algorithms for Efficient Near-Perfect
                                  Phylogenetic Tree Reconstruction in
                                  Theory and Practice  . . . . . . . . . . 561--571
               Jinmiao Chen and   
             Narendra Chaudhari   Cascaded Bidirectional Recurrent Neural
                                  Networks for Protein Secondary Structure
                                  Prediction . . . . . . . . . . . . . . . 572--582
               Huilin Xiong and   
                   Ya Zhang and   
                   Xue-Wen Chen   Data-Dependent Kernel Machines for
                                  Microarray Data Classification . . . . . 583--595
              Shahar Michal and   
                   Tor Ivry and   
                 Omer Cohen and   
               Moshe Sipper and   
                   Danny Barash   Finding a Common Motif of RNA Sequences
                                  Using Genetic Programming: The GeRNAMo
                                  System . . . . . . . . . . . . . . . . . 596--610
              Tara McIntosh and   
                  Sanjay Chawla   High Confidence Rule Mining for
                                  Microarray Analysis  . . . . . . . . . . 611--623
            Ignacio Ponzoni and   
           Francisco Azuaje and   
               Juan Augusto and   
                    David Glass   Inferring Adaptive Regulation Thresholds
                                  and Association Rules from Gene
                                  Expression Data through Combinatorial
                                  Optimization Learning  . . . . . . . . . 624--634
              Nasimul Noman and   
                    Hitoshi Iba   Inferring Gene Regulatory Networks using
                                  Differential Evolution with Local Search
                                  Heuristics . . . . . . . . . . . . . . . 634--647
              Shinn-Ying Ho and   
            Chih-Hung Hsieh and   
                Fu-Chieh Yu and   
                 Hui-Ling Huang   An Intelligent Two-Stage Evolutionary
                                  Algorithm for Dynamic Pathway
                                  Identification From Gene Expression
                                  Profiles . . . . . . . . . . . . . . . . 648--704
               Sergey Bereg and   
                   Yuanyi Zhang   Phylogenetic Networks Based on the
                                  Molecular Clock Hypothesis . . . . . . . 661--667
            Jacek Blazewicz and   
               Edmund Burke and   
             Marta Kasprzak and   
           Alexandr Kovalev and   
               Mikhail Kovalyov   Simplified Partial Digest Problem:
                                  Enumerative and Dynamic Programming
                                  Algorithms . . . . . . . . . . . . . . . 668--680
                     Rui Xu and   
           Donald Wunsch II and   
                   Ronald Frank   Inference of Genetic Regulatory Networks
                                  with Recurrent Neural Network Models
                                  Using Particle Swarm Optimization  . . . 681--692
              Phaedra Agius and   
           Barry Kreiswirth and   
              Steve Naidich and   
                Kristin Bennett   Typing \bionameStaphylococcus aureus
                                  Using the spa Gene and Novel Distance
                                  Measures . . . . . . . . . . . . . . . . 693--704


IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 5, Number 1, January, 2008

        Clare Bates Congdon and   
             Joseph C. Aman and   
            Gerardo M. Nava and   
             H. Rex Gaskins and   
           Carolyn J. Mattingly   An Evaluation of Information Content as
                                  a Metric for the Inference of Putative
                                  Conserved Noncoding Regions in DNA
                                  Sequences Using a Genetic Algorithms
                                  Approach . . . . . . . . . . . . . . . . 1--14
           Riccardo Boscolo and   
              James C. Liao and   
          Vwani P. Roychowdhury   An Information Theoretic Exploratory
                                  Method for Learning Patterns of
                                  Conditional Gene Coexpression from
                                  Microarray Data  . . . . . . . . . . . . 15--24
               Kay C. Wiese and   
         Alain A. Deschenes and   
             Andrew G. Hendriks   RnaPredict---An Evolutionary Algorithm
                                  for RNA Secondary Structure Prediction   25--41
               Diego Rother and   
           Guillermo Sapiro and   
                    Vijay Pande   Statistical Characterization of Protein
                                  Ensembles  . . . . . . . . . . . . . . . 42--55
                    Yun Cui and   
               Lusheng Wang and   
                 Daming Zhu and   
                    Xiaowen Liu   A $ (1.5 + {\epsilon }) $-Approximation
                                  Algorithm for Unsigned Translocation
                                  Distance . . . . . . . . . . . . . . . . 56--66
               Tuan Zea Tan and   
                Geok See Ng and   
                      Chai Quek   A Novel Biologically and Psychologically
                                  Inspired Fuzzy Decision Support System:
                                  Hierarchical Complementary Learning  . . 67--79
        Federica Ciocchetta and   
             Corrado Priami and   
                  Paola Quaglia   An Automatic Translation of SBML into
                                  Beta-Binders . . . . . . . . . . . . . . 80--90
           Sebastian Bocker and   
                   Veli Makinen   Combinatorial Approaches for Mass
                                  Spectra Recalibration  . . . . . . . . . 91--100
              Tamar Barzuza and   
        Jacques S. Beckmann and   
                 Ron Shamir and   
                    Itsik Pe'er   Computational Problems in Perfect
                                  Phylogeny Haplotyping: Typing without
                                  Calling the Allele . . . . . . . . . . . 101--109
               Francis Chin and   
              Henry C. M. Leung   DNA Motif Representation with Nucleotide
                                  Dependency . . . . . . . . . . . . . . . 110--119
              Zong-Xian Yin and   
              Jung-Hsien Chiang   Novel Algorithm for Coexpression
                                  Detection in Time-Varying Microarray
                                  Data Sets  . . . . . . . . . . . . . . . 120--135
             Adrien Goeffon and   
         Jean-Michel Richer and   
                    Jin-Kao Hao   Progressive Tree Neighborhood Applied to
                                  the Maximum Parsimony Problem  . . . . . 136--145
                      Anonymous   2007 Reviewers List  . . . . . . . . . . 146--147
                      Anonymous   2007 Annual Index  . . . . . . . . . . . 148--158
                      Anonymous   Call for Applications for
                                  Editor-in-Chief  . . . . . . . . . . . . 159--159

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 5, Number 2, April, 2008

        Benjamin N. Jackson and   
        Patrick S. Schnable and   
                 Srinivas Aluru   Consensus Genetic Maps as Median Orders
                                  from Inconsistent Sources  . . . . . . . 161--171
               Anupam Gupta and   
                 Ziv Bar-Joseph   Extracting Dynamics from Static Cancer
                                  Expression Data  . . . . . . . . . . . . 172--182
                John Thomas and   
         Naren Ramakrishnan and   
           Chris Bailey-Kellogg   Graphical Models of Residue Coupling in
                                  Protein Families . . . . . . . . . . . . 183--197
          Jesus Mena-Chalco and   
             Helaine Carrer and   
                 Yossi Zana and   
           Roberto M. Cesar Jr.   Identification of Protein Coding Regions
                                  Using the Modified Gabor-Wavelet
                                  Transform  . . . . . . . . . . . . . . . 198--207
              Hidde de Jong and   
                    Michel Page   Search for Steady States of
                                  Piecewise-Linear Differential Equation
                                  Models of Genetic Regulatory Networks    208--222
               Avital Sadot and   
              Jasmin Fisher and   
                  Dan Barak and   
             Yishai Admanit and   
           Michael J. Stern and   
     E. Jane Albert Hubbard and   
                    David Harel   Toward Verified Biological Models  . . . 223--234
           Andreas Spillner and   
             Binh T. Nguyen and   
                Vincent Moulton   Computing Phylogenetic Diversity for
                                  Split Systems  . . . . . . . . . . . . . 235--244
            Giuseppe Lancia and   
                    R. Ravi and   
                    Romeo Rizzi   Haplotyping for Disease Association: a
                                  Combinatorial Approach . . . . . . . . . 245--251
            Alexander Gusev and   
      Ion I. Mãndoiu and   
              Bogdan Pa\csaniuc   Highly Scalable Genotype Phasing by
                                  Entropy Minimization . . . . . . . . . . 252--261
                Wentao Zhao and   
            Erchin Serpedin and   
            Edward R. Dougherty   Inferring Connectivity of Genetic
                                  Regulatory Networks Using
                                  Information-Theoretic Criteria . . . . . 262--274
           Magnus Bordewich and   
                 Charles Semple   Nature Reserve Selection Problem: a
                                  Tight Approximation Algorithm  . . . . . 275--280
          Yong-Hsiang Hsieh and   
             Chih-Chiang Yu and   
                Biing-Feng Wang   Optimal Algorithms for the Interval
                                  Location Problem with Range Constraints
                                  on Length and Average  . . . . . . . . . 281--290
          Susanna L. Lamers and   
               Marco Salemi and   
         Michael S. McGrath and   
                  Gary B. Fogel   Prediction of R5, X4, and R5X4 HIV-1
                                  Coreceptor Usage with Evolved Neural
                                  Networks . . . . . . . . . . . . . . . . 291--300
             Leo van Iersel and   
            Judith Keijsper and   
                Steven Kelk and   
                   Leen Stougie   Shorelines of Islands of Tractability:
                                  Algorithms for Parsimony and Minimum
                                  Perfect Phylogeny Haplotyping Problems   301--312
             Dumitru Brinza and   
           Alexander Zelikovsky   2SNP: Scalable Phasing Method for Trios
                                  and Unrelated Individuals  . . . . . . . 313--318

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 5, Number 3, July, 2008

             Ion I. Mandoiu and   
                     Yi Pan and   
           Alexander Zelikovsky   Guest Editors' Introduction to the
                                  Special Section on Bioinformatics
                                  Research and Applications  . . . . . . . 321--322
            Srinath Sridhar and   
                  Fumei Lam and   
            Guy E. Blelloch and   
                    R. Ravi and   
               Russell Schwartz   Mixed Integer Linear Programming for
                                  Maximum-Parsimony Phylogeny Inference    323--331
             Matthias Bernt and   
              Daniel Merkle and   
              Martin Middendorf   Solving the Preserving Reversal Median
                                  Problem  . . . . . . . . . . . . . . . . 332--347
 Marília D. V. Braga and   
         Marie-France Sagot and   
         Celine Scornavacca and   
                   Eric Tannier   Exploring the Solution Space of Sorting
                                  by Reversals, with Experiments and an
                                  Application to Evolution . . . . . . . . 348--356
              Marco Vassura and   
            Luciano Margara and   
             Pietro Di Lena and   
              Filippo Medri and   
            Piero Fariselli and   
                   Rita Casadio   Reconstruction of $3$D Structures From
                                  Protein Contact Maps . . . . . . . . . . 357--367
                 George Lee and   
           Carlos Rodriguez and   
               Anant Madabhushi   Investigating the Efficacy of Nonlinear
                                  Dimensionality Reduction Schemes in
                                  Classifying Gene and Protein Expression
                                  Studies  . . . . . . . . . . . . . . . . 368--384
                   Hyuk Cho and   
            Inderjit S. Dhillon   Coclustering of Human Cancer Microarrays
                                  Using Minimum Sum-Squared Residue
                                  Coclustering . . . . . . . . . . . . . . 385--400
                   Peng Wei and   
                        Wei Pan   Incorporating Gene Functions into
                                  Regression Analysis of DNA-Protein
                                  Binding Data and Gene Expression Data to
                                  Construct Transcriptional Networks . . . 401--415
                Man-Wai Mak and   
                   Jian Guo and   
                  Sun-Yuan Kung   PairProSVM: Protein Subcellular
                                  Localization Based on Local Pairwise
                                  Profile Alignment and SVM  . . . . . . . 416--422
               Laura L. Elo and   
                Sanna Filen and   
            Riitta Lahesmaa and   
               Tero Aittokallio   Reproducibility-Optimized Test Statistic
                                  for Ranking Genes in Microarray Studies  423--431
      Douglass Stott Parker and   
            Ruey-Lung Hsiao and   
                    Yi Xing and   
            Alissa M. Resch and   
             Christopher J. Lee   Solving the Problem of Trans-Genomic
                                  Query with Alignment Tables  . . . . . . 432--447
                 Zaher Dawy and   
              Michel Sarkis and   
          Joachim Hagenauer and   
               Jakob C. Mueller   Fine-Scale Genetic Mapping Using
                                  Independent Component Analysis . . . . . 448--460
           Michael D. Hendy and   
                      Sagi Snir   Hadamard Conjugation for the Kimura 3ST
                                  Model: Combinatorial Proof Using Path
                                  Sets . . . . . . . . . . . . . . . . . . 461--471
          Philippe Gambette and   
                Daniel H. Huson   Improved Layout of Phylogenetic Networks 472--479

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 5, Number 4, October, 2008

                   Dan Gusfield   EIC Editorial  . . . . . . . . . . . . . 481--481
         Raffaele Giancarlo and   
            Sridhar Hannenhalli   Guest Editors' Introduction to the
                                  Special Section on Algorithms in
                                  Bioinformatics . . . . . . . . . . . . . 482--483
                Jieun Jeong and   
               Piotr Berman and   
            Teresa M. Przytycka   Improving Strand Pairing Prediction
                                  through Exploring Folding Cooperativity  484--491
       Loredana M. Genovese and   
             Filippo Geraci and   
               Marco Pellegrini   SpeedHap: An Accurate Heuristic for the
                                  Single Individual SNP Haplotyping
                                  Problem with Many Gaps, High Reading
                                  Error Rate and Low Coverage  . . . . . . 492--502
              Antoni Lozano and   
              Ron Y. Pinter and   
             Oleg Rokhlenko and   
           Gabriel Valiente and   
             Michal Ziv-Ukelson   Seeded Tree Alignment  . . . . . . . . . 503--513
            Mukul S. Bansal and   
              Oliver Eulenstein   An $ \Omega (n^2 / \log n) $ Speed-Up of
                                  TBR Heuristics for the Gene-Duplication
                                  Problem  . . . . . . . . . . . . . . . . 514--524
                 Xueyi Wang and   
                  Jack Snoeyink   Defining and Computing Optimum RMSD for
                                  Gapped and Weighted Multiple-Structure
                                  Alignment  . . . . . . . . . . . . . . . 525--533
                  Peggy Yao and   
               Ankur Dhanik and   
                Nathan Marz and   
               Ryan Propper and   
                Charles Kou and   
               Guanfeng Liu and   
        Henry van den Bedem and   
        Jean-Claude Latombe and   
   Inbal Halperin-Landsberg and   
                 Russ B. Altman   Efficient Algorithms to Explore
                                  Conformation Spaces of Flexible Protein
                                  Loops  . . . . . . . . . . . . . . . . . 534--545
                   Eagu Kim and   
                John Kececioglu   Learning Scoring Schemes for Sequence
                                  Alignment from Partial Examples  . . . . 546--556
          Alexander Schliep and   
                  Roland Krause   Efficient Algorithms for the
                                  Computational Design of Optimal Tiling
                                  Arrays . . . . . . . . . . . . . . . . . 557--567
                   Zeyun Yu and   
               Chandrajit Bajaj   Computational Approaches for Automatic
                                  Structural Analysis of Large
                                  Biomolecular Complexes . . . . . . . . . 568--582
            Yann Christinat and   
             Bernd Wachmann and   
                      Lei Zhang   Gene Expression Data Analysis Using a
                                  Novel Approach to Biclustering Combining
                                  Discrete and Continuous Data . . . . . . 583--593
            Vincent Lacroix and   
            Ludovic Cottret and   
   Patricia Thébault and   
             Marie-France Sagot   An Introduction to Metabolic Networks
                                  and Their Structural Analysis  . . . . . 594--617
          Ravi Vijaya Satya and   
                 Amar Mukherjee   The Undirected Incomplete Perfect
                                  Phylogeny Problem  . . . . . . . . . . . 618--629
              Cedric Gondro and   
              Brian P. Kinghorn   Optimization of cDNA Microarray
                                  Experimental Designs Using an
                                  Evolutionary Algorithm . . . . . . . . . 630--638


IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 6, Number 1, January, 2009

                   Dan Gusfield   Final, Five-Year End, Editorial  . . . . 1--2
             Marie-France Sagot   New EIC Editorial  . . . . . . . . . . . 3--3
            Daniel H. Huson and   
            Vincent Moulton and   
                     Mike Steel   Special Section: Phylogenetics . . . . . 4--6
                  Kevin Liu and   
             Serita Nelesen and   
            Sindhu Raghavan and   
           C. Randal Linder and   
                   Tandy Warnow   Barking Up The Wrong Treelength: The
                                  Impact of Gap Penalty on Alignment and
                                  Tree Accuracy  . . . . . . . . . . . . . 7--21
             Bui Quang Minh and   
                Fabio Pardi and   
             Steffen Klaere and   
             Arndt von Haeseler   Budgeted Phylogenetic Diversity on
                                  Circular Split Systems . . . . . . . . . 22--29
                Simone Linz and   
                 Charles Semple   Hybridization in Nonbinary Trees . . . . 30--45
            Gabriel Cardona and   
     Merc\`e Llabrés and   
   Francesc Rosselló and   
               Gabriel Valiente   Metrics for Phylogenetic Networks I:
                                  Generalizations of the Robinson--Foulds
                                  Metric . . . . . . . . . . . . . . . . . 46--61
             Stephen J. Willson   Robustness of Topological Supertree
                                  Methods for Reconciling Dense
                                  Incompatible Data  . . . . . . . . . . . 62--75
        Elizabeth S. Allman and   
                 John A. Rhodes   The Identifiability of Covarion Models
                                  in Phylogenetics . . . . . . . . . . . . 76--88
            Frederick A. Matsen   Fourier Transform Inequalities for
                                  Phylogenetic Trees . . . . . . . . . . . 89--95
                   Dan Gusfield   Outgoing EIC Editorial for this Special
                                  Section of TCBB with the Theme of
                                  Phylogenetics  . . . . . . . . . . . . . 96--96
      Stefan Grünewald and   
                Vincent Moulton   Maximum Parsimony for Tree Mixtures  . . 97--102
                Daniel H. Huson   Drawing Rooted Phylogenetic Networks . . 103--109
           Magnus Bordewich and   
            Olivier Gascuel and   
         Katharina T. Huber and   
                Vincent Moulton   Consistency of Topological Moves Based
                                  on the Balanced Minimum Evolution
                                  Principle of Phylogenetic Inference  . . 110--117
                 Taoyang Wu and   
            Vincent Moulton and   
                     Mike Steel   Refining Phylogenetic Trees Given
                                  Additional Data: An Algorithm Based on
                                  Parsimony  . . . . . . . . . . . . . . . 118--125
            Elchanan Mossel and   
             Sebastien Roch and   
                     Mike Steel   Shrinkage Effect in Ancestral Maximum
                                  Likelihood . . . . . . . . . . . . . . . 126--133
                 Jianmin Ma and   
             Minh N. Nguyen and   
            Jagath C. Rajapakse   Gene Classification Using Codon Usage
                                  and Support Vector Machines  . . . . . . 134--143
                  Ranjan Maitra   Initializing Partition-Optimization
                                  Algorithms . . . . . . . . . . . . . . . 144--157
   Sridharakumar Narasimhan and   
     Raghunathan Rengaswamy and   
        Rajanikanth Vadigepalli   Structural Properties of Gene Regulatory
                                  Networks: Definitions and Connections    158--170
                      Anonymous   2008 Reviewers List  . . . . . . . . . . 171--173

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 6, Number 2, April, 2009

             Marie-France Sagot   EIC Editorial  . . . . . . . . . . . . . 177--177
                Ion Mandoiu and   
                     Yi Pan and   
            Raj Sunderraman and   
           Alexander Zelikovsky   Guest Editors' Introduction to the
                                  Special Section on Bioinformatics
                                  Research and Applications  . . . . . . . 178--179
           Todd J. Treangen and   
           Aaron E. Darling and   
            Guillaume Achaz and   
              Mark A. Ragan and   
           Xavier Messeguer and   
            Eduardo P. C. Rocha   A Novel Heuristic for Local Multiple
                                  Alignment of Interspersed DNA Repeats    180--189
                 Shibin Qiu and   
                    Terran Lane   A Framework for Multiple Kernel Support
                                  Vector Regression and Its Applications
                                  to siRNA Efficacy Prediction . . . . . . 190--199
               Yongjin Park and   
           Stanley Shackney and   
               Russell Schwartz   Network-Based Inference of Cancer
                                  Progression from Microarray Data . . . . 200--212
                   Qian Zhu and   
                  Zaky Adam and   
                 Vicky Choi and   
                  David Sankoff   Generalized Gene Adjacencies, Graph
                                  Bandwidth, and Clusters in Yeast
                                  Evolution  . . . . . . . . . . . . . . . 213--220
            Mukul S. Bansal and   
          Oliver Eulenstein and   
              André Wehe   The Gene-Duplication Problem:
                                  Near-Linear Time Algorithms for
                                  NNI-Based Local Searches . . . . . . . . 221--231
                  Yanni Sun and   
                  Jeremy Buhler   Designing Patterns and Profiles for
                                  Faster HMM Search  . . . . . . . . . . . 232--243
           Jahangheer Shaik and   
                Mohammed Yeasin   Fuzzy-Adaptive-Subspace-Iteration-Based
                                  Two-Way Clustering of Microarray Data    244--259
            Matthieu Vignes and   
                Florence Forbes   Gene Clustering via Integrated Markov
                                  Models Combining Individual and Pairwise
                                  Features . . . . . . . . . . . . . . . . 260--270
           Lenwood S. Heath and   
                Allan A. Sioson   Semantics of Multimodal Network Models   271--280
            Ana Arribas-Gil and   
               Dirk Metzler and   
           Jean-Louis Plouhinec   Statistical Alignment with a Sequence
                                  Evolution Model Allowing Rate
                                  Heterogeneity along the Sequence . . . . 281--295
           Gunther H. Weber and   
               Oliver Rubel and   
               Min-Yu Huang and   
           Angela H. DePace and   
        Charless C. Fowlkes and   
        Soile V. E. Keranen and   
    Cris L. Luengo Hendriks and   
                 Hans Hagen and   
           David W. Knowles and   
             Jitendra Malik and   
             Mark D. Biggin and   
                   Bernd Hamann   Visual Exploration of Three-Dimensional
                                  Gene Expression Using Physical Views and
                                  Linked Abstract Views  . . . . . . . . . 296--309
        Edward R. Dougherty and   
                Marcel Brun and   
           Jeffrey M. Trent and   
             Michael L. Bittner   Conditioning-Based Modeling of
                                  Contextual Genomic Regulation  . . . . . 310--320
           Lenwood S. Heath and   
                Allan A. Sioson   Multimodal Networks: Structure and
                                  Operations . . . . . . . . . . . . . . . 321--332
             Naoto Yukinawa and   
              Shigeyuki Oba and   
                Kikuya Kato and   
                     Shin Ishii   Optimal Aggregation of Binary
                                  Classifiers for Multiclass Cancer
                                  Diagnosis Using Gene Expression Profiles 333--343
               Victor Olman and   
                Fenglou Mao and   
                 Hongwei Wu and   
                        Ying Xu   Parallel Clustering Algorithm for Large
                                  Data Sets with Applications in
                                  Bioinformatics . . . . . . . . . . . . . 344--352
           Topon Kumar Paul and   
                    Hitoshi Iba   Prediction of Cancer Class with Majority
                                  Voting Genetic Programming Classifier
                                  Using Gene Expression Data . . . . . . . 353--367

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 6, Number 3, July, 2009

             Marie-France Sagot   EIC Editorial: Introducing New Associate
                                  Editors  . . . . . . . . . . . . . . . . 369--369
                   Chengpeng Bi   A Monte Carlo EM Algorithm for De Novo
                                  Motif Discovery in Biomolecular
                                  Sequences  . . . . . . . . . . . . . . . 370--386
                 Jens Stoye and   
                 Roland Wittler   A Unified Approach for Reconstructing
                                  Ancient Gene Clusters  . . . . . . . . . 387--400
                   Xin Chen and   
                        Yun Cui   An Approximation Algorithm for the
                                  Minimum Breakpoint Linearization Problem 401--409
                Zidong Wang and   
                Xiaohui Liu and   
                 Yurong Liu and   
              Jinling Liang and   
             Veronica Vinciotti   An Extended Kalman Filtering Approach to
                                  Modeling Nonlinear Dynamic Gene
                                  Regulatory Networks via Short Gene
                                  Expression Time Series . . . . . . . . . 410--419
               David Bryant and   
                     Mike Steel   Computing the Distribution of a Tree
                                  Metric . . . . . . . . . . . . . . . . . 420--426
               Marc Hulsman and   
      Marcel J. T. Reinders and   
                 Dick de Ridder   Evolutionary Optimization of Kernel
                                  Weights Improves Protein Complex
                                  Comembership Prediction  . . . . . . . . 427--437
             Zhi-Zhong Chen and   
                   Lusheng Wang   Improved Approximation Algorithms for
                                  Reconstructing the History of Tandem
                                  Repeats  . . . . . . . . . . . . . . . . 438--453
            Gabriel Cardona and   
              Merce Llabres and   
          Francesc Rossello and   
               Gabriel Valiente   Metrics for Phylogenetic Networks II:
                                  Nodal and Triplets Metrics . . . . . . . 454--469
     Vassilios Sotiropoulos and   
Marrie-Nathalie Contou-Carrere and   
        Prodromos Daoutidis and   
           Yiannis N. Kaznessis   Model Reduction of Multiscale Chemical
                                  Langevin Equations: a Numerical Case
                                  Study  . . . . . . . . . . . . . . . . . 470--482
           Mikhail Roytberg and   
                Anna Gambin and   
                Laurent Noe and   
            Slawomir Lasota and   
          Eugenia Furletova and   
               Ewa Szczurek and   
               Gregory Kucherov   On Subset Seeds for Protein Alignment    483--494
                 Guohua Jin and   
               Luay Nakhleh and   
                  Sagi Snir and   
                   Tamir Tuller   Parsimony Score of Phylogenetic
                                  Networks: Hardness Results and a
                                  Linear-Time Heuristic  . . . . . . . . . 495--505
                John Thomas and   
         Naren Ramakrishnan and   
           Chris Bailey-Kellogg   Protein Design by Sampling an Undirected
                                  Graphical Model of Residue Constraints   506--516
              Jennifer A. Smith   RNA Search with Decision Trees and
                                  Partial Covariance Models  . . . . . . . 517--527

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 6, Number 4, October, 2009

                   Jie Chen and   
                   Yu-Ping Wang   A Statistical Change Point Model
                                  Approach for the Detection of DNA Copy
                                  Number Variations in Array CGH Data  . . 529--541
               Amol Prakash and   
                   Martin Tompa   Assessing the Discordance of Multiple
                                  Sequence Alignments  . . . . . . . . . . 542--551
            Gabriel Cardona and   
          Francesc Rossello and   
               Gabriel Valiente   Comparison of Tree-Child Phylogenetic
                                  Networks . . . . . . . . . . . . . . . . 552--569
              Changjin Hong and   
                Ahmed H. Tewfik   Heuristic Reusable Dynamic Programming:
                                  Efficient Updates of Local Sequence
                                  Alignment  . . . . . . . . . . . . . . . 570--582
                  Yong Wang and   
                Wu Ling-Yun and   
              Ji-Hong Zhang and   
             Zhong-Wei Zhan and   
            Zhang Xiang-Sun and   
                    Chen Luonan   Evaluating Protein Similarity from
                                  Coarse Structures  . . . . . . . . . . . 583--593
             Miquel Salicru and   
                Sergi Vives and   
                     Tian Zheng   Inferential Clustering Approach for
                                  Microarray Experiments with Replicated
                                  Measurements . . . . . . . . . . . . . . 594--604
            Satoshi Niijima and   
                  Yasushi Okuno   Laplacian Linear Discriminant Analysis
                                  Approach to Unsupervised Feature
                                  Selection  . . . . . . . . . . . . . . . 605--614
             Carl Rasmussen and   
         Bernard de la Cruz and   
          Zoubin Ghahramani and   
                     David Wild   Modeling and Visualizing Uncertainty in
                                  Gene Expression Clusters Using Dirichlet
                                  Process Mixtures . . . . . . . . . . . . 615--628
            Gabriel Cardona and   
              Merce Llabres and   
          Francesc Rossello and   
               Gabriel Valiente   On Nakhleh's Metric for Reduced
                                  Phylogenetic Networks  . . . . . . . . . 629--638
         Pradeep Chowriappa and   
                 Sumeet Dua and   
                Jinko Kanno and   
             Hilary W. Thompson   Protein Structure Classification Based
                                  on Conserved Hydrophobic Residues  . . . 639--651
             Hiroaki Uehara and   
                 Masakazu Jimbo   A Positive Detecting Code and Its
                                  Decoding Algorithm for DNA Library
                                  Screening  . . . . . . . . . . . . . . . 652--666
             Leo van Iersel and   
            Judith Keijsper and   
                Steven Kelk and   
               Leen Stougie and   
                Ferry Hagen and   
                  Teun Boekhout   Constructing Level-2 Phylogenetic
                                  Networks from Triplets . . . . . . . . . 667--681
                  Saad Mneimneh   On the Approximation of Optimal
                                  Structures for RNA--RNA Interaction  . . 682--688
              Luis A. Diago and   
                 Ernesto Moreno   Evaluation of Geometric Complementarity
                                  between Molecular Surfaces Using
                                  Compactly Supported Radial Basis
                                  Functions  . . . . . . . . . . . . . . . 689--694
            Ana M. Gonzalez and   
        Francisco J. Azuaje and   
            Jose L. Ramirez and   
        Jose F. da Silveira and   
             Jose R. Dorronsoro   Machine Learning Techniques for the
                                  Automated Classification of Adhesin-Like
                                  Proteins in the Human Protozoan Parasite
                                  \bionameTrypanosoma cruzi  . . . . . . . 695--702
                      Anonymous   Call for Papers: Special Issue of
                                  Transactions in Computational Biology
                                  and Bioinformatics: Special Issue on
                                  BioCreative II.5 . . . . . . . . . . . . 703
                      Anonymous   2009 TCBB Annual Index . . . . . . . . . Not in Print


IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 7, Number 1, January, 2010

                      Anonymous   Editor's Note  . . . . . . . . . . . . . 1--1
                 Ester Diaz and   
            Guillermo Ayala and   
       Maria Diaz-Fernandez and   
                 Liang Gong and   
                   Derek Toomre   Automatic Detection of Large Dense-Core
                                  Vesicles in Secretory Cells and
                                  Statistical Analysis of Their
                                  Intracellular Distribution . . . . . . . 2--11
            Carol Lushbough and   
         Michael K. Bergman and   
        Carolyn J. Lawrence and   
             Doug Jennewein and   
                 Volker Brendel   BioExtract Server --- an Integrated
                                  Workflow-Enabling System to Access and
                                  Analyze Heterogeneous, Distributed
                                  Biomolecular Data  . . . . . . . . . . . 12--24
               Shenghuo Zhu and   
              Dingding Wang and   
                     Kai Yu and   
                     Tao Li and   
                    Yihong Gong   Feature Selection for Gene Expression
                                  Using Model-Based Entropy  . . . . . . . 25--36
             Petri Pehkonen and   
                 Garry Wong and   
                  Petri Toronen   Heuristic Bayesian Segmentation for
                                  Discovery of Coexpressed Genes within
                                  Genomic Regions  . . . . . . . . . . . . 37--49
               Rafal Kustra and   
                 Adam Zagdanski   Data-Fusion in Clustering Microarray
                                  Data: Balancing Discovery and
                                  Interpretability . . . . . . . . . . . . 50--63
               Oliver Rubel and   
           Gunther H. Weber and   
               Min-Yu Huang and   
              E. Wes Bethel and   
             Mark D. Biggin and   
        Charless C. Fowlkes and   
    Cris L. Luengo Hendriks and   
        Soile V. E. Keranen and   
           Michael B. Eisen and   
           David W. Knowles and   
             Jitendra Malik and   
                 Hans Hagen and   
                   Bernd Hamann   Integrating Data Clustering and
                                  Visualization for the Analysis of $3$D
                                  Gene Expression Data . . . . . . . . . . 64--79
                     Ju Han and   
                 Hang Chang and   
          Kumari Andarawewa and   
                Paul Yaswen and   
  Mary Helen Barcellos-Hoff and   
                  Bahram Parvin   Multidimensional Profiling of Cell
                                  Surface Proteins and Nuclear Markers . . 80--90
                Bogdan Done and   
             Purvesh Khatri and   
                 Arina Done and   
                 Sorin Draghici   Predicting Novel Human Gene Ontology
                                  Annotations Using Semantic Analysis  . . 91--99
                Zhenqiu Liu and   
                  Shili Lin and   
                       Ming Tan   Sparse Support Vector Machines with $
                                  L_p $ Penalty for Biomarker
                                  Identification . . . . . . . . . . . . . 100--107
               Yukyee Leung and   
                  Yeungsam Hung   A Multiple-Filter-Multiple-Wrapper
                                  Approach to Gene Selection and
                                  Microarray Data Classification . . . . . 108--117
        Theodore J. Perkins and   
             Michael T. Hallett   A Trade-Off between Sample Complexity
                                  and Computational Complexity in Learning
                                  Boolean Networks from Time-Series Data   118--125
            Richard Pelikan and   
               Milos Hauskrecht   Efficient Peak-Labeling Algorithms for
                                  Whole-Sample Mass Spectrometry
                                  Proteomics . . . . . . . . . . . . . . . 126--137
                  Pritha Mahata   Exploratory Consensus of Hierarchical
                                  Clusterings for Melanoma and Breast
                                  Cancer . . . . . . . . . . . . . . . . . 138--152
            Sara C. Madeira and   
         Miguel C. Teixeira and   
          Isabel Sa-Correia and   
            Arlindo L. Oliveira   Identification of Regulatory Modules in
                                  Time Series Gene Expression Data Using a
                                  Linear Time Biclustering Algorithm . . . 153--165
            Elchanan Mossel and   
                 Sebastien Roch   Incomplete Lineage Sorting: Consistent
                                  Phylogeny Estimation from Multiple Loci  166--171
            Alex A. Freitas and   
          Daniela C. Wieser and   
                  Rolf Apweiler   On the Importance of Comprehensible
                                  Classification Models for Protein
                                  Function Prediction  . . . . . . . . . . 172--182
                  Noga Alon and   
                 Benny Chor and   
                Fabio Pardi and   
                  Anat Rapoport   Approximate Maximum Parsimony and
                                  Ancestral Maximum Likelihood . . . . . . 183--187
                      Anonymous   2009 Reviewer's List . . . . . . . . . . 188--190

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 7, Number 2, April, 2010

             Marie-France Sagot   EIC Editorial  . . . . . . . . . . . . . 193--194
            Stefano Lonardi and   
                      Jake Chen   Data Mining in Bioinformatics: Selected
                                  Papers from BIOKDD . . . . . . . . . . . 195--196
              Aaron Smalter and   
                   Jun Huan and   
                     Yi Jia and   
              Gerald Lushington   GPD: a Graph Pattern Diffusion Kernel
                                  for Accurate Graph Classification with
                                  Applications in Cheminformatics  . . . . 197--207
             Petko Bogdanov and   
                 Ambuj K. Singh   Molecular Function Prediction Using
                                  Neighborhood Features  . . . . . . . . . 208--217
                   Luay Nakhleh   A Metric on the Space of Reduced
                                  Phylogenetic Networks  . . . . . . . . . 218--222
               Gunjan Gupta and   
              Alexander Liu and   
                  Joydeep Ghosh   Automated Hierarchical Density Shaving:
                                  a Robust Automated Clustering and
                                  Visualization Framework for Large
                                  Biological Data Sets . . . . . . . . . . 223--237
         Douglas W. Raiford and   
               Dan E. Krane and   
             Travis E. Doom and   
              Michael L. Raymer   Automated Isolation of Translational
                                  Efficiency Bias That Resists the
                                  Confounding Effect of GC(AT)-Content . . 238--250
           Arthur Tenenhaus and   
          Vincent Guillemot and   
              Xavier Gidrol and   
                 Vincent Frouin   Gene Association Networks from
                                  Microarray Data Using a Regularized
                                  Estimation of Partial Correlation Based
                                  on PLS Regression  . . . . . . . . . . . 251--262
                 Zexuan Zhu and   
               Yew-Soon Ong and   
                Jacek M. Zurada   Identification of Full and Partial Class
                                  Relevant Genes . . . . . . . . . . . . . 263--277
            Ranjit Randhawa and   
              Cliff Shaffer and   
                     John Tyson   Model Composition for Macromolecular
                                  Regulatory Networks  . . . . . . . . . . 278--287
          Shahid H. Bokhari and   
                  Daniel Janies   Reassortment Networks for Investigating
                                  the Evolution of Segmented Viruses . . . 288--298
         Tracy L. Bergemann and   
                  Lue Ping Zhao   Signal Quality Measurements for cDNA
                                  Microarray Data  . . . . . . . . . . . . 299--308
             Guillaume Blin and   
               Alain Denise and   
               Serge Dulucq and   
            Claire Herrbach and   
                 Heleene Touzet   Alignments of RNA Structures . . . . . . 309--322
                  Minghui Jiang   Approximation Algorithms for Predicting
                                  RNA Secondary Structures with Arbitrary
                                  Pseudoknots  . . . . . . . . . . . . . . 323--332
                 Tetsuo Shibuya   Fast Hinge Detection Algorithms for
                                  Flexible Protein Structures  . . . . . . 333--341
          Sylvain Guillemot and   
                  Vincent Berry   Fixed-Parameter Tractability of the
                                  Maximum Agreement Supertree Problem  . . 342--353
                Xiaowen Liu and   
                  Jinyan Li and   
                   Lusheng Wang   Modeling Protein Interacting Groups by
                                  Quasi-Bicliques: Complexity, Algorithm,
                                  and Application  . . . . . . . . . . . . 354--364
                 Xingqin Qi and   
                  Guojun Li and   
                Shuguang Li and   
                        Ying Xu   Sorting Genomes by Reciprocal
                                  Translocations, Insertions, and
                                  Deletions  . . . . . . . . . . . . . . . 365--374
                Giora Unger and   
                     Benny Chor   Linear Separability of Gene Expression
                                  Data Sets  . . . . . . . . . . . . . . . 375--381

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 7, Number 3, July, 2010

            Florian Leitner and   
            Scott A. Mardis and   
          Martin Krallinger and   
            Gianni Cesareni and   
       Lynette A. Hirschman and   
               Alfonso Valencia   An Overview of BioCreative II.5  . . . . 385--399
          Artemy Kolchinsky and   
            Alaa Abi-Haidar and   
               Jasleen Kaur and   
         Ahmed Abdeen Hamed and   
                  Luis M. Rocha   Classification of Protein-Protein
                                  Interaction Full-Text Documents Using
                                  Text and Citation Network Features . . . 400--411
               Hong-Jie Dai and   
                Po-Ting Lai and   
         Richard Tzong-Han Tsai   Multistage Gene Normalization and
                                  SVM-Based Ranking for Protein Interactor
                                  Extraction in Full-Text Articles . . . . 412--420
                    Man Lan and   
                        Jian Su   Empirical Investigations into Full-Text
                                  Protein Interaction Article
                                  Categorization Task (ACT) in the
                                  BioCreative II.5 Challenge . . . . . . . 421--427
                 Yifei Chen and   
                   Feng Liu and   
              Bernard Manderick   BioLMiner System: Interaction
                                  Normalization Task and Interaction Pair
                                  Task in the BioCreative II.5 Challenge   428--441
           Rune Sætre and   
           Kazuhiro Yoshida and   
                Makoto Miwa and   
           Takuya Matsuzaki and   
             Yoshinobu Kano and   
                Jun'ichi Tsujii   Extracting Protein Interactions from
                                  Text with the Unified AkaneRE Event
                                  Extraction System  . . . . . . . . . . . 442--453
              Yong-gang Cao and   
                 Zuofeng Li and   
                 Feifan Liu and   
           Shashank Agarwal and   
                 Qing Zhang and   
                        Hong Yu   An IR-Aided Machine Learning Framework
                                  for the BioCreative II.5 Challenge . . . 454--461
             Karin Verspoor and   
          Christophe Roeder and   
           Helen L. Johnson and   
      Kevin Bretonnel Cohen and   
William A. Baumgartner, Jr. and   
             Lawrence E. Hunter   Exploring Species-Based Strategies for
                                  Gene Normalization . . . . . . . . . . . 462--471
              Fabio Rinaldi and   
           Gerold Schneider and   
           Kaarel Kaljurand and   
            Simon Clematide and   
    Thér\`ese Vachon and   
                Martin Romacker   OntoGene in BioCreative II.5 . . . . . . 472--480
        Jörg Hakenberg and   
              Robert Leaman and   
               Nguyen Ha Vo and   
    Siddhartha Jonnalagadda and   
              Ryan Sullivan and   
         Christopher Miller and   
                  Luis Tari and   
               Chitta Baral and   
              Graciela Gonzalez   Efficient Extraction of Protein-Protein
                                  Interactions from Full-Text Articles . . 481--494
      Rezaul Alan Chowdhury and   
                 Hai-Son Le and   
            Vijaya Ramachandran   Cache-Oblivious Dynamic Programming for
                                  Bioinformatics . . . . . . . . . . . . . 495--510
          Leonardo Tininini and   
           Paola Bertolazzi and   
            Alessandra Godi and   
                Giuseppe Lancia   CollHaps: a Heuristic Approach to
                                  Haplotype Inference by Parsimony . . . . 511--523
        Ronald Jackups, Jr. and   
                      Jie Liang   Combinatorial Analysis for Sequence and
                                  Spatial Motif Discovery in Short
                                  Sequence Fragments . . . . . . . . . . . 524--536
                     Xiaoxu Han   Nonnegative Principal Component Analysis
                                  for Cancer Molecular Pattern Discovery   537--549
                   Jia Zeng and   
               Xiao-Yu Zhao and   
               Xiao-Qin Cao and   
                       Hong Yan   SCS: Signal, Context, and Structure
                                  Features for Genome-Wide Human Promoter
                                  Recognition  . . . . . . . . . . . . . . 550--562
               Arthur Zimek and   
            Fabian Buchwald and   
                 Eibe Frank and   
                  Stefan Kramer   A Study of Hierarchical and Flat
                                  Classification of Proteins . . . . . . . 563--571
          Maria Luisa Bonet and   
             Katherine St. John   On the Complexity of uSPR Distance . . . 572--576

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 7, Number 4, October, 2010

                 Ion Mandou and   
            Giri Narasimhan and   
                     Yi Pan and   
                  Yanqing Zhang   Guest Editors' Introduction to the
                                  Special Section on Bioinformatics
                                  Research and Applications  . . . . . . . 577--578
              Adriana Munoz and   
                  David Sankoff   Rearrangement Phylogeny of Genomes in
                                  Contig Form  . . . . . . . . . . . . . . 579--587
       Balaji Venkatachalam and   
                  Jim Apple and   
         Katherine St. John and   
                Daniel Gusfield   Untangling Tanglegrams: Comparing Trees
                                  by Their Drawings  . . . . . . . . . . . 588--597
            Paola Bonizzoni and   
      Gianluca Della Vedova and   
             Riccardo Dondi and   
                Yuri Pirola and   
                    Romeo Rizzi   Pure Parsimony Xor Haplotyping . . . . . 598--610
                      Yufeng Wu   Exact Computation of Coalescent
                                  Likelihood for Panmictic and Subdivided
                                  Populations under the Infinite Sites
                                  Model  . . . . . . . . . . . . . . . . . 611--618
    Sanguthevar Rajasekaran and   
             Sahar Al Seesi and   
                  Reda A. Ammar   Improved Algorithms for Parsing ESLTAGs:
                                  a Grammatical Model Suitable for RNA
                                  Pseudoknots  . . . . . . . . . . . . . . 619--627
             Guillaume Blin and   
             Florian Sikora and   
              Stephane Vialette   Querying Graphs in Protein-Protein
                                  Interactions Networks Using Feedback
                                  Vertex Set . . . . . . . . . . . . . . . 628--635
                    Qiang Cheng   A Sparse Learning Machine for
                                  High-Dimensional Data with Application
                                  to Microarray Gene Analysis  . . . . . . 636--646
              W. B. Langdon and   
             G. J. G. Upton and   
        R. da Silva Camargo and   
                 A. P. Harrison   A Survey of Spatial Defects in Homo
                                  Sapiens Affymetrix GeneChips . . . . . . 647--653
                    Gang Li and   
              Tak-Ming Chan and   
            Kwong-Sak Leung and   
                   Kin-Hong Lee   A Cluster Refinement Algorithm for Motif
                                  Discovery  . . . . . . . . . . . . . . . 654--668
               Jianjun Zhou and   
                Jorg Sander and   
                Zhipeng Cai and   
               Lusheng Wang and   
                     Guohui Lin   Finding the Nearest Neighbors in
                                  Biological Databases Using Less Distance
                                  Computations . . . . . . . . . . . . . . 669--680
          Liang-Tsung Huang and   
                Lien-Fu Lai and   
             M. Michael Gromiha   Human-Readable Rule Generator for
                                  Integrating Amino Acid Sequence
                                  Information and Stability of Mutant
                                  Proteins . . . . . . . . . . . . . . . . 681--687
           Christophe Godin and   
                 Pascal Ferraro   Quantifying the Degree of
                                  Self-Nestedness of Trees: Application to
                                  the Structural Analysis of Plants  . . . 688--703
                  Sagi Snir and   
                     Satish Rao   Quartets MaxCut: a Divide and Conquer
                                  Quartets Algorithm . . . . . . . . . . . 704--718
                     Xin Lu and   
              Anthony Gamst and   
                     Ronghui Xu   RDCurve: a Nonparametric Method to
                                  Evaluate the Stability of Ranking
                                  Procedures . . . . . . . . . . . . . . . 719--726
           Herbert H. Tsang and   
                   Kay C. Wiese   SARNA-Predict: Accuracy Improvement of
                                  RNA Secondary Structure Prediction Using
                                  Permutation-Based Simulated Annealing    727--740
                  Liwen You and   
            Vladimir Brusic and   
           Marcus Gallagher and   
                   Mikael Boden   Using Gaussian Process with Test
                                  Rejection to Detect T-Cell Epitopes in
                                  Pathogen Genomes . . . . . . . . . . . . 741--751
         Alberto Apostolico and   
               Matteo Comin and   
                   Laxmi Parida   VARUN: Discovering Extensible Motifs
                                  under Saturation Constraints . . . . . . 752--762
              Istvan Miklos and   
             Bence Melykuti and   
                Krister Swenson   The Metropolized Partial Importance
                                  Sampling MCMC Mixes Slowly on Minimum
                                  Reversal Rearrangement Paths . . . . . . 763--767
                      Anonymous   2010 TCBB Annual Index . . . . . . . . . 763--767


IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 8, Number 1, January, 2011

             Marie-France Sagot   EIC Editorial  . . . . . . . . . . . . . 1--1
                 Megan Owen and   
                J. Scott Provan   A Fast Algorithm for Computing Geodesic
                                  Distances in Tree Space  . . . . . . . . 2--13
                 Mohak Shah and   
                Jacques Corbeil   A General Framework for Analyzing Data
                                  from Two Short Time-Series Microarray
                                  Experiments  . . . . . . . . . . . . . . 14--26
                 Sean Mauch and   
                   Mark Stalzer   Efficient Formulations for Exact
                                  Stochastic Simulation of Chemical
                                  Systems  . . . . . . . . . . . . . . . . 27--35
             Dario Gasbarra and   
         Sangita Kulathinal and   
              Matti Pirinen and   
             Mikko J. Sillanpaa   Estimating Haplotype Frequencies by
                                  Combining Data from Large DNA Pools with
                                  Database Information . . . . . . . . . . 36--44
        Chandrajit L. Bajaj and   
           Rezaul Chowdhury and   
           Vinay Siddahanavalli   $ F^2 $Dock: Fast Fourier
                                  Protein-Protein Docking  . . . . . . . . 45--58
              Joachim Giard and   
      Patrice Rondao Alface and   
              Jean-Luc Gala and   
                    Benoit Macq   Fast Surface-Based Travel Depth
                                  Estimation Algorithm for Macromolecule
                                  Surface Shape Description  . . . . . . . 59--68
               Cinzia Pizzi and   
                Pasi Rastas and   
                   Esko Ukkonen   Finding Significant Matches of Position
                                  Weight Matrices in Linear Time . . . . . 69--79
             Razvan Andonie and   
     Levente Fabry-Asztalos and   
 Christopher B. Abdul-Wahid and   
          Sarah Abdul-Wahid and   
            Grant I. Barker and   
                Lukas C. Magill   Fuzzy ARTMAP Prediction of Biological
                                  Activities for Potential HIV-1 Protease
                                  Inhibitors Using a Small Molecular Data
                                  Set  . . . . . . . . . . . . . . . . . . 80--93
             Sushmita Mitra and   
                Ranajit Das and   
                 Yoichi Hayashi   Genetic Networks and Soft Computing  . . 94--107
                Wenxue Wang and   
             Bijoy K. Ghosh and   
                Himadri Pakrasi   Identification and Modeling of Genes
                                  with Diurnal Oscillations from
                                  Microarray Time Series Data  . . . . . . 108--121
                Lin-Kai Luo and   
            Deng-Feng Huang and   
                Ling-Jun Ye and   
               Qi-Feng Zhou and   
              Gui-Fang Shao and   
                      Hong Peng   Improving the Computational Efficiency
                                  of Recursive Cluster Elimination for
                                  Gene Selection . . . . . . . . . . . . . 122--129
                 Mehmet Tan and   
        Mohammed Alshalalfa and   
                Reda Alhajj and   
                    Faruk Polat   Influence of Prior Knowledge in
                                  Constraint-Based Learning of Gene
                                  Regulatory Networks  . . . . . . . . . . 130--142
               Liuling Gong and   
           Nidhal Bouaynaya and   
                  Dan Schonfeld   Information-Theoretic Model of Evolution
                                  over Protein Communication Channel . . . 143--151
           Nathan A. Barker and   
             Chris J. Myers and   
              Hiroyuki Kuwahara   Learning Genetic Regulatory Network
                                  Connectivity from Time Series Data . . . 152--165
            Delphine Ropers and   
         Valentina Baldazzi and   
                  Hidde de Jong   Model Reduction Using Piecewise-Linear
                                  Approximations Preserves Dynamic
                                  Properties of the Carbon Starvation
                                  Response in \bionameEscherichia coli . . 166--181
                      Yufeng Wu   New Methods for Inference of Local Tree
                                  Topologies with Recombinant SNP
                                  Sequences in Populations . . . . . . . . 182--193
              Ankit Agrawal and   
                  Xiaoqiu Huang   Pairwise Statistical Significance of
                                  Local Sequence Alignment Using
                                  Sequence-Specific and Position-Specific
                                  Substitution Matrices  . . . . . . . . . 194--205
     Rogier J. P. van Berlo and   
             Dick de Ridder and   
            Jean-Marc Daran and   
Pascale A. S. Daran-Lapujade and   
                Bas Teusink and   
          Marcel J. T. Reinders   Predicting Metabolic Fluxes Using Gene
                                  Expression Differences As Constraints    206--216
                  Leo Lahti and   
               Laura L. Elo and   
           Tero Aittokallio and   
                   Samuel Kaski   Probabilistic Analysis of Probe
                                  Reliability in Differential Gene
                                  Expression Studies with Short
                                  Oligonucleotide Arrays . . . . . . . . . 217--225
                Dukka B. Kc and   
              Dennis R. Livesay   Topology Improves Phylogenetic Motif
                                  Functional Site Predictions  . . . . . . 226--233
          Md Tamjidul Hoque and   
               Madhu Chetty and   
               Andrew Lewis and   
                   Abdul Sattar   Twin Removal in Genetic Algorithms for
                                  Protein Structure Prediction Using
                                  Low-Resolution Model . . . . . . . . . . 234--245
  Joaquim F. Pinto da Costa and   
                Hugo Alonso and   
                     Luis Roque   A Weighted Principal Component Analysis
                                  and Its Application to Gene Expression
                                  Data . . . . . . . . . . . . . . . . . . 246--252
                    Ping Li and   
                      James Lam   Disturbance Analysis of Nonlinear
                                  Differential Equation Models of Genetic
                                  SUM Regulatory Networks  . . . . . . . . 253--259
              Cheng-Wei Luo and   
           Ming-Chiang Chen and   
              Yi-Ching Chen and   
           Roger W. L. Yang and   
              Hsiao-Fei Liu and   
                   Kun-Mao Chao   Linear-Time Algorithms for the Multiple
                                  Gene Duplication Problems  . . . . . . . 260--265
               Kezhi Z. Mao and   
                    Wenyin Tang   Recursive Mahalanobis Separability
                                  Measure for Gene Subset Selection  . . . 266--272
       Vikram Krishnamurthy and   
                    Kai-Yiu Luk   Semi-Markov Models for Brownian Dynamics
                                  Permeation in Biological Ion Channels    273--281
       Vikram Krishnamurthy and   
                    Kai-Yiu Luk   2010 TCBB Reviewers List . . . . . . . . 282--284

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 8, Number 2, March, 2011

             Marie-France Sagot   EIC Editorial  . . . . . . . . . . . . . 289--291
              Fang-Xiang Wu and   
                       Jun Huan   Guest Editorial: Special Focus on
                                  Bioinformatics and Systems Biology . . . 292--293
                 Yanpeng Li and   
                 Xiaohua Hu and   
                Hongfei Lin and   
                    Zhiahi Yang   A Framework for Semisupervised Feature
                                  Generation and Its Applications in
                                  Biomedical Literature Mining . . . . . . 294--307
           Jong Cheol Jeong and   
               Xiaotong Lin and   
                   Xue-wen Chen   On Position-Specific Scoring Matrix for
                                  Protein Function Prediction  . . . . . . 308--315
                Sangyoon Oh and   
                 Min Su Lee and   
               Byoung-Tak Zhang   Ensemble Learning with Active Example
                                  Selection for Imbalanced Biomedical Data
                                  Classification . . . . . . . . . . . . . 316--325
               Zina Ibrahim and   
               Alioune Ngom and   
                Ahmed Y. Tawfik   Using Qualitative Probability in
                                  Reverse-Engineering Gene Regulatory
                                  Networks . . . . . . . . . . . . . . . . 326--334
                Amit Sabnis and   
             Robert W. Harrison   A Continuous-Time, Discrete-State Method
                                  for Simulating the Dynamics of
                                  Biochemical Systems  . . . . . . . . . . 335--341
         Douglas W. Raiford and   
               Dan E. Krane and   
             Travis E. Doom and   
              Michael L. Raymer   A Genetic Optimization Approach for
                                  Isolating Translational Efficiency Bias  342--352
                 Ramesh Ram and   
                   Madhu Chetty   A Markov-Blanket-Based Model for Gene
                                  Regulatory Network Inference . . . . . . 353--367
                 Zengyou He and   
                   Can Yang and   
                    Weichuan Yu   A Partial Set Covering Model for Protein
                                  Mixture Identification Using Mass
                                  Spectrometry Data  . . . . . . . . . . . 368--380
                 Yonghui Wu and   
           Timothy J. Close and   
                Stefano Lonardi   Accurate Construction of Consensus
                                  Genetic Maps via Integer Linear
                                  Programming  . . . . . . . . . . . . . . 381--394
                Zafer Aydin and   
           Yucel Altunbasak and   
                  Hakan Erdogan   Bayesian Models and Algorithms for
                                  Protein $ \beta $-Sheet Prediction . . . 395--409
            Gabriel Cardona and   
              Merce Llabres and   
          Francesc Rossello and   
               Gabriel Valiente   Comparison of Galled Trees . . . . . . . 410--427
             KwongSak Leung and   
                KinHong Lee and   
               JinFeng Wang and   
                Eddie YT Ng and   
              Henry LY Chan and   
            Stephen KW Tsui and   
                Tony SK Mok and   
          Pete Chi-Hang Tse and   
                 Joseph JY Sung   Data Mining on DNA Sequences of
                                  Hepatitis B Virus  . . . . . . . . . . . 428--440
                Tien-ho Lin and   
           Robert F. Murphy and   
                 Ziv Bar-Joseph   Discriminative Motif Finding for
                                  Predicting Protein Subcellular
                                  Localization . . . . . . . . . . . . . . 441--451
           Saras Saraswathi and   
            Suresh Sundaram and   
    Narasimhan Sundararajan and   
         Michael Zimmermann and   
          Marit Nilsen-Hamilton   ICGA-PSO-ELM Approach for Accurate
                                  Multiclass Cancer Classification
                                  Resulting in Reduced Gene Sets in Which
                                  Genes Encoding Secreted Proteins Are
                                  Highly Represented . . . . . . . . . . . 452--463
            Itziar Irigoien and   
                Sergi Vives and   
              Concepcion Arenas   Microarray Time Course Experiments:
                                  Finding Profiles . . . . . . . . . . . . 464--475
                 Qiwen Dong and   
                  Shuigeng Zhou   Novel Nonlinear Knowledge-Based Mean
                                  Force Potentials Based on Machine
                                  Learning . . . . . . . . . . . . . . . . 476--486
           Sebastien Loriot and   
           Sushant Sachdeva and   
             Karine Bastard and   
            Chantal Prevost and   
                Frederic Cazals   On the Characterization and Selection of
                                  Diverse Conformational Ensembles with
                                  Applications to Flexible Docking . . . . 487--498
           Robert Giegerich and   
Christian Hoener zu Siederdissen   Semantics and Ambiguity of Stochastic
                                  RNA Family Models  . . . . . . . . . . . 499--516
                 Ali Tofigh and   
            Michael Hallett and   
                 Jens Lagergren   Simultaneous Identification of
                                  Duplications and Lateral Gene Transfers  517--535
       Michael D. Lieberman and   
                Sima Taheri and   
               whatever Guo and   
          Fatemeh Mirrashed and   
                Inbal Yahav and   
                 Aleks Aris and   
                Ben Shneiderman   Visual Exploration across Biomedical
                                  Databases  . . . . . . . . . . . . . . . 536--550
               Glenn Hickey and   
         Mathieu Blanchette and   
                  Paz Carmi and   
            Anil Maheshwari and   
                    Norbert Zeh   An Approximation Algorithm for the
                                  Noah's Ark Problem with Random Feature
                                  Loss . . . . . . . . . . . . . . . . . . 551--556
                Juan Cortes and   
               Sophie Barbe and   
              Monique Erard and   
                 Thierry Simeon   Encoding Molecular Motions in Voxel Maps 557--563
                       J. Rocha   Graph Comparison by Log-Odds Score
                                  Matrices with Application to Protein
                                  Topology Analysis  . . . . . . . . . . . 564--569
               Andre Fujita and   
          Joao Ricardo Sato and   
      Marcos Almeida Demasi and   
              Rui Yamaguchi and   
           Teppei Shimamura and   
    Carlos Eduardo Ferreira and   
        Mari Cleide Sogayar and   
                  Satoru Miyano   Inferring Contagion in Regulatory
                                  Networks . . . . . . . . . . . . . . . . 570--576

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 8, Number 3, May / June, 2011

              Alfredo Benso and   
           Stefano Di Carlo and   
            Gianfranco Politano   A cDNA Microarray Gene Expression Data
                                  Classifier for Clinical Diagnostics
                                  Based on Graph Theory  . . . . . . . . . 577--591
                Erdem Yoruk and   
            Michael F. Ochs and   
               Donald Geman and   
                 Laurent Younes   A Comprehensive Statistical Model for
                                  Cell Signaling . . . . . . . . . . . . . 592--606
               Jianxin Wang and   
                     Min Li and   
                Jianer Chen and   
                         Yi Pan   A Fast Hierarchical Clustering Algorithm
                                  for Functional Modules Discovery in
                                  Protein Interaction Networks . . . . . . 607--620
              Jianxing Feng and   
                  Rui Jiang and   
                      Tao Jiang   A Max-Flow-Based Approach to the
                                  Identification of Protein Complexes
                                  Using Protein Interaction and Microarray
                                  Data . . . . . . . . . . . . . . . . . . 621--634
         Katharina T. Huber and   
             Leo van Iersel and   
                Steven Kelk and   
             Rados\law Suchecki   A Practical Algorithm for Reconstructing
                                  Level-1 Phylogenetic Networks  . . . . . 635--649
            James T. Murphy and   
                 Ray Walshe and   
                 Marc Devocelle   A Theoretical Analysis of the Prodrug
                                  Delivery System for Treating
                                  Antibiotic-Resistant Bacteria  . . . . . 650--658
             Santanu Ghorai and   
          Anirban Mukherjee and   
       Sanghamitra Sengupta and   
                Pranab K. Dutta   Cancer Classification from Gene
                                  Expression Data by NPPC Ensemble . . . . 659--671
                 Gregor Gossler   Component-Based Modeling and
                                  Reachability Analysis of Genetic
                                  Networks . . . . . . . . . . . . . . . . 672--682
           Yoshinori Tamada and   
                Seiya Imoto and   
            Hiromitsu Araki and   
             Masao Nagasaki and   
              Cristin Print and   
  D. Stephen Charnock-Jones and   
                  Satoru Miyano   Estimating Genome-Wide Gene Networks
                                  Using Nonparametric Bayesian Network
                                  Models on Massively Parallel Computers   683--697
         Alexander K. Hudek and   
                Daniel G. Brown   FEAST: Sensitive Local Alignment with
                                  Multiple Rates of Evolution  . . . . . . 698--709
        Elizabeth S. Allman and   
           Sonja Petrovi\'c and   
             John A. Rhodes and   
                 Seth Sullivant   Identifiability of Two-Tree Mixtures for
                                  Group-Based Models . . . . . . . . . . . 710--722
                 Tianwei Yu and   
                 Hesen Peng and   
                        Wei Sun   Incorporating Nonlinear Relationships in
                                  Microarray Missing Value Imputation  . . 723--731
                   Bin Song and   
\.I Esra Büyüktahtakin and   
               Sanjay Ranka and   
                  Tamer Kahveci   Manipulating the Steady State of
                                  Metabolic Pathways . . . . . . . . . . . 732--747
                    Qian Xu and   
           Sinno Jialin Pan and   
            Hannah Hong Xue and   
                     Qiang Yang   Multitask Learning for Protein
                                  Subcellular Location Prediction  . . . . 748--759
           Ruben Armananzas and   
                 Yvan Saeys and   
                 Inaki Inza and   
       Miguel Garcia-Torres and   
              Concha Bielza and   
           Yves van de Peer and   
                Pedro Larranaga   Peakbin Selection in Mass Spectrometry
                                  Data Using a Consensus Approach with
                                  Estimation of Distribution Algorithms    760--774
       Antonina Mitrofanova and   
          Vladimir Pavlovic and   
                     Bud Mishra   Prediction of Protein Functions with
                                  Gene Ontology and Interspecies Protein
                                  Homology Data  . . . . . . . . . . . . . 775--784
             Stephen J. Willson   Regular Networks Can be Uniquely
                                  Constructed from Their Trees . . . . . . 785--796
                    Tilo Strutz   $3$D Shape Reconstruction of Loop
                                  Objects in X-Ray Protein Crystallography 797--807
                  Banu Dost and   
                 Chunlei Wu and   
                  Andrew Su and   
                   Vineet Bafna   TCLUST: a Fast Method for Clustering
                                  Genome-Scale Expression Data . . . . . . 808--818
Jayendra Gnanaskandan Venkateswaran and   
                   Bin Song and   
              Tamer Kahveci and   
           Christopher Jermaine   TRIAL: a Tool for Finding Distant
                                  Structural Similarities  . . . . . . . . 819--831
              Giorgio Valentini   True Path Rule Hierarchical Ensembles
                                  for Genome-Wide Gene Function Prediction 832--847
            Mukul S. Bansal and   
                     Ron Shamir   A Note on the Fixed Parameter
                                  Tractability of the Gene-Duplication
                                  Problem  . . . . . . . . . . . . . . . . 848--850
        Aditya Kumar Sehgal and   
                 Sanmay Das and   
                 Keith Noto and   
       Milton H. Saier, Jr. and   
                  Charles Elkan   Identifying Relevant Data for a
                                  Biological Database: Handcrafted Rules
                                  versus Machine Learning  . . . . . . . . 851--857
             Minh N. Nguyen and   
            Jacek M. Zurada and   
            Jagath C. Rajapakse   Toward Better Understanding of Protein
                                  Secondary Structure: Extracting
                                  Prediction Rules . . . . . . . . . . . . 858--864

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 8, Number 4, July, 2011

            Mark Borodovsky and   
        Teresa M. Przytycka and   
    Sanguthevar Rajasekaran and   
           Alexander Zelikovsky   Guest Editors' Introduction to the
                                  Special Section on Bioinformatics
                                  Research and Applications  . . . . . . . 865--866
              Yosi Shibberu and   
                   Allen Holder   A Spectral Approach to Protein Structure
                                  Alignment  . . . . . . . . . . . . . . . 867--875
             Nicola Ferraro and   
             Luigi Palopoli and   
               Simona Panni and   
                Simona E. Rombo   Asymmetric Comparison and Querying of
                                  Biological Networks  . . . . . . . . . . 876--889
           John Wiedenhoeft and   
              Roland Krause and   
              Oliver Eulenstein   The Plexus Model for the Inference of
                                  Ancestral Multidomain Proteins . . . . . 890--901
        Nicholas Pattengale and   
               Andre Aberer and   
            Krister Swenson and   
      Alexandros Stamatakis and   
                  Bernard Moret   Uncovering Hidden Phylogenetic Consensus
                                  in Large Data Sets . . . . . . . . . . . 902--911
                  Rob Gysel and   
                Daniel Gusfield   Extensions and Improvements to the
                                  Chordal Graph Approach to the Multistate
                                  Perfect Phylogeny Problem  . . . . . . . 912--917
              Ming-Chi Tsai and   
            Guy E. Blelloch and   
                    R. Ravi and   
               Russell Schwartz   A Consensus Tree Approach for
                                  Reconstructing Human Evolutionary
                                  History and Detecting Population
                                  Substructure . . . . . . . . . . . . . . 918--928
  Sanghamitra Bandyopadhyay and   
            Malay Bhattacharyya   A Biologically Inspired Measure for
                                  Coexpression Analysis  . . . . . . . . . 929--942
             Nuno Tenazinha and   
                   Susana Vinga   A Survey on Methods for Modeling and
                                  Analyzing Integrated Biological Networks 943--958
             Chao-Wen Huang and   
              Wun-Shiun Lee and   
                 Sun-Yuan Hsieh   An Improved Heuristic Algorithm for
                                  Finding Motif Signals in DNA Sequences   959--975
           Sebastian Bocker and   
                 Birte Kehr and   
                 Florian Rasche   Determination of Glycan Structure from
                                  Tandem Mass Spectra  . . . . . . . . . . 976--986
          Samuel S. Y. Wong and   
                 Weimin Luo and   
               Keith C. C. Chan   EvoMD: An Algorithm for Evolutionary
                                  Molecular Design . . . . . . . . . . . . 987--1003
               Ivan Merelli and   
                Paolo Cozzi and   
         Daniele D'Agostino and   
            Andrea Clematis and   
               Luciano Milanesi   Image-Based Surface Matching Algorithm
                                  Oriented to Structural Biology . . . . . 1004--1016
             Pietro Di Lena and   
            Piero Fariselli and   
            Luciano Margara and   
              Marco Vassura and   
                   Rita Casadio   Is There an Optimal Substitution Matrix
                                  for Contact Prediction with Correlated
                                  Mutations? . . . . . . . . . . . . . . . 1017--1028
         Katharina T. Huber and   
           Andreas Spillner and   
         Rados law Suchecki and   
                Vincent Moulton   Metrics on Multilabeled Trees:
                                  Interrelationships and Diameter Bounds   1029--1040
                   Xin Zhao and   
            Leo Wang-Kit Cheung   Multiclass Kernel-Imbedded Gaussian
                                  Processes for Microarray Data Analysis   1041--1053
                 Peng Zhang and   
                Houqiang Li and   
               Honghui Wang and   
               Wong Stephen and   
                    Xiaobo Zhou   Peak Tree: a New Tool for Multiscale
                                  Hierarchical Representation and Peak
                                  Detection of Mass Spectrometry Data  . . 1054--1066
        Yasser El-Manzalawy and   
                Drena Dobbs and   
                 Vasant Honavar   Predicting MHC-II Binding Affinity Using
                                  Multiple Instance Regression . . . . . . 1067--1079
                  Feng Yang and   
                      K. Z. Mao   Robust Feature Selection for Microarray
                                  Data Based on Multicriterion Fusion  . . 1080--1092
               Peter Ti\vno and   
                Hongya Zhao and   
                       Hong Yan   Searching for Coexpressed Genes in
                                  Three-Color cDNA Microarray Data Using a
                                  Probabilistic Model-Based Hough
                                  Transform  . . . . . . . . . . . . . . . 1093--1107
                Li-San Wang and   
           Jim Leebens-Mack and   
               P. Kerr Wall and   
             Kevin Beckmann and   
      Claude W. dePamphilis and   
                   Tandy Warnow   The Impact of Multiple Protein Sequence
                                  Alignment on Phylogenetic Estimation . . 1108--1119
              Bashir Sadjad and   
                  Zsolt Zsoldos   Toward a Robust Search Method for the
                                  Protein--Drug Docking Problem  . . . . . 1120--1133
                  Yang Chen and   
                      Jinglu Hu   Accurate Reconstruction for DNA
                                  Sequencing by Hybridization Based on a
                                  Constructive Heuristic . . . . . . . . . 1134--1140
          Sylvain Guillemot and   
             Jesper Jansson and   
                  Wing-Kin Sung   Computing a Smallest Multilabeled
                                  Phylogenetic Tree from Rooted Triplets   1141--1147
                 Tim Peters and   
            David W. Bulger and   
                  To-ha Loi and   
          Jean Yee Hwa Yang and   
                       David Ma   Two-Step Cross-Entropy Feature Selection
                                  for Microarrays --- Power Through
                                  Complementarity  . . . . . . . . . . . . 1148--1151

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 8, Number 5, September, 2011

               Dongxiao Zhu and   
               Lipi Acharya and   
                      Hui Zhang   A Generalized Multivariate Approach to
                                  Pattern Discovery from Replicated and
                                  Incomplete Genome-Wide Measurements  . . 1153--1169
                  Rui Chang and   
           Robert Shoemaker and   
                       Wei Wang   A Novel Knowledge-Driven Systems Biology
                                  Approach for Phenotype Prediction upon
                                  Genetic Intervention . . . . . . . . . . 1170--1182
            Ekhine Irurozki and   
                Borja Calvo and   
                 Jose A. Lozano   A Preprocessing Procedure for Haplotype
                                  Inference by Pure Parsimony  . . . . . . 1183--1195
         Simone Battagliero and   
            Giuseppe Puglia and   
            Saverio Vicario and   
           Francesco Rubino and   
           Gaetano Scioscia and   
                     Pietro Leo   An Efficient Algorithm for Approximating
                                  Geodesic Distances in Tree Space . . . . 1196--1207
              David J. John and   
        Jacquelyn S. Fetrow and   
                James L. Norris   Continuous Cotemporal Probabilistic
                                  Modeling of Systems Biology Networks
                                  from Sparse Data . . . . . . . . . . . . 1208--1222
         Carito Guziolowski and   
            Sylvain Blachon and   
        Tatiana Baumuratova and   
              Gautier Stoll and   
           Ovidiu Radulescu and   
                    Anne Siegel   Designing Logical Rules to Model the
                                  Response of Biomolecular Networks with
                                  Complex Interactions: An Application to
                                  Cancer Modeling  . . . . . . . . . . . . 1223--1234
       Sitanshu Sekhar Sahu and   
                 Ganapati Panda   Efficient Localization of Hot Spots in
                                  Proteins Using a Novel $S$-Transform
                                  Based Filtering Approach . . . . . . . . 1235--1246
    Samuel Coulbourn Flores and   
            Michael Sherman and   
       Christopher M. Bruns and   
              Peter Eastman and   
                 Russ B. Altman   Fast Flexible Modeling of RNA Structure
                                  Using Internal Coordinates . . . . . . . 1247--1257
            Biing-Feng Wang and   
                 Chien-Hsin Lin   Improved Algorithms for Finding Gene
                                  Teams and Constructing Gene Team Trees   1258--1272
             Chun-Hou Zheng and   
                  Lei Zhang and   
                  To-Yee Ng and   
             Chi Keung Shiu and   
                De-Shuang Huang   Metasample-Based Sparse Representation
                                  for Tumor Classification . . . . . . . . 1273--1282
                  Qian Peng and   
                Andrew D. Smith   Multiple Sequence Assembly from Reads
                                  Alignable to a Common Reference Genome   1283--1295
              Nadja Betzler and   
            Rene van Bevern and   
         Michael R. Fellows and   
      Christian Komusiewicz and   
               Rolf Niedermeier   Parameterized Algorithmics for Finding
                                  Connected Motifs in Biological Networks  1296--1308
            Jong Kyoung Kim and   
                  Seungjin Choi   Probabilistic Models for Semisupervised
                                  Discriminative Motif Discovery in DNA
                                  Sequences  . . . . . . . . . . . . . . . 1309--1317
               Pedro Feijao and   
                  Joao Meidanis   SCJ: a Breakpoint-Like Distance that
                                  Simplifies Several Rearrangement
                                  Problems . . . . . . . . . . . . . . . . 1318--1329
           Marco Mernberger and   
              Gerhard Klebe and   
               Eyke Hullermeier   SEGA: Semiglobal Graph Alignment for
                                  Structure-Based Protein Comparison . . . 1330--1343
                Peter Boyen and   
             Dries Van Dyck and   
                Frank Neven and   
   Roeland C. H. J. van Ham and   
            Aalt D. J. van Dijk   SLIDER: a Generic Metaheuristic for the
                                  Discovery of Correlated Motifs in
                                  Protein-Protein Interaction Networks . . 1344--1357
              Harry Buhrman and   
  Peter T. S. van der Gulik and   
             Steven M. Kelk and   
           Wouter M. Koolen and   
                   Leen Stougie   Some Mathematical Refinements Concerning
                                  Error Minimization in the Genetic Code   1358--1372
         William W. L. Wong and   
            Forbes J. Burkowski   Using Kernel Alignment to Select
                                  Features of Molecular Descriptors in a
                                  QSAR Study . . . . . . . . . . . . . . . 1373--1384
              Marco Muselli and   
            Alberto Bertoni and   
               Marco Frasca and   
         Alessandro Beghini and   
          Francesca Ruffino and   
              Giorgio Valentini   A Mathematical Model for the Validation
                                  of Gene Selection Methods  . . . . . . . 1385--1392
              Elena Dubrova and   
                 Maxim Teslenko   A SAT-Based Algorithm for Finding
                                  Attractors in Synchronous Boolean
                                  Networks . . . . . . . . . . . . . . . . 1393--1399
             Zhi-Zhong Chen and   
                   Lusheng Wang   Fast Exact Algorithms for the Closest
                                  String and Substring Problems with
                                  Application to the Planted $ (L, d)
                                  $-Motif Model  . . . . . . . . . . . . . 1400--1410
                  Simona Grusea   On the Distribution of the Number of
                                  Cycles in the Breakpoint Graph of a
                                  Random Signed Permutation  . . . . . . . 1411--1416
       Getachew K. Befekadu and   
          Mahlet G. Tadesse and   
            Tsung-Heng Tsai and   
               Habtom W. Ressom   Probabilistic Mixture Regression Models
                                  for Alignment of LC-MS Data  . . . . . . 1417--1424
                Paolo Magni and   
             Angela Simeone and   
               Sandra Healy and   
          Antonella Isacchi and   
                Roberta Bosotti   Summarizing Probe Intensities of
                                  Affymetrix GeneChip 3' Expression Arrays
                                  Taking into Account Day-to-Day
                                  Variability  . . . . . . . . . . . . . . 1425--1430
               Ehud Aharoni and   
              Hani Neuvirth and   
                 Saharon Rosset   The Quality Preserving Database: a
                                  Computational Framework for Encouraging
                                  Collaboration, Enhancing Power and
                                  Controlling False Discovery  . . . . . . 1431--1437

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 8, Number 6, November, 2011

      Apostolos Axenopoulos and   
               Petros Daras and   
      Georgios Papadopoulos and   
                  Elias Houstis   A Shape Descriptor for Fast
                                  Complementarity Matching in Molecular
                                  Docking  . . . . . . . . . . . . . . . . 1441--1457
                 Wenqi Zhao and   
                Guoliang Xu and   
            Chandrajit L. Bajaj   An Algebraic Spline Model of Molecular
                                  Surfaces for Energetic Computations  . . 1458--1467
            Markus E. Nebel and   
                   Scheid Anika   Analysis of the Free Energy in a
                                  Stochastic RNA Secondary Structure Model 1468--1482
                 Liang Zhao and   
               Limsoon Wong and   
                      Jinyan Li   Antibody-Specified B-Cell Epitope
                                  Prediction in Line with the Principle of
                                  Context-Awareness  . . . . . . . . . . . 1483--1494
        Murat Can Cobanoglu and   
               Yucel Saygin and   
                  Ugur Sezerman   Classification of GPCRs Using Family
                                  Specific Motifs  . . . . . . . . . . . . 1495--1508
                      Qi Li and   
            Chandra Kambhamettu   Contour Extraction of \bionameDrosophila
                                  Embryos  . . . . . . . . . . . . . . . . 1509--1521
                Jung Hun Oh and   
                       Jean Gao   Fast Kernel Discriminant Analysis for
                                  Classification of Liver Cancer Mass
                                  Spectra  . . . . . . . . . . . . . . . . 1522--1534
              Qingfeng Chen and   
            Yi-Ping Phoebe Chen   Function Annotation for Pseudoknot Using
                                  Structure Similarity . . . . . . . . . . 1535--1544
         Georgios Chalkidis and   
             Masao Nagasaki and   
                  Satoru Miyano   High Performance Hybrid Functional Petri
                                  Net Simulations of Biological Pathway
                                  Models on CUDA . . . . . . . . . . . . . 1545--1556
                  Helong Li and   
                  Sam Kwong and   
                 Lihua Yang and   
                Daren Huang and   
                  Dongping Xiao   Hilbert--Huang Transform for Analysis of
                                  Heart Rate Variability in Cardiac Health 1557--1567
               Jinhua Sheng and   
              Hong-Wen Deng and   
              Vince Calhoun and   
                   Yu-Ping Wang   Integrated Analysis of Gene Expression
                                  and Copy Number Data on Gene Shaving
                                  Using Independent Component Analysis . . 1568--1579
           Carla C. M. Chen and   
           Holger Schwender and   
              Jonthan Keith and   
            Robin Nunkesser and   
           Kerrie Mengersen and   
                Paula Macrossan   Methods for Identifying SNP
                                  Interactions: a Review on Variations of
                                  Logic Regression, Random Forest and
                                  Bayesian Logistic Regression . . . . . . 1580--1591
             Chun-Hou Zheng and   
                  Lei Zhang and   
          Vincent To-Yee Ng and   
             Chi Keung Shiu and   
                    D.-S. Huang   Molecular Pattern Discovery Based on
                                  Penalized Matrix Decomposition . . . . . 1592--1603
         Xavier Le Faucheur and   
            Eli Hershkovits and   
            Rina Tannenbaum and   
               Allen Tannenbaum   Nonparametric Clustering for Studying
                                  RNA Conformations  . . . . . . . . . . . 1604--1619
                  Ivan Dotu and   
             Manuel Cebrian and   
      Pascal Van Hentenryck and   
                    Peter Clote   On Lattice Protein Structure Prediction
                                  Revisited  . . . . . . . . . . . . . . . 1620--1632
               Hong-Dong Li and   
              Yi-Zeng Liang and   
               Qing-Song Xu and   
             Dong-Sheng Cao and   
                Bin-Bin Tan and   
             Bai-Chuan Deng and   
                  Chen-Chen Lin   Recipe for Uncovering Predictive Genes
                                  Using Support Vector Machines Based on
                                  Model Population Analysis  . . . . . . . 1633--1641
      Christoph Hafemeister and   
              Roland Krause and   
              Alexander Schliep   Selecting Oligonucleotide Probes for
                                  Whole-Genome Tiling Arrays with a
                                  Cross-Hybridization Potential  . . . . . 1642--1652
               Thomas Fober and   
             Gerghei Glinca and   
              Gerhard Klebe and   
               Eyke Hullermeier   Superposition and Alignment of Labeled
                                  Point Clouds . . . . . . . . . . . . . . 1653--1666
               Tamir Tuller and   
                Elchanan Mossel   Co-evolution Is Incompatible with the
                                  Markov Assumption in Phylogenetics . . . 1667--1670
                Bing-Yu Sun and   
                Zhi-Hua Zhu and   
                 Jiuyong Li and   
                     Bin Linghu   Combined Feature Selection and Cancer
                                  Prognosis Using Support Vector Machine
                                  Regression . . . . . . . . . . . . . . . 1671--1677
                 Weiguo Liu and   
             Bertil Schmidt and   
         Wolfgang Muller-Wittig   CUDA-BLASTP: Accelerating BLASTP on
                                  CUDA-Enabled Graphics Hardware . . . . . 1678--1684
                   Louxin Zhang   From Gene Trees to Species Trees II:
                                  Species Tree Inference by Minimizing
                                  Deep Coalescence Events  . . . . . . . . 1685--1691
         Michael R. Fellows and   
             Tzvika Hartman and   
             Danny Hermelin and   
              Gad M. Landau and   
           Frances Rosamond and   
                 Liat Rozenberg   Haplotype Inference Constrained by
                                  Plausible Haplotype Data . . . . . . . . 1692--1699
            Jerome Ambroise and   
              Joachim Giard and   
              Jean-Luc Gala and   
                    Benoit Macq   Identification of Relevant Properties
                                  for Epitopes Detection Using a
                                  Regression Model . . . . . . . . . . . . 1700--1707
               Qingguo Wang and   
                   Yi Shang and   
                        Dong Xu   Improving a Consensus Approach for
                                  Protein Structure Selection by Removing
                                  Redundancy . . . . . . . . . . . . . . . 1708--1715
            Aleksandar Poleksic   Optimizing a Widely Used Protein
                                  Structure Alignment Measure in Expected
                                  Polynomial Time  . . . . . . . . . . . . 1716--1720
  Thiago de Souza Rodrigues and   
    Fernanda Caldas Cardoso and   
Santuza Maria Ribeiro Teixeira and   
      Sergio Costa Oliveira and   
            Antonio Padua Braga   Protein Classification with
                                  Extended-Sequence Coding by Sliding
                                  Window . . . . . . . . . . . . . . . . . 1721--1726


IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 9, Number 1, January, 2012

            Daniel DeBlasio and   
            Jocelyne Bruand and   
                  Shaojie Zhang   A Memory Efficient Method for
                                  Structure-Based RNA Multiple Alignment   1--11
                Yuri Pirola and   
            Paola Bonizzoni and   
                      Tao Jiang   An Efficient Algorithm for Haplotype
                                  Inference on Pedigrees with
                                  Recombinations and Mutations . . . . . . 12--25
        Jean-Philippe Doyon and   
               Sylvie Hamel and   
                  Cedric Chauve   An Efficient Method for Exploring the
                                  Space of Gene Tree/Species Tree
                                  Reconciliations in a Probabilistic
                                  Framework  . . . . . . . . . . . . . . . 26--39
                 Chong Wang and   
            Peter Beyerlein and   
             Heike Pospisil and   
               Antje Krause and   
               Chris Nugent and   
                Werner Dubitzky   An Efficient Method for Modeling Kinetic
                                  Behavior of Channel Proteins in
                                  Cardiomyocytes . . . . . . . . . . . . . 40--51
                 Bane Vasic and   
             Vida Ravanmehr and   
         Anantha Raman Krishnan   An Information Theoretic Approach to
                                  Constructing Robust Boolean Gene
                                  Regulatory Networks  . . . . . . . . . . 52--65
        Mahendra Piraveenan and   
         Mikhail Prokopenko and   
                  Albert Zomaya   Assortative Mixing in Directed
                                  Biological Networks  . . . . . . . . . . 66--78
            Raymond H. Chan and   
               Tony H. Chan and   
              Hau Man Yeung and   
                 Roger Wei Wang   Composition Vector Method Based on
                                  Maximum Entropy Principle for Sequence
                                  Comparison . . . . . . . . . . . . . . . 79--87
            Jose R. Quevedo and   
          Antonio Bahamonde and   
        Miguel Perez-Enciso and   
                   Oscar Luaces   Disease Liability Prediction from Large
                                  Scale Genotyping Data Using Classifiers
                                  with a Reject Option . . . . . . . . . . 88--97
                Ying-Xin Li and   
                Shuiwang Ji and   
               Sudhir Kumar and   
                 Jieping Ye and   
                   Zhi-Hua Zhou   \bionameDrosophila Gene Expression
                                  Pattern Annotation through
                                  Multi-Instance Multi-Label Learning  . . 98--112
          David R. Paoletti and   
               Dan E. Krane and   
          Michael L. Raymer and   
                 Travis E. Doom   Inferring the Number of Contributors to
                                  Mixed DNA Profiles . . . . . . . . . . . 113--122
              Xiaoning Qian and   
            Edward R. Dougherty   Intervention in Gene Regulatory Networks
                                  via Phenotypically Constrained Control
                                  Policies Based on Long-Run Behavior  . . 123--136
            Shanika Kuruppu and   
      Bryan Beresford-Smith and   
              Thomas Conway and   
                   Justin Zobel   Iterative Dictionary Construction for
                                  Compression of Large DNA Data Sets . . . 137--149
         Damian Bogdanowicz and   
                Krzysztof Giaro   Matching Split Distance for Unrooted
                                  Binary Phylogenetic Trees  . . . . . . . 150--160
          Thomas K. F. Wong and   
                 Y. S. Chiu and   
                  T. W. Lam and   
                      S. M. Yiu   Memory Efficient Algorithms for
                                  Structural Alignment of RNAs with
                                  Pseudoknots  . . . . . . . . . . . . . . 161--168
          Arthur W. Mahoney and   
       Gregory J. Podgorski and   
              Nicholas S. Flann   Multiobjective Optimization
                                  Based-Approach for Discovering Novel
                                  Cancer Therapies . . . . . . . . . . . . 169--184
               Jianyong Sun and   
      Jonathan M. Garibaldi and   
                Charlie Hodgman   Parameter Estimation Using
                                  Metaheuristics in Systems Biology: a
                                  Comprehensive Review . . . . . . . . . . 185--202
           Andrea Passerini and   
                Marco Lippi and   
                 Paolo Frasconi   Predicting Metal-Binding Sites from
                                  Protein Sequence . . . . . . . . . . . . 203--213
          Shahid H. Bokhari and   
           Laura W. Pomeroy and   
               Daniel A. Janies   Reassortment Networks and the Evolution
                                  of Pandemic H1N1 Swine-Origin Influenza  214--227
                  Lingyu Ma and   
              Marco Reisert and   
                 Hans Burkhardt   RENNSH: a Novel $ \alpha $-Helix
                                  Identification Approach for Intermediate
                                  Resolution Electron Density Maps . . . . 228--239
             Shuai Cheng Li and   
                  Dongbo Bu and   
                        Ming Li   Residues with Similar Hexagon
                                  Neighborhoods Share Similar Side-Chain
                                  Conformations  . . . . . . . . . . . . . 240--248
                   Hong Sun and   
                Ahmet Sacan and   
      Hakan Ferhatosmanoglu and   
                      Yusu Wang   Smolign: a Spatial Motifs-Based Protein
                                  Multiple Structural Alignment Method . . 249--261
                     Lei Yu and   
                    Yue Han and   
              Michael E. Berens   Stable Gene Selection from Microarray
                                  Data via Sample Weighting  . . . . . . . 262--272
          Maria Luisa Bonet and   
                Simone Linz and   
             Katherine St. John   The Complexity of Finding Multiple
                                  Solutions to Betweenness and Quartet
                                  Compatibility  . . . . . . . . . . . . . 273--285
               Noah Daniels and   
                Anoop Kumar and   
               Lenore Cowen and   
                     Matt Menke   Touring Protein Space with Matt  . . . . 286--293
                 Yang Xiang and   
         Philip R. O. Payne and   
                      Kun Huang   Transactional Database Transformation
                                  and Its Application in Prioritizing
                                  Human Disease Genes  . . . . . . . . . . 294--304
             Kyle H. Ambert and   
                 Aaron M. Cohen   $k$-Information Gain Scaled Nearest
                                  Neighbors: a Novel Approach to
                                  Classifying Protein-Protein
                                  Interaction-Related Documents  . . . . . 305--310
                     Yun Xu and   
                    Da Teng and   
                     Yiming Lei   MinePhos: a Literature Mining System for
                                  Protein Phoshphorylation Information
                                  Extraction . . . . . . . . . . . . . . . 311--315
                     Yun Xu and   
                    Da Teng and   
                     Yiming Lei   2011 Reviewers List  . . . . . . . . . . 316--318
                     Yun Xu and   
                    Da Teng and   
                     Yiming Lei   2011 Annual Index  . . . . . . . . . . . ??

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 9, Number 2, March, 2012

               Lipi Acharya and   
                Thair Judeh and   
             Zhansheng Duan and   
             Michael Rabbat and   
                   Dongxiao Zhu   GSGS: a Computational Approach to
                                  Reconstruct Signaling Pathway Structures
                                  from Gene Sets . . . . . . . . . . . . . 438--450
           Sandro Andreotti and   
             Gunnar W. Klau and   
                   Knut Reinert   Antilope --- a Lagrangian Relaxation
                                  Approach to the de novo Peptide
                                  Sequencing Problem . . . . . . . . . . . 385--394
         Ulavappa B. Angadi and   
                 M. Venkatesulu   Structural SCOP Superfamily Level
                                  Classification Using Unsupervised
                                  Machine Learning . . . . . . . . . . . . 601--608
         Barbara Di Camillo and   
                Marco Falda and   
             Gianna Toffolo and   
                Claudio Cobelli   SimBioNeT: a Simulator of Biological
                                  Network Topology . . . . . . . . . . . . 592--600
             Zhi-Zhong Chen and   
                   Lusheng Wang   Algorithms for Reticulate Networks of
                                  Multiple Phylogenetic Trees  . . . . . . 372--384
              Yi-Ming Cheng and   
     Srinivasa Murthy Gopal and   
                Sean M. Law and   
                   Michael Feig   Molecular Dynamics Trajectory
                                  Compression with a Coarse-Grained Model  476--486
                Ola ElBakry and   
             M. Omair Ahmad and   
                 M. N. S. Swamy   Identification of Differentially
                                  Expressed Genes for Time-Course
                                  Microarray Data Based on Modified RM
                                  ANOVA  . . . . . . . . . . . . . . . . . 451--466
               Zeny Z. Feng and   
              Xiaojian Yang and   
            Sanjeena Subedi and   
             Paul D. McNicholas   The LASSO and Sparse Least Squares
                                  Regression Methods for SNP Selection in
                                  Predicting Quantitative Traits . . . . . 629--636
          Martin Hopfensitz and   
           Christoph Mussel and   
            Christian Wawra and   
             Markus Maucher and   
               Michael Kuhl and   
              Heiko Neumann and   
                Hans A. Kestler   Multiscale Binarization of Gene
                                  Expression Data for Reconstructing
                                  Boolean Networks . . . . . . . . . . . . 487--498
              Qinghua Huang and   
                Dacheng Tao and   
                 Xuelong Li and   
                      Alan Liew   Parallelized Evolutionary Learning for
                                  Detection of Biclusters in Gene
                                  Expression Data  . . . . . . . . . . . . 560--570
        Ioannis G. Karafyllidis   Quantum Gate Circuit Model of Signal
                                  Integration in Bacterial Quorum Sensing  571--579
                Steven Kelk and   
         Celine Scornavacca and   
                 Leo van Iersel   On the Elusiveness of Clusters . . . . . 517--534
    Kyriakos Kentzoglanakis and   
                  Matthew Poole   A Swarm Intelligence Framework for
                                  Reconstructing Gene Networks: Searching
                                  for Biologically Plausible Architectures 358--371
         M. Oguzhan Kulekci and   
       Jeffrey Scott Vitter and   
                      Bojian Xu   Efficient Maximal Repeat Finding Using
                                  the Burrows-Wheeler Transform and
                                  Wavelet Tree . . . . . . . . . . . . . . 421--429
                   Wenji Ma and   
                  Yong Yang and   
             Zhi-Zhong Chen and   
                   Lusheng Wang   Mutation Region Detection for Closely
                                  Related Individuals without a Known
                                  Pedigree . . . . . . . . . . . . . . . . 499--510
            Selim Mimaroglu and   
                 Emin Aksehirli   DICLENS: Divisive Clustering Ensemble
                                  with Automatic Cluster Number  . . . . . 408--420
                Loris Nanni and   
          Alessandra Lumini and   
               Dinesh Gupta and   
                     Aarti Garg   Identifying Bacterial Virulent Proteins
                                  by Fusing a Set of Classifiers Based on
                                  Variants of Chou's Pseudo Amino Acid
                                  Composition and on Evolutionary
                                  Information  . . . . . . . . . . . . . . 467--475
                Paul Phipps and   
                   Sergey Bereg   Optimizing Phylogenetic Networks for
                                  Circular Split Systems . . . . . . . . . 535--547
            Aleksandar Poleksic   On Complexity of Protein Structure
                                  Alignment Problem under Distance
                                  Constraint . . . . . . . . . . . . . . . 511--516
           Andreas Spillner and   
                Binh Nguyen and   
                Vincent Moulton   Constructing and Drawing Regular Planar
                                  Split Networks . . . . . . . . . . . . . 395--407
           Sascha Steinbiss and   
                   Stefan Kurtz   A New Efficient Data Structure for
                                  Storage and Retrieval of Multiple
                                  Biosequences . . . . . . . . . . . . . . 345--357
               Chien-Hao Su and   
                Tse-Yi Wang and   
             Ming-Tsung Hsu and   
   Francis Cheng-Hsuan Weng and   
              Cheng-Yan Kao and   
                 Daryi Wang and   
                Huai-Kuang Tsai   The Impact of Normalization and
                                  Phylogenetic Information on Estimating
                                  the Distance for Metagenomes . . . . . . 619--628
               Daifeng Wang and   
              Mia K. Markey and   
             Claus O. Wilke and   
               Ari Arapostathis   Eigen-Genomic System Dynamic-Pattern
                                  Analysis (ESDA): Modeling mRNA
                                  Degradation and Self-Regulation  . . . . 430--437
            Biing-Feng Wang and   
             Chung-Chin Kuo and   
               Shang-Ju Liu and   
                 Chien-Hsin Lin   A New Efficient Algorithm for the
                                  Gene-Team Problem on General Sequences   330--344
                Biing-Feng Wang   Output-Sensitive Algorithms for Finding
                                  the Nested Common Intervals of Two
                                  General Sequences  . . . . . . . . . . . 548--559
               Shu-Lin Wang and   
                 Yi-Hai Zhu and   
                    Wei Jia and   
                De-Shuang Huang   Robust Classification Method of Tumor
                                  Subtype by Using Correlation Filters . . 580--591
              Yongwook Yoon and   
               Gary Geunbae Lee   Subcellular Localization Prediction
                                  through Boosting Association Rules . . . 609--618
               Nianyin Zeng and   
                Zidong Wang and   
                  Yurong Li and   
                     Min Du and   
                    Xiaohui Liu   A Hybrid EKF and Switching PSO Algorithm
                                  for Joint State and Parameter Estimation
                                  of Lateral Flow Immunoassay Models . . . 321--329

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 9, Number 3, May, 2012

                  Tommaso Mazza   High Performance Computational Systems
                                  Biology  . . . . . . . . . . . . . . . . 641--642
               Mark Burkitt and   
                Dawn Walker and   
         Daniella M. Romano and   
                 Alireza Fazeli   Constructing Complex $3$D Biological
                                  Environments from Medical Imaging Using
                                  High Performance Computing . . . . . . . 643--654
                Lorenzo Dematte   Smoldyn on Graphics Processing Units:
                                  Massively Parallel Brownian Dynamics
                                  Simulations  . . . . . . . . . . . . . . 655--667
         Vincenzo Belcastro and   
       Francesco Gregoretti and   
            Velia Siciliano and   
            Michele Santoro and   
          Giovanni D'Angelo and   
              Gennaro Oliva and   
              Diego di Bernardo   Reverse Engineering and Analysis of
                                  Genome-Wide Gene Regulatory Networks
                                  from Gene Expression Profiles Using
                                  High-Performance Computing . . . . . . . 668--678
            Alhadi Bustamam and   
              Kevin Burrage and   
           Nicholas A. Hamilton   Fast Parallel Markov Clustering in
                                  Bioinformatics Using Massively Parallel
                                  Computing on GPU with CUDA and ELLPACK-R
                                  Sparse Format  . . . . . . . . . . . . . 679--692
                Jiri Barnat and   
                 Lubos Brim and   
                Adam Krejci and   
                Adam Streck and   
             David Safranek and   
              Martin Vejnar and   
                Tomas Vejpustek   On Parameter Synthesis by Parallel Model
                                  Checking . . . . . . . . . . . . . . . . 693--705
         Georgina Stegmayer and   
            Diego H. Milone and   
           Laura Kamenetzky and   
           Mariana G. Lopez and   
               Fernando Carrari   A Biologically Inspired Validity Measure
                                  for Comparison of Clustering Methods
                                  over Metabolic Data Sets . . . . . . . . 706--716
              Clara Pizzuti and   
                Simona E. Rombo   A Coclustering Approach for Mining Large
                                  Protein-Protein Interaction Networks . . 717--730
          Petros Kountouris and   
      Michalis Agathocleous and   
       Vasilis J. Promponas and   
      Georgia Christodoulou and   
          Simos Hadjicostas and   
       Vassilis Vassiliades and   
            Chris Christodoulou   A Comparative Study on Filtering Protein
                                  Secondary Structure Prediction . . . . . 731--739
             Xiao-Fei Zhang and   
                   Dao-Qing Dai   A Framework for Incorporating Functional
                                  Interrelationships into Protein Function
                                  Prediction Algorithms  . . . . . . . . . 740--753
                Alok Sharma and   
                Seiya Imoto and   
                  Satoru Miyano   A Top-r Feature Selection Algorithm for
                                  Microarray Gene Expression Data  . . . . 754--764
             Shuai Cheng Li and   
                  Dongbo Bu and   
                        Ming Li   Clustering 100,000 Protein Structure
                                  Decoys in Minutes  . . . . . . . . . . . 765--773
                  Yanni Sun and   
              Jeremy Buhler and   
                     Cheng Yuan   Designing Filters for Fast-Known NcRNA
                                  Identification . . . . . . . . . . . . . 774--787
              Milos Krejnik and   
                     Jiri Klema   Empirical Evidence of the Applicability
                                  of Functional Clustering through Gene
                                  Expression Classification  . . . . . . . 788--798
            Giuliano Armano and   
                  Filippo Ledda   Exploiting Intrastructure Information
                                  for Secondary Structure Prediction with
                                  Multifaceted Pipelines . . . . . . . . . 799--808
              Oliver Serang and   
        William Stratford Noble   Faster Mass Spectrometry-Based Protein
                                  Inference: Junction Trees Are More
                                  Efficient than Sampling and
                                  Marginalization by Enumeration . . . . . 809--817
                 Hong Huang and   
                  Hailiang Feng   Gene Classification Using Parameter-Free
                                  Semi-Supervised Manifold Learning  . . . 818--827
               Peter Jarvis and   
                  Jeremy Sumner   Markov Invariants for Phylogenetic Rate
                                  Matrices Derived from Embedded Submodels 828--836
            Cheng-Hong Yang and   
              Yu-Huei Cheng and   
            Cheng-Huei Yang and   
                  Li-Yeh Chuang   Mutagenic Primer Design for Mismatch
                                  PCR-RFLP SNP Genotyping Using a Genetic
                                  Algorithm  . . . . . . . . . . . . . . . 837--845
           Mindaugas Norkus and   
                 Damien Fay and   
             Mary J. Murphy and   
                Frank Barry and   
           Gearoid OLaighin and   
                 Liam Kilmartin   On the Application of Active Learning
                                  and Gaussian Processes in
                                  Postcryopreservation Cell Membrane
                                  Integrity Experiments  . . . . . . . . . 846--856
             Xiao-Fei Zhang and   
               Dao-Qing Dai and   
                    Xiao-Xin Li   Protein Complexes Discovery Based on
                                  Protein-Protein Interaction Data via a
                                  Regularized Sparse Generative Network
                                  Model  . . . . . . . . . . . . . . . . . 857--870
                 Yong Zhang and   
                    Peng Li and   
                    Garng Huang   Quantifying Dynamic Stability of Genetic
                                  Memory Circuits  . . . . . . . . . . . . 871--884
             Eugen Czeizler and   
             Andrzej Mizera and   
             Elena Czeizler and   
           Ralph-Johan Back and   
           John E. Eriksson and   
                      Ion Petre   Quantitative Analysis of the
                                  Self-Assembly Strategies of Intermediate
                                  Filaments from Tetrameric Vimentin . . . 885--898
             Michael Mooney and   
                Beth Wilmot and   
   The Bipolar Genome Study and   
               Shannon McWeeney   The GA and the GWAS: Using Genetic
                                  Algorithms to Search for Multilocus
                                  Associations . . . . . . . . . . . . . . 899--910
              Tommaso Mazza and   
            Paolo Ballarini and   
               Rosita Guido and   
                  Davide Prandi   The Relevance of Topology in Parallel
                                  Simulation of Biological Networks  . . . 911--923
           Debarka Sengupta and   
              Ujjwal Maulik and   
      Sanghamitra Bandyopadhyay   Weighted Markov Chain Based Aggregation
                                  of Biomolecule Orderings . . . . . . . . 924--933
               Italo Zoppis and   
             Erica Gianazza and   
       Massimiliano Borsani and   
            Clizia Chinello and   
           Veronica Mainini and   
           Carmen Galbusera and   
            Carlo Ferrarese and   
          Gloria Galimberti and   
               Sandro Sorbi and   
            Barbara Borroni and   
               Fulvio Magni and   
           Marco Antoniotti and   
                Giancarlo Mauri   Mutual Information Optimization for Mass
                                  Spectra Data Alignment . . . . . . . . . 934--939
       Denise Fagundes-Lima and   
                   Gerald Weber   Comment on ``SCS: Signal, Context, and
                                  Structure Features for Genome-Wide Human
                                  Promoter Recognition'' . . . . . . . . . 940--941
                      Anonymous   IEEE/ACM Transactions on Computational
                                  Biology and Bioinformatics Seeks New
                                  Editor in Chief for 2013--2014 Terms . . 942--942

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 9, Number 4, July, 2012

                Luonan Chen and   
                  Michael K. Ng   Guest Editorial: Bioinformatics and
                                  Computational Systems Biology  . . . . . 945--946
                Yinyin Yuan and   
           Christina Curtis and   
              Carlos Caldas and   
              Florian Markowetz   A Sparse Regulatory Network of
                                  Copy-Number Driven Gene Expression
                                  Reveals Putative Breast Cancer Oncogenes 947--954
                 Li-Zhi Liu and   
              Fang-Xiang Wu and   
                    W. J. Zhang   Inference of Biological S-System Using
                                  the Separable Estimation Method and the
                                  Genetic Algorithm  . . . . . . . . . . . 955--965
             Shuichi Kawano and   
           Teppei Shimamura and   
              Atsushi Niida and   
                Seiya Imoto and   
              Rui Yamaguchi and   
             Masao Nagasaki and   
                Ryo Yoshida and   
              Cristin Print and   
                  Satoru Miyano   Identifying Gene Pathways Associated
                                  with Cancer Characteristics via Sparse
                                  Statistical Methods  . . . . . . . . . . 966--972
                Haseong Kim and   
                   Erol Gelenbe   Stochastic Gene Expression Modeling with
                                  Hill Function for Switch-Like Gene
                                  Responses  . . . . . . . . . . . . . . . 973--979
                   Xin Chen and   
                 Xiaohua Hu and   
                Tze Yee Lim and   
              Xiajiong Shen and   
                 E. K. Park and   
                  Gail L. Rosen   Exploiting the Functional and Taxonomic
                                  Structure of Genomic Data by
                                  Probabilistic Topic Modeling . . . . . . 980--991
         Alvaro J. Gonzalez and   
                    Li Liao and   
                    Cathy H. Wu   Predicting Ligand Binding Residues and
                                  Functional Sites Using Multipositional
                                  Correlations with Graph Theoretic
                                  Clustering and Kernel CCA  . . . . . . . 992--1001
                Jianer Chen and   
           Alexander Zelikovsky   Guest Editors' Introduction to the
                                  Special Section on Bioinformatics
                                  Research and Applications  . . . . . . . 1002--1003
            Ruchi Chaudhary and   
         J. Gordon Burleigh and   
           David Fernandez-Baca   Fast Local Search for Unrooted
                                  Robinson--Foulds Supertrees  . . . . . . 1004--1013
                     Yu Lin and   
              Vaibhav Rajan and   
            Bernard M. E. Moret   A Metric for Phylogenetic Trees Based on
                                  Matching . . . . . . . . . . . . . . . . 1014--1022
         Krister M. Swenson and   
                  Eric Chen and   
     Nicholas D. Pattengale and   
                  David Sankoff   The Kernel of Maximum Agreement Subtrees 1023--1031
               Xiuwei Zhang and   
            Bernard M. E. Moret   Refining Regulatory Networks through
                                  Phylogenetic Transfer of Information . . 1032--1045
          Luqman Hodgkinson and   
                Richard M. Karp   Algorithms to Detect Multiprotein
                                  Modularity Conserved during Evolution    1046--1058
          Jonathan Q. Jiang and   
                 Lisa J. McQuay   Predicting Protein Function by
                                  Multi-Label Correlated Semi-Supervised
                                  Learning . . . . . . . . . . . . . . . . 1059--1069
               Jianxin Wang and   
                     Min Li and   
                  Huan Wang and   
                         Yi Pan   Identification of Essential Proteins
                                  Based on Edge Clustering Coefficient . . 1070--1080
              Woo-Hyuk Jang and   
              Suk-Hoon Jung and   
                   Dong-Soo Han   A Computational Model for Predicting
                                  Protein Interactions Based on
                                  Multidomain Collaboration  . . . . . . . 1081--1090
                Ickwon Choi and   
          Michael W. Kattan and   
             Brian J. Wells and   
                   Changhong Yu   A Hybrid Approach to Survival Model
                                  Building Using Integration of Clinical
                                  and Molecular Information in Censored
                                  Data . . . . . . . . . . . . . . . . . . 1091--1105
               Cosmin Lazar and   
            Jonatan Taminau and   
              Stijn Meganck and   
            David Steenhoff and   
              Alain Coletta and   
               Colin Molter and   
      Virginie de Schaetzen and   
                Robin Duque and   
             Hugues Bersini and   
                       Ann Nowe   A Survey on Filter Techniques for
                                  Feature Selection in Gene Expression
                                  Microarray Analysis  . . . . . . . . . . 1106--1119
          Claudio Felicioli and   
              Roberto Marangoni   BpMatch: An Efficient Algorithm for a
                                  Segmental Analysis of Genomic Sequences  1120--1127
                Stephen Willson   CSD Homomorphisms between Phylogenetic
                                  Networks . . . . . . . . . . . . . . . . 1128--1138
             Soumi Sengupta and   
      Sanghamitra Bandyopadhyay   De Novo Design of Potential RecA
                                  Inhibitors Using MultiObjective
                                  Optimization . . . . . . . . . . . . . . 1139--1154
                  Peng Chen and   
               Limsoon Wong and   
                      Jinyan Li   Detection of Outlier Residues for
                                  Improving Interface Prediction in
                                  Protein Heterocomplexes  . . . . . . . . 1155--1165
           Georgina Mirceva and   
            Ivana Cingovska and   
                Zoran Dimov and   
                   Danco Davcev   Efficient Approaches for Retrieving
                                  Protein Tertiary Structures  . . . . . . 1166--1179
     Nicoletta De Francesco and   
          Giuseppe Lettieri and   
                   Luca Martini   Efficient Genotype Elimination via
                                  Adaptive Allele Consolidation  . . . . . 1180--1189
                Yijia Zhang and   
                Hongfei Lin and   
                Zhihao Yang and   
                  Jian Wang and   
                     Yanpeng Li   Hash Subgraph Pairwise Kernel for
                                  Protein-Protein Interaction Extraction   1190--1202
                 Amina Noor and   
            Erchin Serpedin and   
             Mohamed Nounou and   
                   Hazem Nounou   Inferring Gene Regulatory Networks via
                                  Nonlinear State-Space Models and
                                  Exploiting Sparsity  . . . . . . . . . . 1203--1211
                  Chao Yang and   
                 Zengyou He and   
                   Can Yang and   
                    Weichuan Yu   Peptide Reranking with Protein-Peptide
                                  Correspondence and Precursor Peak
                                  Intensity Information  . . . . . . . . . 1212--1219
               Haitao Jiang and   
             Chunfang Zheng and   
              David Sankoff and   
                     Binhai Zhu   Scaffold Filling under the Breakpoint
                                  and Related Distances  . . . . . . . . . 1220--1229
                Ranadip Pal and   
             Sonal Bhattacharya   Transient Dynamics of Reduced-Order
                                  Models of Genetic Regulatory Networks    1230--1244
       Jose Salavert Torres and   
    Ignacio Blanquer Espert and   
     Andres Tomas Dominguez and   
          Vicente Hernendez and   
             Ignacio Medina and   
            Joaquin Terraga and   
                 Joaquin Dopazo   Using GPUs for the Exact Alignment of
                                  Short-Read Genetic Sequences by Means of
                                  the Burrows--Wheeler Transform . . . . . 1245--1256
             Shaohong Zhang and   
               Hau-San Wong and   
                  Ying Shen and   
                   Dongqing Xie   A New Unsupervised Feature Ranking
                                  Method for Gene Expression Data Based on
                                  Consensus Affinity . . . . . . . . . . . 1257--1263

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 9, Number 5, September, 2012

            Yi-Ping Phoebe Chen   Guest Editorial: Application and
                                  Development of Bioinformatics  . . . . . 1265
   Stephanus Daniel Handoko and   
             Xuchang Ouyang and   
           Chinh Tran To Su and   
            Chee Keong Kwoh and   
                   Yew Soon Ong   QuickVina: Accelerating AutoDock Vina
                                  Using Gradient-Based Heuristics for
                                  Global Optimization  . . . . . . . . . . 1266--1272
                Pengyi Yang and   
                     Jie Ma and   
               Penghao Wang and   
                Yunping Zhu and   
               Bing B. Zhou and   
                   Yee Hwa Yang   Improving X!Tandem on Peptide
                                  Identification from Mass Spectrometry by
                                  Self-Boosted Percolator  . . . . . . . . 1273--1280
                    Lin Wan and   
                    Fengzhu Sun   CEDER: Accurate Detection of
                                  Differentially Expressed Genes by
                                  Combining Significance of Exons Using
                                  RNA-Seq  . . . . . . . . . . . . . . . . 1281--1292
            Richard Rottger and   
             Ulrich Ruckert and   
                Jan Taubert and   
                   Jan Baumbach   How Little Do We Actually Know? On the
                                  Size of Gene Regulatory Networks . . . . 1293--1300
          Hossam M. Ashtawy and   
             Nihar R. Mahapatra   A Comparative Assessment of Ranking
                                  Accuracies of Conventional and
                                  Machine-Learning-Based Scoring Functions
                                  for Protein-Ligand Binding Affinity
                                  Prediction . . . . . . . . . . . . . . . 1301--1313
      François Fages and   
                Sylvain Soliman   Guest Editors' Introduction to the
                                  Special Section on Computational Methods
                                  in Systems Biology . . . . . . . . . . . 1314--1315
                Jimmy Omony and   
      Astrid R. Mach-Aigner and   
           Leo H. de Graaff and   
         Gerrit van Straten and   
         Anton J. B. van Boxtel   Evaluation of Design Strategies for Time
                                  Course Experiments in Genetic Networks:
                                  Case Study of the XlnR Regulon in
                                  \bionameAspergillus niger  . . . . . . . 1316--1325
             Eugen Czeizler and   
           Vladimir Rogojin and   
                      Ion Petre   The Phosphorylation of the Heat Shock
                                  Factor as a Modulator for the Heat Shock
                                  Response . . . . . . . . . . . . . . . . 1326--1337
             Hannes Klarner and   
              Heike Siebert and   
             Alexander Bockmayr   Time Series Dependent Analysis of
                                  Unparametrized Thomas Networks . . . . . 1338--1351
  Sucheendra K. Palaniappan and   
                  S. Akshay and   
                   Bing Liu and   
              Blaise Genest and   
              P. S. Thiagarajan   A Hybrid Factored Frontier Algorithm for
                                  Dynamic Bayesian Networks with a
                                  Biopathways Application  . . . . . . . . 1352--1365
            Nicola Paoletti and   
                 Pietro Lio and   
           Emanuela Merelli and   
                Marco Viceconti   Multilevel Computational Modeling and
                                  Quantitative Analysis of Bone Remodeling 1366--1378
             Blaise Hanczar and   
                  Avner Bar-Hen   A New Measure of Classifier Performance
                                  for Gene Expression Data . . . . . . . . 1379--1386
                Uday Kamath and   
               Jack Compton and   
      Rezarta Islamaj Dogan and   
            Kenneth De Jong and   
                   Amarda Shehu   An Evolutionary Algorithm Approach for
                                  Feature Generation from Sequence Data
                                  and Its Application to DNA Splice Site
                                  Prediction . . . . . . . . . . . . . . . 1387--1398
           Nadeem A. Ansari and   
                  Riyue Bao and   
             Calin Voichita and   
                 Sorin Draghici   Detecting Phenotype-Specific
                                  Interactions between Biological
                                  Processes from Microarray Data and
                                  Annotations  . . . . . . . . . . . . . . 1399--1409
             Tatsuya Akutsu and   
                 Sven Kosub and   
         Avraham A. Melkman and   
                Takeyuki Tamura   Finding a Periodic Attractor of a
                                  Boolean Network  . . . . . . . . . . . . 1410--1421
               Herbert Pang and   
          Stephen L. George and   
                    Ken Hui and   
                    Tiejun Tong   Gene Selection Using Iterative Feature
                                  Elimination Random Forests for Survival
                                  Outcomes . . . . . . . . . . . . . . . . 1422--1431
                 Bilge Karacali   Hierarchical Motif Vectors for
                                  Prediction of Functional Sites in Amino
                                  Acid Sequences Using Quasi-Supervised
                                  Learning . . . . . . . . . . . . . . . . 1432--1441
  Pablo H. Hennings-Yeomans and   
              Gregory F. Cooper   Improving the Prediction of Clinical
                                  Outcomes from Genomic Data Using
                                  Multiresolution Analysis . . . . . . . . 1442--1450
             Nicolas Bonnel and   
 Pierre-François Marteau   LNA: Fast Protein Structural Comparison
                                  Using a Laplacian Characterization of
                                  Tertiary Structure . . . . . . . . . . . 1451--1458
            Francesco Sambo and   
     Marco A. Montes de Oca and   
         Barbara Di Camillo and   
             Gianna Toffolo and   
                 Thomas Stutzle   MORE: Mixed Optimization for Reverse
                                  Engineering --- an Application to
                                  Modeling Biological Networks Response
                                  via Sparse Systems of Nonlinear
                                  Differential Equations . . . . . . . . . 1459--1471
               Neil Jacklin and   
                   Zhi Ding and   
                   Wei Chen and   
                   Chunqi Chang   Noniterative Convex Optimization Methods
                                  for Network Component Analysis . . . . . 1472--1481
           Silvana Badaloni and   
         Barbara Di Camillo and   
                Francesco Sambo   Qualitative Reasoning for Biological
                                  Network Inference from Systematic
                                  Perturbation Experiments . . . . . . . . 1482--1491
            John C. Hawkins and   
                 Hongbo Zhu and   
                 Joan Teyra and   
            M. Teresa Pisabarro   Reduced False Positives in PDZ Binding
                                  Prediction Using Sequence and Structural
                                  Descriptors  . . . . . . . . . . . . . . 1492--1503
               Jianyong Sun and   
      Jonathan M. Garibaldi and   
                     Kim Kenobi   Robust Bayesian Clustering for
                                  Replicated Gene Expression Data  . . . . 1504--1514
             Zhi-Zhong Chen and   
                   Fei Deng and   
                   Lusheng Wang   Simultaneous Identification of
                                  Duplications, Losses, and Lateral Gene
                                  Transfers  . . . . . . . . . . . . . . . 1515--1528
                    Bo Liao and   
                   Xiong Li and   
                    Wen Zhu and   
                        Zhi Cao   A Novel Method to Select Informative
                                  SNPs and Their Application in Genetic
                                  Association Studies  . . . . . . . . . . 1529--1534
              Shaini Joseph and   
             Shreyas Karnik and   
              Pravin Nilawe and   
            V. K. Jayaraman and   
           Susan Idicula-Thomas   ClassAMP: a Prediction Tool for
                                  Classification of Antimicrobial Peptides 1535--1538
               M. N. Nounou and   
               H. N. Nounou and   
                  N. Meskin and   
                   A. Datta and   
                E. R. Dougherty   Multiscale Denoising of Biological Data:
                                  a Comparative Analysis . . . . . . . . . 1539--1545
          Michael Margaliot and   
                   Tamir Tuller   Stability Analysis of the Ribosome Flow
                                  Model  . . . . . . . . . . . . . . . . . 1545--1552

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 9, Number 6, November, 2012

             Marie-France Sagot   EIC Editorial  . . . . . . . . . . . . . 1553--1557
            James H. Degnan and   
          Noah A. Rosenberg and   
                  Tanja Stadler   A Characterization of the Set of Species
                                  Trees that Produce Anomalous Ranked Gene
                                  Trees  . . . . . . . . . . . . . . . . . 1558--1568
                  Yang Tang and   
                Zidong Wang and   
                 Huijun Gao and   
              Stephen Swift and   
                  Jurgen Kurths   A Constrained Evolutionary Computation
                                  Method for Detecting Controlling Regions
                                  of Cortical Networks . . . . . . . . . . 1569--1581
                Yuri Pirola and   
      Gianluca Della Vedova and   
            Stefano Biffani and   
          Alessandra Stella and   
                Paola Bonizzoni   A Fast and Practical Approach to
                                  Genotype Phasing and Imputation on a
                                  Pedigree with Erroneous and Incomplete
                                  Information  . . . . . . . . . . . . . . 1582--1594
                   N. Kazmi and   
              M. A. Hossain and   
                 R. M. Phillips   A Hybrid Cellular Automaton Model of
                                  Solid Tumor Growth and Bioreductive Drug
                                  Transport  . . . . . . . . . . . . . . . 1595--1606
           Alessandro Abate and   
           Stephane Vincent and   
                 Roel Dobbe and   
           Alberto Silletti and   
                Neal Master and   
         Jeffrey D. Axelrod and   
               Claire J. Tomlin   A Mathematical Model to Study the
                                  Dynamics of Epithelial Cellular Networks 1607--1620
             Gizem Cavuslar and   
               Bulent Catay and   
          Mehmet Serkan Apaydin   A Tabu Search Approach for the NMR
                                  Protein Structure-Based Assignment
                                  Problem  . . . . . . . . . . . . . . . . 1621--1628
             Christopher Ma and   
          Thomas K. F. Wong and   
                  T. W. Lam and   
                  W. K. Hon and   
                K. Sadakane and   
                      S. M. Yiu   An Efficient Alignment Algorithm for
                                  Searching Simple Pseudoknots over Long
                                  Genomic Sequence . . . . . . . . . . . . 1629--1638
                I. Burak Ozyurt   Automatic Identification and
                                  Classification of Noun Argument
                                  Structures in Biomedical Literature  . . 1639--1648
                Meng-Yun Wu and   
               Dao-Qing Dai and   
                     Yu Shi and   
                   Hong Yan and   
                 Xiao-Fei Zhang   Biomarker Identification and Cancer
                                  Classification Based on Microarray Data
                                  Using Laplace Naive Bayes Model with
                                  Mean Shrinkage . . . . . . . . . . . . . 1649--1662
                 Ozan Irsoy and   
         Olcay Taner Yildiz and   
                 Ethem Alpaydin   Design and Analysis of Classifier
                                  Learning Experiments in Bioinformatics:
                                  Survey and Case Studies  . . . . . . . . 1663--1675
              Wendy Ashlock and   
                Suprakash Datta   Distinguishing Endogenous Retroviral
                                  LTRs from SINE Elements Using Features
                                  Extracted from Evolved Side Effect
                                  Machines . . . . . . . . . . . . . . . . 1676--1689
         Richard Tzong-Han Tsai   Improving Protein-Protein Interaction
                                  Pair Ranking with an Integrated Global
                                  Association Score  . . . . . . . . . . . 1690--1695
   Seyedsasan Hashemikhabir and   
           Eyup Serdar Ayaz and   
             Yusuf Kavurucu and   
                  Tolga Can and   
                  Tamer Kahveci   Large-Scale Signaling Network
                                  Reconstruction . . . . . . . . . . . . . 1696--1708
           Khachik Sargsyan and   
               Cosmin Safta and   
           Bert Debusschere and   
                     Habib Najm   Multiparameter Spectral Representation
                                  of Noise-Induced Competence in
                                  \bionameBacillus Subtilis  . . . . . . . 1709--1723
          Michael Margaliot and   
                   Tamir Tuller   On the Steady-State Distribution in the
                                  Homogeneous Ribosome Flow Model  . . . . 1724--1736
           Tobias Marschall and   
                 Inke Herms and   
    Hans-Michael Kaltenbach and   
                   Sven Rahmann   Probabilistic Arithmetic Automata and
                                  Their Applications . . . . . . . . . . . 1737--1750
                  Zhiwen Yu and   
                      Le Li and   
                   Jane You and   
               Hau-San Wong and   
                   Guoqiang Han   SC$^3$: Triple Spectral Clustering-Based
                                  Consensus Clustering Framework for Class
                                  Discovery from Cancer Gene Expression
                                  Profiles . . . . . . . . . . . . . . . . 1751--1765
                     Xin Ma and   
                   Jing Guo and   
                Hong-De Liu and   
              Jian-Ming Xie and   
                       Xiao Sun   Sequence-Based Prediction of DNA-Binding
                                  Residues in Proteins with Conservation
                                  and Correlation Information  . . . . . . 1766--1775
               Jianxin Wang and   
              Yuannan Huang and   
              Fang-Xiang Wu and   
                         Yi Pan   Symmetry Compression Method for
                                  Discovering Network Motifs . . . . . . . 1776--1789
      Mohammad Shafkat Amin and   
     Russell L. Finley, Jr. and   
                 Hasan M. Jamil   Top-$k$ Similar Graph Matching Using
                                  TraM in Biological Networks  . . . . . . 1790--1804
          Zachary L. Dwight and   
              Robert Palais and   
                Carl T. Wittwer   uAnalyze: Web-Based High-Resolution DNA
                                  Melting Analysis with Comparison to
                                  Thermodynamic Predictions  . . . . . . . 1805--1811
                  Matteo Re and   
               Marco Mesiti and   
              Giorgio Valentini   A Fast Ranking Algorithm for Predicting
                                  Gene Functions in Biomolecular Networks  1812--1818
            Hazem N. Nounou and   
          Mohamed N. Nounou and   
               Nader Meskin and   
            Aniruddha Datta and   
            Edward R. Dougherty   Fuzzy Intervention in Biological
                                  Phenomena  . . . . . . . . . . . . . . . 1819--1825
           George Papadakis and   
                 Electra Gizeli   In Silico Search of DNA Drugs Targeting
                                  Oncogenes  . . . . . . . . . . . . . . . 1826--1830
             Manuele Bicego and   
              Pietro Lovato and   
          Alessandro Perina and   
            Marianna Fasoli and   
         Massimo Delledonne and   
             Mario Pezzotti and   
         Annalisa Polverari and   
                Vittorio Murino   Investigating Topic Models' Capabilities
                                  in Expression Microarray Data
                                  Classification . . . . . . . . . . . . . 1831--1836
               Elena Grassi and   
       Federico Di Gregorio and   
                 Ivan Molineris   KungFQ: a Simple and Powerful Approach
                                  to Compress \tt fastq Files  . . . . . . 1837--1842
          Christina Boucher and   
                   Mohamed Omar   On the Hardness of Counting and Sampling
                                  Center Strings . . . . . . . . . . . . . 1843--1846
             Daniel Gyorffy and   
            Peter Zavodszky and   
                Andras Szilagyi   ``Pull Moves'' for Rectangular Lattice
                                  Polymer Models Are Not Fully Reversible  1847--1849
  Ricardo J. G. B. Campello and   
             Davoud Moulavi and   
                   Joerg Sander   A Simpler and More Accurate AUTO--HDS
                                  Framework for Clustering and
                                  Visualization of Biological Data . . . . 1850--1852
   Stephanus Daniel Handoko and   
             Xuchang Ouyang and   
           Chinh Tran To Su and   
            Chee Keong Kwoh and   
                   Yew Soon Ong   Erratum to ``QuickVina: Accelerating
                                  AutoDock Vina Using Gradient-Based
                                  Heuristics for Global Optimization'' . . 1853
                      Anonymous   Call for Papers: Special Issue on
                                  `-Omics' Based Companion Diagnostics for
                                  Personalized Medicine  . . . . . . . . . 1855--1855


IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 10, Number 1, January, 2013

                        Ying Xu   Editorial from the New Editor-in--Chief  1--1
         Shubhra Sankar Ray and   
                  Sankar K. Pal   RNA Secondary Structure Prediction Using
                                  Soft Computing . . . . . . . . . . . . . 2--17
            Teresa Piovesan and   
                    Steven Kelk   A Simple Fixed Parameter Tractable
                                  Algorithm for Computing the
                                  Hybridization Number of Two (Not
                                  Necessarily Binary) Trees  . . . . . . . 18--25
              Inken Wohlers and   
              Rumen Andonov and   
                 Gunnar W. Klau   DALIX: Optimal DALI Protein Structure
                                  Alignment  . . . . . . . . . . . . . . . 26--36
          Carlos H. A. Higa and   
           Tales P. Andrade and   
        Ronaldo Fumio Hashimoto   Growing Seed Genes from Time Series Data
                                  and Thresholded Boolean Networks with
                                  Perturbation . . . . . . . . . . . . . . 37--49
             Daniele Muraro and   
                    Ute Vob and   
             Michael Wilson and   
            Malcolm Bennett and   
                Helen Byrne and   
                Ive De Smet and   
            Charlie Hodgman and   
                      John King   Inference of the Genetic Network
                                  Regulating Lateral Root Initiation in
                                  \bionameArabidopsis thaliana . . . . . . 50--60
              Cuong V. Than and   
              Noah A. Rosenberg   Mathematical Properties of the Deep
                                  Coalescence Cost . . . . . . . . . . . . 61--72
                Peter Boyen and   
                Frank Neven and   
             Dries Van Dyck and   
            Felipe Valentim and   
                  Aalt van Dijk   Mining Minimal Motif Pair Sets Maximally
                                  Covering Interactions in a
                                  Protein-Protein Interaction Network  . . 73--86
        Jagath C. Rajapakse and   
          Piyushkumar A. Mundra   Multiclass Gene Selection Using
                                  Pareto-Fronts  . . . . . . . . . . . . . 87--97
                    Ye Yang and   
  Farnoosh A. Aghababazadeh and   
                David R. Bickel   Parametric Estimation of the Local False
                                  Discovery Rate for Identifying Genetic
                                  Associations . . . . . . . . . . . . . . 98--108
               Andrei Todor and   
                 Alin Dobra and   
                  Tamer Kahveci   Probabilistic Biological Network
                                  Alignment  . . . . . . . . . . . . . . . 109--121
            Priscila Biller and   
               Pedro Feijao and   
                  Joao Meidanis   Rearrangement-Based Phylogeny Using the
                                  Single-Cut-or-Join Operation . . . . . . 122--134
      Apostolos Axenopoulos and   
               Petros Daras and   
   Georgios E. Papadopoulos and   
                  Elias Houstis   SP-Dock: Protein-Protein Docking Using
                                  Shape and Physicochemical
                                  Complementarity  . . . . . . . . . . . . 135--150
           Stefan Grunewald and   
           Andreas Spillner and   
           Sarah Bastkowski and   
          Anja Bogershausen and   
                Vincent Moulton   SuperQ: Computing Supernetworks from
                                  Quartets . . . . . . . . . . . . . . . . 151--160
            Itziar Irigoien and   
           Francesc Mestres and   
              Concepcion Arenas   The Depth Problem: Identifying the Most
                                  Representative Units in a Data Group . . 161--172
                     Xia Wu and   
                    Juan Li and   
      Napatkamon Ayutyanont and   
             Hillary Protas and   
             William Jagust and   
              Adam Fleisher and   
                Eric Reiman and   
                     Li Yao and   
                     Kewei Chen   The Receiver Operational Characteristic
                                  for Binary Classification with Multiple
                                  Indices and Its Application to the
                                  Neuroimaging Study of Alzheimer's
                                  Disease  . . . . . . . . . . . . . . . . 173--180
              Gui-Fang Shao and   
                   Fan Yang and   
                 Qian Zhang and   
               Qi-Feng Zhou and   
                    Lin-Kai Luo   Using the Maximum Between-Class Variance
                                  for Automatic Gridding of cDNA
                                  Microarray Images  . . . . . . . . . . . 181--192
            Alexis Lamiable and   
           Franck Quessette and   
              Sandrine Vial and   
            Dominique Barth and   
                   Alain Denise   An Algorithmic Game-Theory Approach for
                                  Coarse-Grain Prediction of RNA $3$D
                                  Structure  . . . . . . . . . . . . . . . 193--199
            Kristian Ovaska and   
                 Lauri Lyly and   
            Biswajyoti Sahu and   
              Olli A. Janne and   
              Sampsa Hautaniemi   Genomic Region Operation Kit for
                                  Flexible Processing of Deep Sequencing
                                  Data . . . . . . . . . . . . . . . . . . 200--206
                  Xiang Wan and   
                   Can Yang and   
                 Qiang Yang and   
                Hongyu Zhao and   
                    Weichuan Yu   HapBoost: a Fast Approach to Boosting
                                  Haplotype Association Analyses in
                                  Genome-Wide Association Studies  . . . . 207--212
                   Mark Howison   High-Throughput Compression of FASTQ
                                  Data with SeqDB  . . . . . . . . . . . . 213--218
                   Yuan Zhu and   
             Xiao-Fei Zhang and   
               Dao-Qing Dai and   
                    Meng-Yun Wu   Identifying Spurious Interactions and
                                  Predicting Missing Interactions in the
                                  Protein-Protein Interaction Networks via
                                  a Generative Network Model . . . . . . . 219--225
            Aleksandar Poleksic   Improved Algorithms for Matching
                                  $r$-Separated Sets with Applications to
                                  Protein Structure Alignment  . . . . . . 226--229
               Xiaowei Zhou and   
                   Can Yang and   
                  Xiang Wan and   
                Hongyu Zhao and   
                    Weichuan Yu   Multisample aCGH Data Analysis via Total
                                  Variation and Spectral Regularization    230--235
     Alan Joseph J. Caceres and   
              Juan Castillo and   
                 Jinnie Lee and   
             Katherine St. John   Walks on SPR Neighborhoods . . . . . . . 236--239
                      Anonymous   2012 Reviewers List  . . . . . . . . . . 240--243
                          Title   2012 Annual Index  . . . . . . . . . . . 244--270

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 10, Number 2, March, 2013

            Yi-Ping Phoebe Chen   Guest Editorial: Advanced Algorithms of
                                  Bioinformatics . . . . . . . . . . . . . 273--273
                  Jikai Lei and   
    Prapaporn Techa-angkoon and   
                      Yanni Sun   Chain-RNA: a Comparative ncRNA Search
                                  Tool Based on the Two-Dimensional Chain
                                  Algorithm  . . . . . . . . . . . . . . . 274--285
              Pradipta Maji and   
                  Sushmita Paul   Rough-Fuzzy Clustering for Grouping
                                  Functionally Similar Genes from
                                  Microarray Data  . . . . . . . . . . . . 286--299
                 Ngoc Tu Le and   
                  Tu Bao Ho and   
                    Bich Hai Ho   Computational Reconstruction of
                                  Transcriptional Relationships from
                                  ChIP-Chip Data . . . . . . . . . . . . . 300--307
      François Fages and   
                Sylvain Soliman   Guest Editors' Introduction to the
                                  Special Section on Computational Methods
                                  in Systems Biology . . . . . . . . . . . 308--309
        Thomas A. Henzinger and   
                 Maria Mateescu   The Propagation Approach for Computing
                                  Biochemical Reaction Networks  . . . . . 310--322
            Abhishek Murthy and   
              Ezio Bartocci and   
           Flavio H. Fenton and   
                James Glimm and   
            Richard A. Gray and   
        Elizabeth M. Cherry and   
            Scott A. Smolka and   
                     Radu Grosu   Curvature Analysis of Cardiac Excitation
                                  Wavefronts . . . . . . . . . . . . . . . 323--336
                   Qian Gao and   
              David Gilbert and   
              Monika Heiner and   
                    Fei Liu and   
         Daniele Maccagnola and   
                     David Tree   Multiscale Modeling and Analysis of
                                  Planar Cell Polarity in the
                                  \bionameDrosophila Wing  . . . . . . . . 337--351
              Serdar Bozdag and   
           Timothy J. Close and   
                Stefano Lonardi   A Graph-Theoretical Approach to the
                                  Selection of the Minimum Tiling Path
                                  from a Physical Map  . . . . . . . . . . 352--360
            Cheng-Hong Yang and   
                  Yu-Da Lin and   
              Li-Yeh Chaung and   
                Hsueh-Wei Chang   Evaluation of Breast Cancer
                                  Susceptibility Using Improved Genetic
                                  Algorithms to Generate Genotype SNP
                                  Barcodes . . . . . . . . . . . . . . . . 361--371
               Jiaoyun Yang and   
                     Yun Xu and   
                Xiaohui Yao and   
                  Guoliang Chen   FNphasing: a Novel Fast Heuristic
                                  Algorithm for Haplotype Phasing Based on
                                  Flow Network Model . . . . . . . . . . . 372--382
               Cosmin Lazar and   
            Jonatan Taminau and   
              Stijn Meganck and   
            David Steenhoff and   
              Alain Coletta and   
       David Y. Weiss Solis and   
               Colin Molter and   
                Robin Duque and   
             Hugues Bersini and   
                       Ann Nowe   GENESHIFT: a Nonparametric Approach for
                                  Integrating Microarray Gene Expression
                                  Data Based on the Inner Product as a
                                  Distance Measure between the
                                  Distributions of Genes . . . . . . . . . 383--392
         Camilla Bernardini and   
             Federica Censi and   
             Wanda Lattanzi and   
        Giovanni Calcagnini and   
            Alessandro Giuliani   Gene Regulation Networks in Early Phase
                                  of Duchenne Muscular Dystrophy . . . . . 393--400
              Ariel E. Baya and   
              Pablo M. Granitto   How Many Clusters: a Validation Index
                                  for Arbitrary-Shaped Clusters  . . . . . 401--414
              Qingfeng Chen and   
                    Wei Lan and   
                   Jianxin Wang   Mining Featured Patterns of MiRNA
                                  Interaction Based on Sequence and
                                  Structure Similarity . . . . . . . . . . 415--422
              Ujjwal Maulik and   
       Anirban Mukhopadhyay and   
        Malay Bhattacharyya and   
              Lars Kaderali and   
             Benedikt Brors and   
  Sanghamitra Bandyopadhyay and   
                    Roland Eils   Mining Quasi-Bicliques from HIV-1-Human
                                  Protein Interaction Network: a
                                  Multiobjective Biclustering Approach . . 423--435
                  Xiao Wang and   
                   Guo-Zheng Li   Multilabel Learning via Random Label
                                  Selection for Protein Subcellular
                                  Multilocations Prediction  . . . . . . . 436--446
                  Yifeng Li and   
                   Alioune Ngom   Nonnegative Least-Squares Methods for
                                  the Classification of High-Dimensional
                                  Biological Data  . . . . . . . . . . . . 447--456
                Hong-Jie Yu and   
                De-Shuang Huang   Normalized Feature Vectors: a Novel
                                  Alignment-Free Sequence Comparison
                                  Method Based on the Numbers of Adjacent
                                  Amino Acids  . . . . . . . . . . . . . . 457--467
                Chien-Ta Tu and   
                   Bor-Sen Chen   On the Increase in Network Robustness
                                  and Decrease in Network Response Ability
                                  during the Aging Process: a Systems
                                  Biology Approach via Microarray Data . . 468--480
           Kevin W. DeRonne and   
                 George Karypis   Pareto Optimal Pairwise Sequence
                                  Alignment  . . . . . . . . . . . . . . . 481--493
            Tsung-Heng Tsai and   
          Mahlet G. Tadesse and   
                   Yue Wang and   
               Habtom W. Ressom   Profile-Based LC-MS Data Alignment --- a
                                  Bayesian Approach  . . . . . . . . . . . 494--503
            Ali Gholami Rud and   
           Saeed Shahrivari and   
               Saeed Jalili and   
 Zahra Razaghi Moghadam Kashani   RANGI: a Fast List-Colored Graph Motif
                                  Finding Algorithm  . . . . . . . . . . . 504--513
                    Wei Liu and   
                    Dong Li and   
                Yunping Zhu and   
                Hongwei Xie and   
                       Fuchu He   Reconstruction of Signaling Network from
                                  Protein Interactions Based on Function
                                  Annotations  . . . . . . . . . . . . . . 514--521
              Pawel Gorecki and   
          Oliver Eulenstein and   
                   Jerzy Tiuryn   Unrooted Tree Reconciliation: a Unified
                                  Approach . . . . . . . . . . . . . . . . 522--536
                  N. Meskin and   
                  H. Nounou and   
                  M. Nounou and   
                       A. Datta   Parameter Estimation of Biological
                                  Phenomena: an Unscented Kalman Filter
                                  Approach . . . . . . . . . . . . . . . . 537--543
                      Anonymous   Call for Papers: Special issue on
                                  sofware and databases in TCBB  . . . . . 544--544

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 10, Number 3, May, 2013

              Saima Rathore and   
          Mutawarra Hussain and   
                  Ahmad Ali and   
                 Asifullah Khan   A Recent Survey on Colon Cancer
                                  Detection Techniques . . . . . . . . . . 545--563
          Abdollah Dehzangi and   
             Kuldip Paliwal and   
                Alok Sharma and   
              Omid Dehzangi and   
                   Abdul Sattar   A Combination of Feature Extraction
                                  Methods with an Ensemble of Different
                                  Classifiers for Protein Structural Class
                                  Prediction Problem . . . . . . . . . . . 564--575
           Magnus Bordewich and   
                  Radu Mihaescu   Accuracy Guarantees for Phylogeny
                                  Reconstruction Algorithms Based on
                                  Balanced Minimum Evolution . . . . . . . 576--583
                    Yi Ming Zou   Boolean Networks with Multiexpressions
                                  and Parameters . . . . . . . . . . . . . 584--592
                Hsi-Che Liu and   
              Pei-Chen Peng and   
          Tzung-Chien Hsieh and   
               Ting-Chi Yeh and   
               Chih-Jen Lin and   
              Chien-Yu Chen and   
                Jen-Yin Hou and   
              Lee-Yung Shih and   
               Der-Cherng Liang   Comparison of Feature Selection Methods
                                  for Cross-Laboratory Microarray Analysis 593--604
                 Hasan M. Jamil   Designing Integrated Computational
                                  Biology Pipelines Visually . . . . . . . 605--618
            Francesco Abate and   
           Andrea Acquaviva and   
              Elisa Ficarra and   
               Roberto Piva and   
                   Enrico Macii   Gelsius: a Literature-Based Workflow for
                                  Determining Quantitative Associations
                                  between Genes and Biological Processes   619--631
         Md. Muksitul Haque and   
         Lawrence B. Holder and   
         Michael K. Skinner and   
                  Diane J. Cook   Generalized Query-Based Active Learning
                                  to Identify Differentially Methylated
                                  Regions in DNA . . . . . . . . . . . . . 632--644
              Gordon Gremme and   
           Sascha Steinbiss and   
                   Stefan Kurtz   GenomeTools: a Comprehensive Software
                                  Library for Efficient Processing of
                                  Structured Genome Annotations  . . . . . 645--656
                  Zhiwen Yu and   
                Hantao Chen and   
                   Jane You and   
               Guoqiang Han and   
                          Le Li   Hybrid Fuzzy Cluster Ensemble Framework
                                  for Tumor Clustering from Biomolecular
                                  Data . . . . . . . . . . . . . . . . . . 657--670
                Ola ElBakry and   
             M. Omair Ahmad and   
                 M. N. S. Swamy   Inference of Gene Regulatory Networks
                                  with Variable Time Delay from
                                  Time-Series Microarray Data  . . . . . . 671--687
                   Xiong Li and   
                    Bo Liao and   
                  Lijun Cai and   
                    Zhi Cao and   
                        Wen Zhu   Informative SNPs Selection Based on
                                  Two-Locus and Multilocus Linkage
                                  Disequilibrium: Criteria of
                                  Max-Correlation and Min-Redundancy . . . 688--695
              Tak-Ming Chan and   
               Leung-Yau Lo and   
              Ho-Yin Sze-To and   
            Kwong-Sak Leung and   
                Xinshu Xiao and   
                   Man-Hon Wong   Modeling Associated Protein-DNA Pattern
                                  Discovery with Unified Scores  . . . . . 696--707
                  Yang Tang and   
                 Huijun Gao and   
                  Jurgen Kurths   Multiobjective Identification of
                                  Controlling Areas in Neuronal Networks   708--720
         Peter J. Humphries and   
                     Taoyang Wu   On the Neighborhoods of Trees  . . . . . 721--728
                Yijia Zhang and   
                Hongfei Lin and   
                Zhihao Yang and   
                  Jian Wang and   
                 Yanpeng Li and   
                          Bo Xu   Protein Complex Prediction in Large
                                  Ontology Attributed Protein-Protein
                                  Interaction Networks . . . . . . . . . . 729--741
           Debarka Sengupta and   
             Aroonalok Pyne and   
              Ujjwal Maulik and   
      Sanghamitra Bandyopadhyay   Reformulated Kemeny Optimal Aggregation
                                  with Application in Consensus Ranking of
                                  microRNA Targets . . . . . . . . . . . . 742--751
              Jian-Sheng Wu and   
                   Zhi-Hua Zhou   Sequence-Based Prediction of
                                  microRNA-Binding Residues in Proteins
                                  Using Cost-Sensitive Laplacian Support
                                  Vector Machines  . . . . . . . . . . . . 752--759
                Fiete Haack and   
              Kevin Burrage and   
              Ronald Redmer and   
          Adelinde M. Uhrmacher   Studying the Role of Lipid Rafts on
                                  Protein Receptor Bindings with Cellular
                                  Automata . . . . . . . . . . . . . . . . 760--770
                  Wei Zhang and   
                     Xiufen Zou   Systematic Analysis of the Mechanisms of
                                  Virus-Triggered Type I IFN Signaling
                                  Pathways through Mathematical Modeling   771--779
                Allen L. Hu and   
               Keith C. C. Chan   Utilizing Both Topological and Attribute
                                  Information for Protein Complex
                                  Identification in PPI Networks . . . . . 780--792
             Sara P. Garcia and   
    Joao M. O. S. Rodrigues and   
              Sergio Santos and   
               Diogo Pratas and   
               Vera Afreixo and   
              Carlos Bastos and   
    Paulo J. S. G. Ferreira and   
               Armando J. Pinho   A Genomic Distance for Assembly
                                  Comparison Based on Compressed Maximal
                                  Exact Matches  . . . . . . . . . . . . . 793--798
                     Osman Goni   A New Approach to Implement Absorbing
                                  Boundary Condition in Biomolecular
                                  Electrostatics . . . . . . . . . . . . . 799--804
            Edoardo Milotti and   
      Vladislav Vyshemirsky and   
               Michela Sega and   
             Sabrina Stella and   
              Federico Dogo and   
               Roberto Chignola   Computer-Aided Biophysical Modeling: a
                                  Quantitative Approach to Complex
                                  Biological Systems . . . . . . . . . . . 805--810
              Stefan Ivanov and   
              Ivan Dimitrov and   
              Irina Doytchinova   Quantitative Prediction of Peptide
                                  Binding to HLA-DP1 Protein . . . . . . . 811--815
                      Anonymous   Call for Papers: Special Issue on
                                  Software and Databases in TCBB . . . . . 816--816

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 10, Number 4, July, 2013

                 Guoxian Yu and   
            Huzefa Rangwala and   
        Carlotta Domeniconi and   
                Guoji Zhang and   
                      Zhiwen Yu   Protein Function Prediction using
                                  Multi-label Ensemble Classification  . . 1--1
    Marcilio C. P. de Souto and   
                   Maricel Kann   Guest Editorial for Special Section on
                                  BSB 2012 . . . . . . . . . . . . . . . . 817--818
               Pedro Feijao and   
                  Joao Meidanis   Extending the Algebraic Formalism for
                                  Genome Rearrangements to Include Linear
                                  Chromosomes  . . . . . . . . . . . . . . 819--831
               Ronny Lorenz and   
        Stephan H. Bernhart and   
                   Jing Qin and   
Christian Honer zu Siederdissen and   
              Andrea Tanzer and   
               Fabian Amman and   
            Ivo L. Hofacker and   
               Peter F. Stadler   $2$D Meets $4$G: $G$-Quadruplexes in RNA
                                  Secondary Structure Prediction . . . . . 832--844
         Pablo A. Jaskowiak and   
  Ricardo J. G. B. Campello and   
            Ivan G. Costa Filho   Proximity Measures for Clustering Gene
                                  Expression Microarray Data: a Validation
                                  Methodology and a Comparative Analysis   845--857
              Surajit Panja and   
               Sourav Patra and   
          Anirban Mukherjee and   
             Madhumita Basu and   
       Sanghamitra Sengupta and   
                Pranab K. Dutta   A Closed-Loop Control Scheme for
                                  Steering Steady States of Glycolysis and
                                  Glycogenolysis Pathway . . . . . . . . . 858--868
            Oyku Eren Ozsoy and   
                      Tolga Can   A Divide and Conquer Approach for
                                  Construction of Large-Scale Signaling
                                  Networks from PPI and RNAi Data Using
                                  Linear Programming . . . . . . . . . . . 869--883
              Ken D. Nguyen and   
                         Yi Pan   A Knowledge-Based Multiple-Sequence
                                  Alignment Algorithm  . . . . . . . . . . 884--896
                    Nan Liu and   
               Haitao Jiang and   
                 Daming Zhu and   
                     Binhai Zhu   An Improved Approximation Algorithm for
                                  Scaffold Filling to Maximize the Common
                                  Adjacencies  . . . . . . . . . . . . . . 905--913
                  Mouli Das and   
               C. A. Murthy and   
                    Rajat K. De   An Optimization Rule for In Silico
                                  Identification of Targeted
                                  Overproduction in Metabolic Pathways . . 914--926
                   Chao Luo and   
                  Xingyuan Wang   Algebraic Representation of Asynchronous
                                  Multiple-Valued Networks and Its
                                  Dynamics . . . . . . . . . . . . . . . . 927--938
             Adam M. Halasz and   
              Hong-Jian Lai and   
           Meghan M. McCabe and   
     Krishnan Radhakrishnan and   
              Jeremy S. Edwards   Analytical Solution of Steady-State
                                  Equations for Chemical Reaction Networks
                                  with Bilinear Rate Laws  . . . . . . . . 957--969
               Andrei Todor and   
                 Alin Dobra and   
                  Tamer Kahveci   Characterizing the Topology of
                                  Probabilistic Biological Networks  . . . 970--983
      Sergio Torres-Sanchez and   
        Nuria Medina-Medina and   
              Chris Gignoux and   
    Maria del Mar Abad-Grau and   
      Esteban Gonzalez-Burchard   GeneOnEarth: Fitting Genetic PC Plots on
                                  the Globe  . . . . . . . . . . . . . . . 1009--1016
                   Yuan Zhu and   
              Weiqiang Zhou and   
               Dao-Qing Dai and   
                       Hong Yan   Identification of DNA-Binding and
                                  Protein-Binding Proteins Using Enhanced
                                  Graph Wavelet Features . . . . . . . . . 1017--1031
            Claudio Angione and   
         Giovanni Carapezza and   
              Jole Costanza and   
                 Pietro Lio and   
               Giuseppe Nicosia   Pareto Optimality in Organelle Energy
                                  Metabolism Analysis  . . . . . . . . . . 1032--1044
       Jose Ignacio Requeno and   
  Gregorio de Miguel Casado and   
             Roberto Blanco and   
              Jose Manuel Colom   Temporal Logics for Phylogenetic
                                  Analysis via Model Checking  . . . . . . 1058--1070
              Farid Rajabli and   
                Unal Goktas and   
                       Gul Inan   Application of Dempster--Schafer Method
                                  in Family-Based Association Studies  . . 1071--1075
            Kevaughn Gordon and   
                  Eric Ford and   
             Katherine St. John   Hamiltonian Walks of Phylogenetic
                                  Treespaces . . . . . . . . . . . . . . . 1076--1079
                 Tianwei Yu and   
                     Hesen Peng   Hierarchical Clustering of
                                  High-Throughput Expression Data Based on
                                  General Dependences  . . . . . . . . . . 1080--1085
                      Anonymous   Call for Papers: Special Issue on
                                  Software and Databases in TCBB . . . . . 1086--1086

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 10, Number 5, September, 2013

             Kuan-Liang Liu and   
                 Tzu-Tsung Wong   Na\"\ive Bayesian Classifiers with
                                  Multinomial Models for rRNA Taxonomic
                                  Assignment . . . . . . . . . . . . . . . 1--1
              Tamer Kahveci and   
                     Mona Singh   Guest Editorial for ACM BCB  . . . . . . 1089--1090
           Reginaldo M. Kuroshu   Nonoverlapping Clone Pooling for
                                  High-Throughput Sequencing . . . . . . . 1091--1097
  K. S. M. Tozammel Hossain and   
         Debprakash Patnaik and   
           Srivatsan Laxman and   
               Prateek Jain and   
       Chris Bailey-Kellogg and   
             Naren Ramakrishnan   Improved Multiple Sequence Alignments
                                  Using Coupled Pattern Mining . . . . . . 1098--1112
             Ahsanur Rahman and   
      Christopher L. Poirel and   
            David J. Badger and   
                Craig Estep and   
                   T. M. Murali   Reverse Engineering Molecular
                                  Hypergraphs  . . . . . . . . . . . . . . 1113--1124
         Mehmet Umut Caglar and   
                    Ranadip Pal   Stochastic Model Simulation Using
                                  Kronecker Product Analysis and
                                  Zassenhaus Formula Approximation . . . . 1125--1136
              Ming-Chi Tsai and   
            Guy E. Blelloch and   
                    R. Ravi and   
               Russell Schwartz   Coalescent-Based Method for Learning
                                  Parameters of Admixture Events from
                                  Large-Scale Genetic Variation Data . . . 1137--1149
              Oben M. Tataw and   
   Gonehal Venugopala Reddy and   
            Eamonn J. Keogh and   
          Amit K. Roy-Chowdhury   Quantitative Analysis of Live-Cell
                                  Growth at the Shoot Apex of
                                  \bionameArabidopsis thaliana: Algorithms
                                  for Feature Measurement and Temporal
                                  Alignment  . . . . . . . . . . . . . . . 1150--1161
               Kevin Molloy and   
                Sameh Saleh and   
                   Amarda Shehu   Probabilistic Search and Energy Guidance
                                  for Biased Decoy Sampling in Ab Initio
                                  Protein Structure Prediction . . . . . . 1162--1175
             Yao-ming Huang and   
                 Chris Bystroff   Expanded Explorations into the
                                  Optimization of an Energy Function for
                                  Protein Design . . . . . . . . . . . . . 1176--1187
            Seth Blumenthal and   
               Yisheng Tang and   
                Wenjie Yang and   
                     Brian Chen   Isolating Influential Regions of
                                  Electrostatic Focusing in Protein and
                                  DNA Structure  . . . . . . . . . . . . . 1188--1198
                 Pavel P. Kuksa   Biological Sequence Classification with
                                  Multivariate String Kernels  . . . . . . 1201--1210
                 Said Bleik and   
           Meenakshi Mishra and   
                   Jun Huan and   
                       Min Song   Text Categorization of Biomedical Data
                                  Sets Using Graph Kernels and a
                                  Controlled Vocabulary  . . . . . . . . . 1211--1217
                     Su Yan and   
          W. Scott Spangler and   
                      Ying Chen   Chemical Name Extraction Based on
                                  Automatic Training Data Generation and
                                  Rich Feature Set . . . . . . . . . . . . 1218--1233
          Liliana D. Florea and   
             Steven L. Salzberg   Genome-Guided Transcriptome Assembly in
                                  the Age of Next-Generation Sequencing    1234--1240
         Devendra K. Shakya and   
               Rajiv Saxena and   
              Sanjeev N. Sharma   An Adaptive Window Length Strategy for
                                  Eukaryotic CDS Prediction  . . . . . . . 1241--1252
              Noah A. Rosenberg   Coalescent Histories for
                                  Caterpillar-Like Families  . . . . . . . 1253--1262
          Sebastian Wandelt and   
                      Ulf Leser   FRESCO: Referential Compression of
                                  Highly Similar Sequences . . . . . . . . 1275--1288
              Kamal Al Nasr and   
                Chunmei Liu and   
          Mugizi Rwebangira and   
               Legand Burge and   
                        Jing He   Intensity-Based Skeletonization of
                                  CryoEM Gray-Scale Images Using a True
                                  Segmentation-Free Algorithm  . . . . . . 1289--1298
              Li-Yeh Chuang and   
            Cheng-Huei Yang and   
              Jui-Hung Tsai and   
                Cheng-Hong Yang   Operon Prediction Using Chaos Embedded
                                  Particle Swarm Optimization  . . . . . . 1299--1309
                Yoram Zarai and   
          Michael Margaliot and   
                   Tamir Tuller   Explicit Expression for the Steady-State
                                  Translation Rate in the
                                  Infinite-Dimensional Homogeneous
                                  Ribosome Flow Model  . . . . . . . . . . 1322--1328
             Christian Bach and   
               Prabir Patra and   
             Jani M. Pallis and   
            William Sherman and   
                   Hassan Bajwa   Strategy for Naturelike Designer
                                  Transcription Factors with Reduced
                                  Toxicity . . . . . . . . . . . . . . . . 1340--1343
                      Anonymous   IEEE Open Access Publishing  . . . . . . 1344--1344

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 10, Number 6, November, 2013

             Ion I. Mandoiu and   
               Jianxin Wang and   
           Alexander Zelikovsky   Guest Editors' Introduction to the
                                  Special Section on Bioinformatics
                                  Research and Applications  . . . . . . . 1345--1346
                    Xi Chen and   
               Jianhua Xuan and   
                  Chen Wang and   
         Ayesha N. Shajahan and   
         Rebecca B. Riggins and   
                  Robert Clarke   Reconstruction of Transcriptional
                                  Regulatory Networks by Stability-Based
                                  Network Component Analysis . . . . . . . 1347--1358
                  Matteo Re and   
              Giorgio Valentini   Network-Based Drug Ranking and
                                  Repositioning with Respect to DrugBank
                                  Therapeutic Categories . . . . . . . . . 1359--1371
                  Tim Wylie and   
                     Binhai Zhu   Protein Chain Pair Simplification under
                                  the Discrete Fréchet Distance . . . . . . 1372--1383
            Laurent Bulteau and   
                  Minghui Jiang   Inapproximability of $ ((1, 2))
                                  $-Exemplar Distance  . . . . . . . . . . 1384--1390
          Daniele Catanzaro and   
              Martine Labbe and   
          Bjarni V. Halldorsson   An Integer Programming Formulation of
                                  the Parsimonious Loss of Heterozygosity
                                  Problem  . . . . . . . . . . . . . . . . 1391--1402
            Yann Christinat and   
            Bernard M. E. Moret   A Transcript Perspective on Evolution    1403--1411
                      Si Li and   
              Kwok Pui Choi and   
                 Taoyang Wu and   
                   Louxin Zhang   Maximum Likelihood Inference of the
                                  Evolutionary History of a PPI Network
                                  from the Duplication History of Its
                                  Proteins . . . . . . . . . . . . . . . . 1412--1421
      Ayshwarya Subramanian and   
           Stanley Shackney and   
               Russell Schwartz   Novel Multisample Scheme for Inferring
                                  Phylogenetic Markers from Whole Genome
                                  Tumor Profiles . . . . . . . . . . . . . 1422--1431
                 Andre Wehe and   
         J. Gordon Burleigh and   
              Oliver Eulenstein   Efficient Algorithms for
                                  Knowledge-Enhanced Supertree and
                                  Supermatrix Phylogenetic Problems  . . . 1432--1441
                   Tao Meng and   
           Ahmed T. Soliman and   
              Mei-Ling Shyu and   
                 Yimin Yang and   
             Shu-Ching Chen and   
              S. S. Iyengar and   
                 John Yordy and   
                Puneeth Iyengar   Wavelet Analysis in Current Cancer
                                  Genome Research: a Survey  . . . . . . . 1442--14359
                Shuiwang Ji and   
                Wenlu Zhang and   
                    Rongjian Li   A Probabilistic Latent Semantic Analysis
                                  Model for Coclustering the Mouse Brain
                                  Atlas  . . . . . . . . . . . . . . . . . 1460--1468
                 Daming Zhu and   
                   Lusheng Wang   An Exact Algorithm for the Zero Exemplar
                                  Breakpoint Distance Problem  . . . . . . 1469--1477
                Ramy Mourad and   
                 Zaher Dawy and   
                  Faruck Morcos   Designing Pooling Systems for Noisy
                                  High-Throughput Protein-Protein
                                  Interaction Experiments Using Boolean
                                  Compressed Sensing . . . . . . . . . . . 1478--1490
              M. K. Ahirwal and   
                   A. Kumar and   
                    G. K. Singh   EEG/ERP Adaptive Noise Canceller Design
                                  with Controlled Search Space (CSS)
                                  Approach in Cuckoo and Other
                                  Optimization Algorithms  . . . . . . . . 1491--1504
         Chanchala D. Kaddi and   
          R. Mitchell Parry and   
                    May D. Wang   Multivariate Hypergeometric Similarity
                                  Measure  . . . . . . . . . . . . . . . . 1505--1516
              Ginny Y. Wong and   
          Frank H. F. Leung and   
                    Sai-Ho Ling   Predicting Protein-Ligand Binding Site
                                  Using Support Vector Machine with
                                  Protein Properties . . . . . . . . . . . 1517--1529
        Fernando A. F. Braz and   
              Jader S. Cruz and   
 Alessandra C. Faria-Campos and   
            Sergio V. A. Campos   Probabilistic Model Checking Analysis of
                                  Palytoxin Effects on Cell Energy
                                  Reactions of the Na+/K+-ATPase . . . . . 1530--1541
                  Chao Yang and   
                 Zengyou He and   
                    Weichuan Yu   A Combinatorial Perspective of the
                                  Protein Inference Problem  . . . . . . . 1542--1547
             Mark T. Oakley and   
 Elizabeth Grace Richardson and   
               Harriet Carr and   
                Roy L. Johnston   Protein Structure Optimization with a
                                  ``Lamarckian'' Ant Colony Algorithm  . . 1548--1552


IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 11, Number 1, January, 2014

                        Ying Xu   Editorial from the Editor-in-Chief . . . 1--1
           Frank Eisenhaber and   
              Wing-Kin Sung and   
                   Limsoon Wong   Guest editorial for the international
                                  conference on genome informatics (GIW
                                  2013)  . . . . . . . . . . . . . . . . . 5--6
                 Liang Zhao and   
           Steven C. H. Hoi and   
                 Zhenhua Li and   
               Limsoon Wong and   
                Hung Nguyen and   
                      Jinyan Li   Coupling graphs, efficient algorithms
                                  and B-cell epitope prediction  . . . . . 7--16
                   Ying Fan and   
                 Ruoshui Lu and   
               Lusheng Wang and   
          Massimo Andreatta and   
                 Shuai Cheng Li   Quantifying significance of MHC II
                                  residues . . . . . . . . . . . . . . . . 17--25
                Paul D. Yoo and   
              Sami Muhaidat and   
                 Kamal Taha and   
             Jamal Bentahar and   
                 Abdallah Shami   Intelligent consensus modeling for
                                  proline cis-trans isomerization
                                  prediction . . . . . . . . . . . . . . . 26--32
       Laleh Soltan Ghoraie and   
           Forbes Burkowski and   
             Shuai Cheng Li and   
                         Mu Zhu   Residue-specific side-chain
                                  polymorphisms via particle belief
                                  propagation  . . . . . . . . . . . . . . 33--41
                 Ruiqi Liao and   
             Ruichang Zhang and   
                Jihong Guan and   
                  Shuigeng Zhou   A new unsupervised binning approach for
                                  metagenomic sequences based on $N$-grams
                                  and automatic feature weighting  . . . . 42--54
             Jui-Chen Hsiao and   
             Chih-Hsuan Wei and   
                    Hung-Yu Kao   Gene name disambiguation using
                                  multi-scope species detection  . . . . . 55--62
                   Jing Guo and   
                Ritika Jain and   
                  Peng Yang and   
                    Rui Fan and   
            Chee Keong Kwoh and   
                      Jie Zheng   Reliable and fast estimation of
                                  recombination rates by convergence
                                  diagnosis and parallel Markov Chain
                                  Monte Carlo  . . . . . . . . . . . . . . 63--72
                Yanglan Gan and   
                Jihong Guan and   
              Shuigeng Zhou and   
                 Weixiong Zhang   Identifying cis-regulatory elements and
                                  modules using conditional random fields  73--82
          Sriganesh Srihari and   
            Venkatesh Raman and   
              Hon Wai Leong and   
                  Mark A. Ragan   Evolution and controllability of cancer
                                  networks: a Boolean perspective  . . . . 83--94
  Sanghamitra Bandyopadhyay and   
              Saurav Mallik and   
           Anirban Mukhopadhyay   A survey and comparative study of
                                  statistical tests for identifying
                                  differential expression from microarray
                                  data . . . . . . . . . . . . . . . . . . 95--115
  Sanghamitra Bandyopadhyay and   
                Koushik Mallick   A new path based hybrid measure for gene
                                  ontology similarity  . . . . . . . . . . 116--127
                Fahad Saeed and   
           Jason D. Hoffert and   
                Mark A. Knepper   CAMS--RS: clustering algorithm for
                                  large-scale mass spectrometry data using
                                  restricted search space and intelligent
                                  random sampling  . . . . . . . . . . . . 128--141
            Vangelis Metsis and   
             Fillia Makedon and   
              Dinggang Shen and   
                     Heng Huang   DNA copy number selection using robust
                                  structured sparsity-inducing norms . . . 138--181
            Biing-Feng Wang and   
             Chien-Hsin Lin and   
                     I-Tse Yang   Constructing a gene team tree in almost
                                  $ O (n \lg n) $ time . . . . . . . . . . 142--153
           Mitsunori Kayano and   
               Motoki Shiga and   
              Hiroshi Mamitsuka   Detecting differentially coexpressed
                                  genes from labeled expression data: a
                                  brief review . . . . . . . . . . . . . . 154--167
        Sandhya Prabhakaran and   
         Mélanie Rey and   
            Osvaldo Zagordi and   
          Niko Beerenwinkel and   
                    Volker Roth   HIV haplotype inference using a
                                  propagating Dirichlet process mixture
                                  model  . . . . . . . . . . . . . . . . . 182--191
                   Leyi Wei and   
              Minghong Liao and   
                    Yue Gao and   
                Rongrong Ji and   
                 Zengyou He and   
                       Quan Zou   Improved and promising identification of
                                  human MicroRNAs by incorporating a
                                  high-quality negative set  . . . . . . . 192--201
 Mohammad Shahrokh Esfahani and   
            Edward R. Dougherty   Incorporation of biological pathway
                                  knowledge in the construction of priors
                                  for optimal Bayesian classification  . . 202--218
                  Mika Amit and   
              Rolf Backofen and   
              Steffen Heyne and   
              Gad M. Landau and   
          Mathias Möhl and   
             Christina Otto and   
                 Sebastian Will   Local exact pattern matching for
                                  non-fixed RNA structures . . . . . . . . 219--230
       Pawel Górecki and   
              Oliver Eulenstein   Maximizing deep coalescence cost . . . . 231--242
                    Jun Sun and   
              Vasile Palade and   
                 Xiaojun Wu and   
                       Wei Fang   Multiple sequence alignment with hidden
                                  Markov models learned by random drift
                                  particle swarm optimization  . . . . . . 243--257
                 John Healy and   
               Desmond Chambers   Approximate $k$-mer matching using fuzzy
                                  hash maps  . . . . . . . . . . . . . . . 258--264
                 Guoxian Yu and   
            Huzefa Rangwala and   
        Carlotta Domeniconi and   
                Guoji Zhang and   
                      Zhiwen Yu   Erratum to ``Protein function prediction
                                  using multilabel ensemble
                                  classification'' . . . . . . . . . . . . 265--265

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 11, Number 2, March, 2014

              Chang-Kug Kim and   
                  Jin-A Kim and   
               Ji-Weon Choi and   
              In-Seon Jeong and   
               Yi-Seul Moon and   
              Dong-Suk Park and   
             Young-Joo Seol and   
               Yong-Kab Kim and   
              Yong-Hwan Kim and   
                    Yeon-Ki Kim   A multi-layered screening method to
                                  identify plant regulatory genes  . . . . 293--303
                  Tom M. W. Nye   An algorithm for constructing principal
                                  geodesics in phylogenetic treespace  . . 304--315
                Abeer Eshra and   
                 Ayman El-Sayed   An odd parity checker prototype using
                                  DNAzyme finite state machine . . . . . . 316--324
              Ruth Davidson and   
                 Seth Sullivant   Distance-based phylogenetic methods
                                  around a polytomy  . . . . . . . . . . . 325--335
       Kristopher L. Patton and   
              David J. John and   
            James L. Norris and   
            Daniel R. Lewis and   
                Gloria K. Muday   Hierarchical probabilistic interaction
                                  modeling for multiple gene expression
                                  replicates . . . . . . . . . . . . . . . 336--346
     Pugalendhi GaneshKumar and   
            Chellasamy Rani and   
           Durairaj Devaraj and   
    T. Aruldoss Albert Victoire   Hybrid ant bee algorithm for fuzzy
                                  expert system based sample
                                  classification . . . . . . . . . . . . . 347--360
                  Shunji Tanaka   Improved exact enumerative algorithms
                                  for the planted $ (l, d)$-motif search
                                  problem  . . . . . . . . . . . . . . . . 361--374
         Jouni Sirén and   
    Niko Välimäki and   
              Veli Mäkinen   Indexing graphs for path queries with
                                  applications in genome research  . . . . 375--388
            Anthony Labarre and   
                   Sicco Verwer   Merging partially labelled trees:
                                  hardness and a declarative programming
                                  solution . . . . . . . . . . . . . . . . 389--397
                 Weiming Li and   
                     Bin Ma and   
                 Kaizhong Zhang   Optimizing spaced $k$-mer neighbors for
                                  efficient filtration in protein
                                  similarity search  . . . . . . . . . . . 398--406
                 Xiwei Tang and   
               Jianxin Wang and   
            Jiancheng Zhong and   
                         Yi Pan   Predicting essential proteins based on
                                  weighted degree centrality . . . . . . . 407--418
              Kamal Al Nasr and   
                Desh Ranjan and   
            Mohammad Zubair and   
                   Lin Chen and   
                        Jing He   Solving the secondary structure matching
                                  problem in cryo-EM de novo modeling
                                  using a constrained $K$-shortest path
                                  graph algorithm  . . . . . . . . . . . . 419--430
                Miha Moskon and   
                      Miha Mraz   Systematic approach to computational
                                  design of gene regulatory networks with
                                  information processing capabilities  . . 431--440
                 Dan Tulpan and   
             Derek H. Smith and   
             Roberto Montemanni   Thermodynamic post-processing versus
                                  GC-content pre-processing for DNA codes
                                  satisfying the Hamming distance and
                                  reverse-complement constraints . . . . . 441--452

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 11, Number 3, May, 2014

                Zhipeng Cai and   
          Oliver Eulenstein and   
                  Cynthia Gibas   Guest editors introduction to the
                                  special section on bioinformatics
                                  research and applications  . . . . . . . 453--454
          Falk Hüffner and   
      Christian Komusiewicz and   
            Adrian Liebtrau and   
               Rolf Niedermeier   Partitioning biological networks into
                                  highly connected clusters with maximum
                                  edge coverage  . . . . . . . . . . . . . 455--467
                 Xuebo Song and   
                     Lin Li and   
          Pradip K. Srimani and   
               Philip S. Yu and   
                  James Z. Wang   Measure the semantic similarity of GO
                                  terms using aggregate information
                                  content  . . . . . . . . . . . . . . . . 468--476
                   Yu Zheng and   
                   Louxin Zhang   Effect of incomplete lineage sorting on
                                  tree-reconciliation-based inference of
                                  gene duplication . . . . . . . . . . . . 477--485
                 Bihai Zhao and   
               Jianxin Wang and   
                     Min Li and   
              Fang-Xiang Wu and   
                         Yi Pan   Detecting protein complexes based on
                                  uncertain graph model  . . . . . . . . . 486--497
            Elena Marchiori and   
               Alioune Ngom and   
                    Raj Acharya   Guest editorial: pattern recognition in
                                  bioinformatics . . . . . . . . . . . . . 498--499
               Matteo Comin and   
               Morris Antonello   Fast entropic profiler: an information
                                  theoretic approach for the discovery of
                                  patterns in genomes  . . . . . . . . . . 500--509
          Abdollah Dehzangi and   
             Kuldip Paliwal and   
                James Lyons and   
                Alok Sharma and   
                   Abdul Sattar   A segmentation-based method to extract
                                  structural and evolutionary features for
                                  protein fold recognition . . . . . . . . 510--519
            Michael F. Ochs and   
            Jason E. Farrar and   
          Michael Considine and   
               Yingying Wei and   
           Soheil Meshinchi and   
               Robert J. Arceci   Outlier analysis and top scoring pair
                                  for integrated data analysis and
                                  biomarker discovery  . . . . . . . . . . 520--532
            Shaurya Jauhari and   
                 S. A. M. Rizvi   Mining gene expression data focusing
                                  cancer therapeutics: a digest  . . . . . 533--547
          Andrew K. C. Wong and   
             En-Shiun Annie Lee   Aligning and clustering patterns to
                                  reveal the protein functionality of
                                  sequences  . . . . . . . . . . . . . . . 548--560
                 Marco Mina and   
             Pietro Hiram Guzzi   Improving the robustness of local
                                  network alignment: design and extensive
                                  assessment of a Markov clustering-based
                                  approach . . . . . . . . . . . . . . . . 561--572
             Qingliang Shen and   
                  Hong Tian and   
                 Daoqi Tang and   
                Wenbing Yao and   
                  Xiangdong Gao   Ligand-K* sequence elimination: a novel
                                  algorithm for ensemble-based redesign of
                                  receptor-ligand binding  . . . . . . . . 573--578
                 Guoxian Yu and   
            Huzefa Rangwala and   
        Carlotta Domeniconi and   
                Guoji Zhang and   
                      Zhiwen Yu   Protein function prediction with
                                  incomplete annotations . . . . . . . . . 579--591
Fernando López-Caamal and   
    Diego A. Oyarzún and   
       Richard H. Middleton and   
 Míriam R. García   Spatial quantification of cytosolic Ca$
                                  {2+} $ accumulation in nonexcitable
                                  cells: an analytical study . . . . . . . 592--603
           Benjamin X. Guan and   
                  Bir Bhanu and   
                Prue Talbot and   
                    Sabrina Lin   Bio-driven cell region detection in
                                  human embryonic stem cell assay  . . . . 604--611

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 11, Number 4, July, 2014

                        Ying Xu   Reviewer appreciation editorial  . . . . 613--613
              Shuigeng Zhou and   
            Yi-Ping Phoebe Chen   Guest editorial for the 12th Asia
                                  Pacific Bioinformatics Conference  . . . 614--615
                     Bin Xu and   
                    Jihong Guan   From function to interaction: a new
                                  paradigm for accurately predicting
                                  protein complexes based on
                                  protein-to-protein interaction networks  616--627
               Matteo Comin and   
                Davide Verzotto   Beyond fixed-resolution alignment-free
                                  measures for mammalian enhancers
                                  sequence comparison  . . . . . . . . . . 628--637
                Yanglan Gan and   
                Guobing Zou and   
                Jihong Guan and   
                    Guangwei Xu   A novel wavelet-based approach for
                                  predicting nucleosome positions using
                                  DNA structural information . . . . . . . 638--647
               Christine Lo and   
            Boyko Kakaradov and   
          Daniel Lokshtanov and   
              Christina Boucher   SeeSite: characterizing relationships
                                  between splice junctions and splicing
                                  enhancers  . . . . . . . . . . . . . . . 648--656
                 Hualong Yu and   
                         Jun Ni   An improved ensemble learning method for
                                  classifying high-dimensional and
                                  imbalanced biomedicine data  . . . . . . 657--666
                     Fei Hu and   
                   Jun Zhou and   
                Lingxi Zhou and   
                     Jijun Tang   Probabilistic reconstruction of
                                  ancestral gene orders with insertions
                                  and deletions  . . . . . . . . . . . . . 667--672
               Minta Thomas and   
            Anneleen Daemen and   
                   Bart De Moor   Maximum likelihood estimation of GEVD:
                                  applications in bioinformatics . . . . . 673--680
            Kazuki Ichikawa and   
             Shinichi Morishita   A simple but powerful heuristic method
                                  for accelerating $k$-means clustering of
                                  large-scale data in life science . . . . 681--692
                   Yuan Gao and   
            Rosa H. M. Chan and   
           Tommy W. S. Chow and   
                Liyun Zhang and   
             Sylvia Bonilla and   
               Chi-Pui Pang and   
              Mingzhi Zhang and   
                  Yuk Fai Leung   A high-throughput zebrafish screening
                                  method for visual mutants by
                                  light-induced locomotor response . . . . 693--701
            Chia-Hua Chuang and   
                 Chun-Liang Lin   A novel synthesizing genetic logic
                                  circuit: frequency multiplier  . . . . . 702--713
                     Hai Su and   
                Fuyong Xing and   
               Jonah D. Lee and   
      Charlotte A. Peterson and   
                       Lin Yang   Automatic myonuclear detection in
                                  isolated single muscle fibers using
                                  robust ellipse fitting and sparse
                                  representation . . . . . . . . . . . . . 714--726
                  Zhiwen Yu and   
             Hongsheng Chen and   
                   Jane You and   
               Hau-San Wong and   
                 Jiming Liu and   
                      Le Li and   
                   Guoqiang Han   Double selection based semi-supervised
                                  clustering ensemble for tumor clustering
                                  from gene expression profiles  . . . . . 727--740
                     Rui Fa and   
                 Asoke K. Nandi   Noise resistant generalized parametric
                                  validity index of clustering for gene
                                  expression data  . . . . . . . . . . . . 741--752
Beatriz García-Jiménez and   
                 Tirso Pons and   
            Araceli Sanchis and   
               Alfonso Valencia   Predicting protein relationships to
                                  human pathways through a relational
                                  learning approach based on simple
                                  sequence features  . . . . . . . . . . . 753--765
                    Ao Kong and   
             Chinmaya Gupta and   
              Mauro Ferrari and   
             Marco Agostini and   
               Chiara Bedin and   
              Ali Bouamrani and   
            Ennio Tasciotti and   
                Robert Azencott   Biomarker signature discovery from mass
                                  spectrometry data  . . . . . . . . . . . 766--772

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 11, Number 5, September, 2014

              Gaurav Pandey and   
                Huzefa Rangwala   Guest editorial for special section on
                                  BIOKDD2013 . . . . . . . . . . . . . . . 773--774
           Shobeir Fakhraei and   
                 Bert Huang and   
             Louiqa Raschid and   
                    Lise Getoor   Network-based drug-target interaction
                                  prediction with probabilistic soft logic 775--787
             Raed I. Seetan and   
             Anne M. Denton and   
              Omar Al-Azzam and   
                 Ajay Kumar and   
             M. Javed Iqbal and   
            Shahryar F. Kianian   Reliable radiation hybrid maps: an
                                  efficient scalable clustering-based
                                  approach . . . . . . . . . . . . . . . . 788--800
  Joana P. Gonçalves and   
                Sara C. Madeira   LateBiclustering: efficient heuristic
                                  algorithm for time-lagged bicluster
                                  identification . . . . . . . . . . . . . 801--813
                 Cheng Zhou and   
             Pieter Meysman and   
                 Boris Cule and   
               Kris Laukens and   
                  Bart Goethals   Discovery of spatially cohesive itemsets
                                  in three-dimensional protein structures  814--825
             Michael Zeller and   
       Christophe N. Magnan and   
            Vishal R. Patel and   
                 Paul Rigor and   
             Leonard Sender and   
                   Pierre Baldi   A genomic analysis pipeline and its
                                  application to pediatric cancers . . . . 826--839
                  Peng Chen and   
                  Chao Wang and   
                      Xi Li and   
                    Xuehai Zhou   Accelerating the next generation long
                                  read mapping with the FPGA-based system  840--852
           Luis A. A. Meira and   
Vinícius R. Máximo and   
   Álvaro L. Fazenda and   
Arlindo F. Da Conceição   Acc-Motif: accelerated network motif
                                  detection  . . . . . . . . . . . . . . . 853--862
             Imen Messaoudi and   
      Afef Elloumi-Oueslati and   
                   Zied Lachiri   Building specific signals from frequency
                                  chaos game and revealing periodicities
                                  using a smoothed Fourier analysis  . . . 863--877
               Timo Krotzky and   
               Thomas Fober and   
      Eyke Hüllermeier and   
                  Gerhard Klebe   Extended graph-based models for enhanced
                                  similarity search in Cavbase . . . . . . 878--890
              Jian-Sheng Wu and   
            Sheng-Jun Huang and   
                   Zhi-Hua Zhou   Genome-wide protein function prediction
                                  through multi-instance multi-label
                                  learning . . . . . . . . . . . . . . . . 891--902
             Tulaya Limpiti and   
Chainarong Amornbunchornvej and   
      Apichart Intarapanich and   
       Anunchai Assawamakin and   
              Sissades Tongsima   iNJclust: iterative neighbor-joining
                                  tree clustering framework for inferring
                                  population structure . . . . . . . . . . 903--914
               Xiaoqing Liu and   
                     Jun Wu and   
               Haipeng Gong and   
             Shengchun Deng and   
                     Zengyou He   Mining conditional phosphorylation
                                  motifs . . . . . . . . . . . . . . . . . 915--927
         Bonnie Kirkpatrick and   
               Kristian Stevens   Perfect phylogeny problems with missing
                                  values . . . . . . . . . . . . . . . . . 928--941
               Danilo Horta and   
      Ricardo J. G. B. Campello   Similarity measures for comparing
                                  biclusterings  . . . . . . . . . . . . . 942--954
          Yulia M. Suvorova and   
         Maria A. Korotkova and   
             Eugene V. Korotkov   Study of the paired change points in
                                  bacterial genes  . . . . . . . . . . . . 955--964
                  Hao Zhang and   
              Xingyuan Wang and   
                    Xiaohui Lin   Synchronization of Boolean networks with
                                  different update schemes . . . . . . . . 965--972
                    Jing Li and   
                     Jun Hu and   
             Matthew Newman and   
                  Kejun Liu and   
                    Huanying Ge   RNA-seq analysis pipeline based on
                                  Oshell environment . . . . . . . . . . . 973--978

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 11, Number 6, November, 2014

                Yufei Huang and   
                Yidong Chen and   
                  Xiaoning Qian   Selected articles from the 2012 IEEE
                                  International Workshop on Genomic Signal
                                  Processing and Statistics (GENSIPS 2012) 981--983
            Karl B. Gregory and   
              Amin A. Momin and   
           Kevin R. Coombes and   
Veerabhadran Baladandayuthapani   Latent feature decompositions for
                                  integrative analysis of multi-platform
                                  genomic data . . . . . . . . . . . . . . 984--994
                Noah Berlow and   
                Saad Haider and   
                   Qian Wan and   
          Mathew Geltzeiler and   
              Lara E. Davis and   
             Charles Keller and   
                    Ranadip Pal   An integrated approach to anti-cancer
                                  drug sensitivity prediction  . . . . . . 995--1008
                    Ye Tian and   
               Sean S. Wang and   
                 Zhen Zhang and   
          Olga C. Rodriguez and   
          Emanuel Petricoin and   
               Ie-Ming Shih and   
                Daniel Chan and   
         Maria Avantaggiati and   
                Guoqiang Yu and   
                Shaozhen Ye and   
              Robert Clarke and   
                  Chao Wang and   
                  Bai Zhang and   
                   Yue Wang and   
                 Chris Albanese   Integration of network biology and
                                  imaging to study cancer phenotypes and
                                  responses  . . . . . . . . . . . . . . . 1009--1019
                    Meng Lu and   
              Hye-Seung Lee and   
               David Hadley and   
           Jianhua Z. Huang and   
                  Xiaoning Qian   Logistic principal component analysis
                                  for rare variants in gene-environment
                                  interaction analysis . . . . . . . . . . 1020--1028
        Seyed Javad Sajjadi and   
              Xiaoning Qian and   
                    Bo Zeng and   
                Amin Ahmadi Adl   Network-based methods to identify highly
                                  discriminating subsets of biomarkers . . 1029--1037
                  Yanxun Xu and   
             Xiaofeng Zheng and   
                  Yuan Yuan and   
          Marcos R. Estecio and   
           Jean-Pierre Issa and   
                   Peng Qiu and   
                    Yuan Ji and   
                  Shoudan Liang   BM-SNP: a Bayesian model for SNP calling
                                  using high throughput sequencing data    1038--1044
                       Peng Qiu   Unfold high-dimensional clouds for
                                  exhaustive gating of flow cytometry data 1045--1051
         Mainá Bitar and   
    Glória Regina Franco   A basic protein comparative
                                  three-dimensional modeling
                                  methodological workflow theory and
                                  practice . . . . . . . . . . . . . . . . 1052--1065
               Choujun Zhan and   
                Wuchao Situ and   
              Lam Fat Yeung and   
       Peter Wai-Ming Tsang and   
                     Genke Yang   A parameter estimation method for
                                  biological systems modelled by ODE/DDE
                                  models using spline approximation and
                                  differential evolution algorithm . . . . 1066--1076
         Fumihide Shiraishi and   
              Erika Yoshida and   
               Eberhard O. Voit   An efficient and very accurate method
                                  for calculating steady-state
                                  sensitivities in metabolic reaction
                                  systems  . . . . . . . . . . . . . . . . 1077--1086
          Anveshi Charuvaka and   
                Huzefa Rangwala   Classifying protein sequences using
                                  regularized multi-task learning  . . . . 1087--1098
               Laszlo David and   
             Alexander Bockmayr   Computing elementary flux modes
                                  involving a set of target reactions  . . 1099--1107
             Ahsan Z. Rizvi and   
                C. Bhattacharya   Detection of replication origin sites in
                                  herpesvirus genomes by clustering and
                                  scoring of palindromes with quadratic
                                  entropy measures . . . . . . . . . . . . 1108--1118
                     Kamal Taha   Determining semantically related
                                  significant genes  . . . . . . . . . . . 1119--1130
              Saima Rathore and   
          Mutawarra Hussain and   
                 Asifullah Khan   GECC: gene expression based ensemble
                                  classification of colon samples  . . . . 1131--1145
                    Bo Liao and   
                  Yan Jiang and   
                  Wei Liang and   
                    Wen Zhu and   
                  Lijun Cai and   
                        Zhi Cao   Gene selection using locality sensitive
                                  Laplacian score  . . . . . . . . . . . . 1146--1156
              Michiel Stock and   
               Thomas Fober and   
      Eyke Hüllermeier and   
             Serghei Glinca and   
              Gerhard Klebe and   
            Tapio Pahikkala and   
               Antti Airola and   
           Bernard De Baets and   
                Willem Waegeman   Identification of functionally related
                                  enzymes by learning-to-rank methods  . . 1157--1169
       Anirban Mukhopadhyay and   
                Monalisa Mandal   Identifying non-redundant gene markers
                                  from microarray data: a multiobjective
                                  variable length PSO-based approach . . . 1170--1183
                Yoram Zarai and   
          Michael Margaliot and   
                   Tamir Tuller   Maximizing protein translation rate in
                                  the ribosome flow model: the homogeneous
                                  case . . . . . . . . . . . . . . . . . . 1184--1195
            Umesh Kalathiya and   
         Monikaben Padariya and   
                Maciej Baginski   Molecular modeling and evaluation of
                                  novel dibenzopyrrole derivatives as
                                  telomerase inhibitors and potential drug
                                  for cancer therapy . . . . . . . . . . . 1196--1207
                   Andri Mirzal   Nonparametric Tikhonov regularized NMF
                                  and its application in cancer clustering 1208--1217
           Parthan Kasarapu and   
   Maria Garcia De La Banda and   
             Arun S. Konagurthu   On representing protein folding patterns
                                  using non-linear parametric curves . . . 1218--1228
            Filippo Disanto and   
              Noah A. Rosenberg   On the number of ranked species trees
                                  producing anomalous ranked gene trees    1229--1238
          Hasin Afzal Ahmed and   
          Priyakshi Mahanta and   
 Dhruba Kumar Bhattacharyya and   
             Jugal Kumar Kalita   Shifting-and-scaling correlation based
                                  biclustering algorithm . . . . . . . . . 1239--1252
           Koichi Kobayashi and   
              Kunihiko Hiraishi   ILP/SMT-based method for design of
                                  Boolean networks based on singleton
                                  attractors . . . . . . . . . . . . . . . 1253--1259
          Loes Olde Loohuis and   
             Andreas Witzel and   
                     Bud Mishra   Improving detection of driver genes:
                                  power-law null model of copy number
                                  variation in cancer  . . . . . . . . . . 1260--1263
               Haiying Wang and   
                    Huiru Zheng   Organized modularity in the interactome:
                                  evidence from the analysis of dynamic
                                  organization in the cell cycle . . . . . 1264--1270


IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 12, Number 1, January, 2015

                        Ying Xu   Editorial from the Editor-in-Chief . . . 1--1
             Srinivas Aluru and   
                Donna K. Slonim   Guest Editors' introduction: selected
                                  papers from ACM-BCB 2013 . . . . . . . . 2--3
            Noah M. Daniels and   
             Andrew Gallant and   
              Norman Ramsey and   
                Lenore J. Cowen   MRFy: remote homology detection for
                                  beta-structural proteins using Markov
                                  random fields and stochastic search  . . 4--16
               Manabu Torii and   
          Cecilia N. Arighi and   
                    Gang Li and   
               Qinghua Wang and   
                Cathy H. Wu and   
               K. Vijay-Shanker   RLIMS-P 2.0: a generalizable rule-based
                                  information extraction system for
                                  literature mining of protein
                                  phosphorylation information  . . . . . . 17--29
                   Kun Wang and   
                Avinash Das and   
            Zheng-Mei Xiong and   
                    Kan Cao and   
            Sridhar Hannenhalli   Phenotype-dependent coexpression gene
                                  clusters: application to normal and
                                  premature ageing . . . . . . . . . . . . 30--39
         Fazle Elahi Faisal and   
                   Han Zhao and   
            Tijana Milenkovi\'c   Global network alignment in the context
                                  of aging . . . . . . . . . . . . . . . . 40--52
               Haitham Gabr and   
               Andrei Todor and   
                 Alin Dobra and   
                  Tamer Kahveci   Reachability analysis in probabilistic
                                  biological networks  . . . . . . . . . . 53--66
                 Yongtao Ye and   
       David Wai-lok Cheung and   
                Yadong Wang and   
               Siu-Ming Yiu and   
                 Qing Zhang and   
                Tak-Wah Lam and   
                 Hing-Fung Ting   GLProbs: aligning multiple sequences
                                  adaptively . . . . . . . . . . . . . . . 67--78
                     Hui Li and   
                  Xiaoyi Li and   
          Murali Ramanathan and   
                   Aidong Zhang   Prediction and informative risk factor
                                  selection of bone diseases . . . . . . . 79--91
         Michael A. DeJesus and   
              Thomas R. Ioerger   Capturing uncertainty by modeling local
                                  transposon insertion frequencies
                                  improves discrimination of essential
                                  genes  . . . . . . . . . . . . . . . . . 92--102
               Matt Spencer and   
             Jesse Eickholt and   
                  Jianlin Cheng   A deep learning network approach to ab
                                  initio protein secondary structure
                                  prediction . . . . . . . . . . . . . . . 103--112
                    Bo Liao and   
                   Xiong Li and   
                  Lijun Cai and   
                    Zhi Cao and   
                    Haowen Chen   A hierarchical clustering method of
                                  selecting kernel SNP to unify
                                  informative SNP and tag SNP  . . . . . . 113--122
            Shing-Chow Chan and   
                   Li Zhang and   
                 Ho-Chun Wu and   
                   Kai-Man Tsui   A maximum a posteriori probability and
                                  time-varying approach for inferring gene
                                  regulatory networks from time course
                                  gene microarray data . . . . . . . . . . 123--135
                 Yetian Fan and   
                     Wei Wu and   
                   Jie Yang and   
                 Wenyu Yang and   
                   Rongrong Liu   An algorithm for motif discovery with
                                  iteration on lengths of motifs . . . . . 136--141
               Man-Hon Wong and   
              Ho-Yin Sze-To and   
               Leung-Yau Lo and   
              Tak-Ming Chan and   
                Kwong-Sak Leung   Discovering binding cores in
                                  Protein--DNA binding using association
                                  rule mining with statistical measures    142--154
        Pawe Górecki and   
              Oliver Eulenstein   Gene tree diameter for deep coalescence  155--165
                  Chao Wang and   
                      Xi Li and   
                  Peng Chen and   
                  Aili Wang and   
                Xuehai Zhou and   
                        Hong Yu   Heterogeneous cloud framework for big
                                  data genome sequencing . . . . . . . . . 166--178
                   Wei Peng and   
               Jianxin Wang and   
                 Bihai Zhao and   
                   Lusheng Wang   Identification of protein complexes
                                  using weighted PageRank--Nibble
                                  algorithm and core-attachment structure  179--192
                     Nan Du and   
             Marc R. Knecht and   
            Mark T. Swihart and   
              Zhenghua Tang and   
           Tiffany R. Walsh and   
                   Aidong Zhang   Identifying affinity classes of
                                  inorganic materials binding sequences
                                  via a graph-based model  . . . . . . . . 193--204
              Xiangyuan Zhu and   
                   Kenli Li and   
                Ahmad Salah and   
                    Lin Shi and   
                       Keqin Li   Parallel implementation of MAFFT on
                                  CUDA-enabled graphics hardware . . . . . 205--218
                 Guoxian Yu and   
            Huzefa Rangwala and   
        Carlotta Domeniconi and   
                Guoji Zhang and   
                     Zili Zhang   Predicting protein function using
                                  multiple kernels . . . . . . . . . . . . 219--233
            Judith Keijsper and   
                 Tim Oosterwijk   Tractable cases of $ (*, 2)$-bounded
                                  parsimony haplotyping  . . . . . . . . . 234--247

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 12, Number 2, March, 2015

                   Feng Luo and   
                      Xintao Wu   Guest editorial for special section on
                                  BIBM 2013  . . . . . . . . . . . . . . . 252--253
             Xingpeng Jiang and   
                 Xiaohua Hu and   
                  Weiwei Xu and   
                     E. K. Park   Predicting microbial interactions using
                                  vector autoregressive model with graph
                                  regularization . . . . . . . . . . . . . 254--261
                    Cen Wan and   
            Alex A. Freitas and   
João Pedro De Magalhães   Predicting the pro-longevity or
                                  anti-longevity effect of model organism
                                  genes with new hierarchical feature
                                  selection methods  . . . . . . . . . . . 262--275
                   Wei Peng and   
               Jianxin Wang and   
             Yingjiao Cheng and   
                      Yu Lu and   
               Fangxiang Wu and   
                         Yi Pan   UDoNC: an algorithm for identifying
                                  essential proteins based on protein
                                  domains and protein--protein interaction
                                  networks . . . . . . . . . . . . . . . . 276--288
                Yongguo Mei and   
                Adria Carbo and   
               Stefan Hoops and   
         Raquel Hontecillas and   
         Josep Bassaganya-Riera   ENISI SDE: a new web-based tool for
                                  modeling stochastic processes  . . . . . 289--297
                   Bin Pang and   
           David Schlessman and   
              Xingyan Kuang and   
                   Nan Zhao and   
                Daniel Shyu and   
              Dmitry Korkin and   
                   Chi-Ren Shyu   An integrated approach to
                                  sequence-independent local alignment of
                                  protein binding sites  . . . . . . . . . 298--308
              Young-Rae Cho and   
                  Yanan Xin and   
                   Greg Speegle   P-Finder: reconstruction of signaling
                                  networks from protein--protein
                                  interactions and GO annotations  . . . . 309--321
           Jong Cheol Jeong and   
                    Xuewen Chen   A new semantic functional similarity
                                  over gene ontology . . . . . . . . . . . 322--334
          Hossam M. Ashtawy and   
             Nihar R. Mahapatra   A comparative assessment of predictive
                                  accuracies of conventional and machine
                                  learning scoring functions for
                                  protein--ligand binding affinity
                                  prediction . . . . . . . . . . . . . . . 335--347
                  Lina Yang and   
              Yuan Yan Tang and   
                    Yang Lu and   
                      Huiwu Luo   A fractal dimension and wavelet
                                  transform based method for protein
                                  sequence similarity analysis . . . . . . 348--369
                Savas Konur and   
                Marian Gheorghe   A property-driven methodology for formal
                                  analysis of synthetic biology systems    360--371
                     Min Li and   
                      Yu Lu and   
               Jianxin Wang and   
              Fang-Xiang Wu and   
                         Yi Pan   A topology potential-based method for
                                  identifying essential proteins from PPI
                                  networks . . . . . . . . . . . . . . . . 372--383
                   Qiang Yu and   
                Hongwei Huo and   
       Jeffrey Scott Vitter and   
                   Jun Huan and   
                  Yakov Nekrich   An efficient exact algorithm for the
                                  motif stem search problem over large
                                  alphabets  . . . . . . . . . . . . . . . 384--397
                 Xian Zhang and   
                  Ligang Wu and   
                   Shaochun Cui   An improved integral inequality to
                                  stability analysis of genetic regulatory
                                  networks with interval time-varying
                                  delays . . . . . . . . . . . . . . . . . 398--409
                 Zhenhua Li and   
                    Ying He and   
               Limsoon Wong and   
                      Jinyan Li   Burial level change defines a high
                                  energetic relevance for protein binding
                                  interfaces . . . . . . . . . . . . . . . 410--421
           Gautam Dasarathy and   
               Robert Nowak and   
                 Sebastien Roch   Data requirement for phylogenetic
                                  inference from multiple loci: a new
                                  distance method  . . . . . . . . . . . . 422--432
                   Jun Meng and   
                 Jing Zhang and   
                     Yushi Luan   Gene selection integrated with
                                  biological knowledge for plant stress
                                  response using neighborhood system and
                                  rough set theory . . . . . . . . . . . . 433--444
           Trevor Cickovski and   
               Tiffany Flor and   
         Galen Irving-Sachs and   
             Philip Novikov and   
                James Parda and   
                Giri Narasimhan   GPUDePiCt: a parallel implementation of
                                  a clustering algorithm for computing
                                  degenerate primers on graphics
                                  processing units . . . . . . . . . . . . 445--454
               Bingjing Cai and   
               Haiying Wang and   
                Huiru Zheng and   
                       Hui Wang   Identification of protein complexes from
                                  tandem affinity purification/mass
                                  spectrometry data via biased random walk 455--466
                Xueming Liu and   
                   Linqiang Pan   Identifying driver nodes in the human
                                  signaling network using structural
                                  controllability analysis . . . . . . . . 467--472
                 Hasan M. Jamil   Improving integration effectiveness of
                                  ID mapping based biological record
                                  linkage  . . . . . . . . . . . . . . . . 473--486
  W. J. R. M. Priyadarshana and   
                Georgy Sofronov   Multiple break-points detection in array
                                  CGH data via the cross-entropy method    487--498

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 12, Number 3, May, 2015

     João C. Setubal and   
                  Nalvo Almeida   TCBB special section on the Brazilian
                                  Symposium on Bioinformatics 2013 . . . . 499--499
 Marília D. V. Braga and   
                     Jens Stoye   Sorting linear genomes with
                                  rearrangements and indels  . . . . . . . 500--506
Christian Höner Zu Siederdissen and   
            Ivo L. Hofacker and   
               Peter F. Stadler   Product grammars for alignment and
                                  folding  . . . . . . . . . . . . . . . . 507--519
               David Hoksza and   
                  Daniel Svozil   Multiple $3$D RNA structure
                                  superposition using neighbor joining . . 520--530
           Hyrum D. Carroll and   
           Alex C. Williams and   
           Anthony G. Davis and   
                 John L. Spouge   Improving retrieval efficacy of homology
                                  searches using the false discovery rate  531--537
           Adriana Birlutiu and   
Florence D'Alché-Buc and   
                     Tom Heskes   A Bayesian framework for combining
                                  protein and network topology information
                                  for predicting protein--protein
                                  interactions . . . . . . . . . . . . . . 538--550
               Yinglei Song and   
                Chunmei Liu and   
                       Zhi Wang   A machine learning approach for accurate
                                  annotation of noncoding RNAs . . . . . . 551--559
              Tahir Mehmood and   
                 Jon Bohlin and   
                    Lars Snipen   A partial least squares based procedure
                                  for upstream sequence classification in
                                  prokaryotes  . . . . . . . . . . . . . . 560--567
                 Liang Dong and   
                   Bing Shi and   
             Guangdong Tian and   
                   YanBo Li and   
                  Bing Wang and   
                   MengChu Zhou   An accurate de novo algorithm for glycan
                                  topology determination from mass spectra 568--578
                   Pei Wang and   
              Jinhu Lü and   
                     Xinghuo Yu   Colored noise induced bistable switch in
                                  the genetic toggle switch systems  . . . 579--589
       Sourya Bhattacharyya and   
              Jayanta Mukherjee   COSPEDTree: couplet supertree by
                                  equivalence partitioning of taxa set and
                                  DAG formation  . . . . . . . . . . . . . 590--603
       Krishnasamy Gopinath and   
      Ramaraj Jayakumararaj and   
          Muthusamy Karthikeyan   DAPD: a knowledgebase for diabetes
                                  associated proteins  . . . . . . . . . . 604--610
                Dong-Jun Yu and   
                    Yang Li and   
                     Jun Hu and   
                 Xibei Yang and   
               Jing-Yu Yang and   
                  Hong-Bin Shen   Disulfide connectivity prediction based
                                  on modelled protein $3$D structural
                                  information and random forest regression 611--621
                  Lei Huang and   
                    Li Liao and   
                    Cathy H. Wu   Evolutionary model selection and
                                  parameter estimation for
                                  protein--protein interaction network
                                  based on differential evolution
                                  algorithm  . . . . . . . . . . . . . . . 622--631
                Saurav Basu and   
                    Chi Liu and   
            Gustavo Kunde Rohde   Extraction of individual filaments from
                                  $2$D confocal microscopy images of flat
                                  cells  . . . . . . . . . . . . . . . . . 632--643
                Yen Kaow Ng and   
                 Linzhi Yin and   
               Hirotaka Ono and   
                 Shuai Cheng Li   Finding all longest common segments in
                                  protein structures efficiently . . . . . 644--655
David L. González-Álvarez and   
Miguel A. Vega-Rodríguez and   
      Álvaro Rubio-Largo   Finding patterns in protein sequences by
                                  using a hybrid multiobjective teaching
                                  learning based optimization algorithm    656--666
              Tommaso Mazza and   
           Caterina Fusilli and   
            Chiara Saracino and   
       Gianluigi Mazzoccoli and   
           Francesca Tavano and   
         Manlio Vinciguerra and   
               Valerio Pazienza   Functional impact of autophagy-related
                                  genes on the homeostasis and dynamics of
                                  pancreatic cancer cell lines . . . . . . 667--678
                   Hong Xia and   
               Yuanning Liu and   
               Minghui Wang and   
                          Ao Li   Identification of genomic aberrations in
                                  cancer subclones from heterogeneous
                                  tumor samples  . . . . . . . . . . . . . 679--685
                Dandan Song and   
               Jiaxing Chen and   
                 Guang Chen and   
                    Ning Li and   
                     Jin Li and   
                    Jun Fan and   
                  Dongbo Bu and   
                 Shuai Cheng Li   Parameterized BLOSUM matrices for
                                  protein alignment  . . . . . . . . . . . 686--694
               Xiaojun Ding and   
               Jianxin Wang and   
            Alex Zelikovsky and   
                   Xuan Guo and   
                 Minzhu Xie and   
                         Yi Pan   Searching high-order SNP combinations
                                  for complex diseases based on energy
                                  distribution difference  . . . . . . . . 695--704
            Marcelo Boareto and   
              Jonatas Cesar and   
          Vitor B. P. Leite and   
                 Nestor Caticha   Supervised variational relevance
                                  learning, an analytic geometric feature
                                  selection with applications to omic
                                  datasets . . . . . . . . . . . . . . . . 705--711
              Chih-Yuan Hsu and   
              Zhen-Ming Pan and   
               Rei-Hsing Hu and   
            Chih-Chun Chang and   
           Hsiao-Chun Cheng and   
                    Che Lin and   
                   Bor-Sen Chen   Systematic biological filter design with
                                  a desired I/O filtering response based
                                  on promoter-RBS libraries  . . . . . . . 712--725

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 12, Number 4, July, 2015

       Sarath Chandra Janga and   
               Dongxiao Zhu and   
               Jake Y. Chen and   
               Mohammed J. Zaki   Knowledge discovery using big data in
                                  biomedical systems . . . . . . . . . . . 726--728
        Suvarna Vani Koneru and   
               Bhavani S. Durga   Divide and conquer approach to contact
                                  map overlap problem using $2$D-pattern
                                  mining of protein contact networks . . . 729--737
              Rui Henriques and   
                Sara C. Madeira   Biclustering with flexible plaid models
                                  to unravel interactions between
                                  biological processes . . . . . . . . . . 738--752
                  Julia E. Vogt   Unsupervised structure detection in
                                  biomedical data  . . . . . . . . . . . . 753--760
             Tetsuo Shibuya and   
              Chuan Yi Tang and   
                Paul Horton and   
                   Kiyoshi Asai   Guest editorial for the 25th
                                  International Conference on Genome
                                  Informatics (GIW/ISCB-Asia 2014) . . . . 761--762
          Omar Y. Al-Jarrah and   
                Paul D. Yoo and   
                 Kamal Taha and   
              Sami Muhaidat and   
             Abdallah Shami and   
                     Nazar Zaki   Randomized subspace learning for proline
                                  cis--trans isomerization prediction  . . 763--769
              Wing-Kin Sung and   
          Kunihiko Sadakane and   
             Tetsuo Shibuya and   
              Abha Belorkar and   
                  Iana Pyrogova   An $ O(m \log m) $-time algorithm for
                                  detecting superbubbles . . . . . . . . . 770--777
                Ho-Sik Seok and   
                Taemin Song and   
               Sek Won Kong and   
                 Kyu-Baek Hwang   An efficient search algorithm for
                                  finding genomic-range overlaps based on
                                  the maximum range length . . . . . . . . 778--784
                  Yi-Yu Hsu and   
                    Hung-Yu Kao   Curatable named-entity recognition using
                                  semantic relations . . . . . . . . . . . 785--792
                    Dong Xu and   
                  Kun Huang and   
               Jeanette Schmidt   Guest editors introduction to the
                                  special section on software and
                                  databases  . . . . . . . . . . . . . . . 793--794
               Weixing Feng and   
               Peichao Sang and   
                Deyuan Lian and   
              Yansheng Dong and   
               Fengfei Song and   
                    Meng Li and   
                      Bo He and   
                Fenglin Cao and   
                    Yunlong Liu   ResSeq: enhancing short-read sequencing
                                  alignment by rescuing error-containing
                                  reads  . . . . . . . . . . . . . . . . . 795--798
           Matthew W. Segar and   
        Cynthia J. Sakofsky and   
               Anna Malkova and   
                    Yunlong Liu   MMBIRFinder: a tool to detect
                                  microhomology-mediated break-induced
                                  replication  . . . . . . . . . . . . . . 799--806
            Suzanne J. Matthews   Heterogeneous compression of large
                                  collections of evolutionary trees  . . . 807--814
               Jianxin Wang and   
            Jiancheng Zhong and   
                  Gang Chen and   
                     Min Li and   
              Fang-xiang Wu and   
                         Yi Pan   ClusterViz: a cytoscape APP for cluster
                                  analysis of biological network . . . . . 815--822
Isabel A. Nepomuceno-Chamorro and   
   Alfonso Marquez-Chamorro and   
          Jesus S. Aguilar-Ruiz   Building transcriptional association
                                  networks in cytoscape with RegNetC . . . 823--824
                 Kamal Taha and   
                Paul D. Yoo and   
               Mohammed Alzaabi   iPFPi: a system for improving protein
                                  function prediction through cumulative
                                  iterations . . . . . . . . . . . . . . . 825--836
              Davide Chicco and   
                Marco Masseroli   Software suite for gene and protein
                                  annotation prediction and similarity
                                  search . . . . . . . . . . . . . . . . . 837--843
             Yan-Ping Xiang and   
                     Ke Liu and   
            Xian-Ying Cheng and   
                Cheng Cheng and   
                  Fang Gong and   
                Jian-Bo Pan and   
                   Zhi-Liang Ji   Rapid assessment of adverse drug
                                  reactions by statistical solution of
                                  gene association network . . . . . . . . 844--850
               Shovan Barma and   
                Bo-Wei Chen and   
                 Ka Lok Man and   
                  Jhing-Fa Wang   Quantitative measurement of split of the
                                  second heart sound (S2)  . . . . . . . . 851--860
          Hosein M. Golshan and   
          Reza P. R. Hasanzadeh   An optimized LMMSE based method for $3$D
                                  MRI denoising  . . . . . . . . . . . . . 861--870
           Blesson Varghese and   
                Ishan Patel and   
                    Adam Barker   RBioCloud: a light-weight framework for
                                  bioconductor and R-based jobs on the
                                  cloud  . . . . . . . . . . . . . . . . . 871--878
                  Wei Zhang and   
                     Xiufen Zou   A new method for detecting protein
                                  complexes based on the three node
                                  cliques  . . . . . . . . . . . . . . . . 879--886
                  Zhiwen Yu and   
                Hantao Chen and   
                   Jane You and   
                 Jiming Liu and   
               Hau-San Wong and   
               Guoqiang Han and   
                          Le Li   Adaptive fuzzy consensus clustering
                                  framework for clustering analysis of
                                  cancer data  . . . . . . . . . . . . . . 887--901
                   Lei Deng and   
                   Zhigang Chen   An integrated framework for functional
                                  annotation of protein structural domains 902--913
 Mohammad R. Nezami Ranjbar and   
          Mahlet G. Tadesse and   
                   Yue Wang and   
               Habtom W. Ressom   Bayesian normalization model for
                                  label-free quantitative analysis by
                                  LC--MS . . . . . . . . . . . . . . . . . 914--927
               Muxuan Liang and   
                Zhizhong Li and   
                  Ting Chen and   
                  Jianyang Zeng   Integrative data analysis of
                                  multi-platform cancer data with a
                                  multimodal deep learning approach  . . . 928--937
      Roozbeh Dehghannasiri and   
             Byung-Jun Yoon and   
            Edward R. Dougherty   Optimal experimental design for gene
                                  regulatory networks in the presence of
                                  uncertainty  . . . . . . . . . . . . . . 938--950
                  Ting Chen and   
          Ulisses M. Braga-Neto   Statistical detection of intrinsically
                                  multivariate predictive genes  . . . . . 951--963
               Jin-Xing Liu and   
                    Yong Xu and   
             Chun-Hou Zheng and   
                  Heng Kong and   
                    Zhi-Hui Lai   RPCA-based tumor classification using
                                  gene expression data . . . . . . . . . . 964--970

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 12, Number 5, September, 2015

       Juan A. Gomez-Pulido and   
             Bertil Schmidt and   
                   Wu-chun Feng   Accelerating bioinformatics applications
                                  via emerging parallel computing systems  971--972
        Edward B. Fernandez and   
           Jason Villarreal and   
            Stefano Lonardi and   
                Walid A. Najjar   FHAST: FPGA-Based Acceleration of Bowtie
                                  in Hardware  . . . . . . . . . . . . . . 973--981
   Jorge Gonzalez-Dominguez and   
            Lars Wienbrandt and   
      Jan Christian Kassens and   
           David Ellinghaus and   
          Manfred Schimmler and   
                 Bertil Schmidt   Parallelizing Epistasis Detection in
                                  GWAS on FPGA and GPU-Accelerated
                                  Computing Systems  . . . . . . . . . . . 982--994
            Hector Martinez and   
            Joaquin Tarraga and   
             Ignacio Medina and   
          Sergio Barrachina and   
           Maribel Castillo and   
             Joaquin Dopazo and   
       Enrique S. Quintana-Orti   Concurrent and Accurate Short Read
                                  Mapping on Multicore Processors  . . . . 995--1007
              Sanchit Misra and   
              Kiran Pamnany and   
                 Srinivas Aluru   Parallel Mutual Information Based
                                  Construction of Genome-Scale Networks on
                                  the Intel Xeon Phi Coprocessor . . . . . 1008--1020
      Anne Jeannin-Girardon and   
              Pascal Ballet and   
                  Vincent Rodin   Large Scale Tissue Morphogenesis
                                  Simulation on Heterogeneous Systems
                                  Based on a Flexible Biomechanical Cell
                                  Model  . . . . . . . . . . . . . . . . . 1021--1033
                    Yao Xin and   
              Will X. Y. Li and   
              Zhaorui Zhang and   
           Ray C. C. Cheung and   
                  Dong Song and   
             Theodore W. Berger   An Application Specific Instruction Set
                                  Processor (ASIP) for Adaptive Filters in
                                  Neural Prosthetics . . . . . . . . . . . 1034--1047
           Alejandro Chacon and   
        Santiago Marco-Sola and   
           Antonio Espinosa and   
               Paolo Ribeca and   
              Juan Carlos Moure   Boosting the FM-Index on the GPU:
                                  Effective Techniques to Mitigate Random
                                  Memory Access  . . . . . . . . . . . . . 1048--1059
           Thuy-Diem Nguyen and   
             Bertil Schmidt and   
                Zejun Zheng and   
                Chee-Keong Kwoh   Efficient and Accurate OTU Clustering
                                  with GPU-Based Sequence Alignment and
                                  Dynamic Dendrogram Cutting . . . . . . . 1060--1073
               Shihua Zhang and   
                    Luonan Chen   Guest Editorial for Special Section on
                                  ISB/TBC 2014 . . . . . . . . . . . . . . 1074--1075
            H. Robert Frost and   
                 Zhigang Li and   
      Folkert W. Asselbergs and   
                 Jason H. Moore   An Independent Filter for Gene Set
                                  Testing Based on Spectral Enrichment . . 1076--1086
              Dominique Chu and   
                  Anton Salykin   Evolutionary Pressures on the Yeast
                                  Transcriptome  . . . . . . . . . . . . . 1087--1093
                   Hao Kang and   
             Kwang-Hyun Cho and   
      Xiaohua Douglas Zhang and   
                   Tao Zeng and   
                    Luonan Chen   Inferring Sequential Order of Somatic
                                  Mutations during Tumorgenesis based on
                                  Markov Chain Model . . . . . . . . . . . 1094--1103
                   Nan Meng and   
            Raghu Machiraju and   
                      Kun Huang   Identify Critical Genes in Development
                                  with Consistent H3K4me2 Patterns across
                                  Multiple Tissues . . . . . . . . . . . . 1104--1111
                Yu-Qing Qiu and   
                   Xue Tian and   
                   Shihua Zhang   Infer Metagenomic Abundance and Reveal
                                  Homologous Genomes Based on the
                                  Structure of Taxonomy Tree . . . . . . . 1112--1122
             Mauro Leoncini and   
         Manuela Montangero and   
           Marco Pellegrini and   
          Karina Panucia Tillan   CMStalker: a Combinatorial Tool for
                                  Composite Motif Discovery  . . . . . . . 1123--1136
                 Jan Zrimec and   
                   Ales Lapanje   Fast Prediction of DNA Melting Bubbles
                                  Using DNA Thermodynamic Stability  . . . 1137--1145
               Shuqin Zhang and   
                Hongyu Zhao and   
                  Michael K. Ng   Functional Module Analysis for Gene
                                  Coexpression Networks with Network
                                  Integration  . . . . . . . . . . . . . . 1146--1160
              Jeong-Rae Kim and   
              Sang-Mok Choo and   
            Hyung-Seok Choi and   
                 Kwang-Hyun Cho   Identification of Gene Networks with
                                  Time Delayed Regulation Based on
                                  Temporal Expression Profiles . . . . . . 1161--1168
               Leung-Yau Lo and   
            Kwong-Sak Leung and   
                   Kin-Hong Lee   Inferring Time-Delayed Causal Gene
                                  Network Using Time-Series Expression
                                  Data . . . . . . . . . . . . . . . . . . 1169--1182
    Dimitrios Kleftogiannis and   
   Konstantinos Theofilatos and   
       Spiros Likothanassis and   
              Seferina Mavroudi   YamiPred: a Novel Evolutionary Method
                                  for Predicting Pre-miRNAs and Selecting
                                  Relevant Features  . . . . . . . . . . . 1183--1192
              Pietro Lovato and   
        Alejandro Giorgetti and   
                 Manuele Bicego   A Multimodal Approach for Protein Remote
                                  Homology Detection . . . . . . . . . . . 1193--1198
                Jure Bordon and   
                Miha Moskon and   
              Nikolaj Zimic and   
                      Miha Mraz   Fuzzy Logic as a Computational Tool for
                                  Quantitative Modelling of Biological
                                  Systems with Uncertain Kinetic Data  . . 1199--1205
               Po-Kuei Chen and   
                 Chun-Liang Lin   Synthesis of Genetic Clock with
                                  Combinational Biologic Circuits  . . . . 1206--1212
  Emmanouil I. Athanasiadis and   
      Marilena M. Bourdakou and   
               George M. Spyrou   ZoomOut: Analyzing Multiple Networks as
                                  Single Nodes . . . . . . . . . . . . . . 1213--1216

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 12, Number 6, November, 2015

             Hsien-Da Huang and   
            Yi-Ping Phoebe Chen   Guest Editorial for the 13th Asia
                                  Pacific Bioinformatics Conference  . . . 1217--1218
                Liang Cheng and   
                     Jie Li and   
                    Yang Hu and   
                  Yue Jiang and   
             Yongzhuang Liu and   
                Yanshuo Chu and   
              Zhenxing Wang and   
                    Yadong Wang   Using Semantic Association to Extend and
                                  Infer Literature-Oriented Relativity
                                  Between Terms  . . . . . . . . . . . . . 1219--1226
            Nicolas Wieseke and   
               Tom Hartmann and   
             Matthias Bernt and   
              Martin Middendorf   Cophylogenetic Reconciliation with ILP   1227--1235
               Huidong Chen and   
                Jihong Guan and   
                  Shuigeng Zhou   DPNuc: Identifying Nucleosome Positions
                                  Based on the Dirichlet Process Mixture
                                  Model  . . . . . . . . . . . . . . . . . 1236--1247
                    Nan Gao and   
                  Yan Zhang and   
                  Bing Feng and   
                     Jijun Tang   A Cooperative Co-Evolutionary Genetic
                                  Algorithm for Tree Scoring and Ancestral
                                  Genome Inference . . . . . . . . . . . . 1248--1254
                 Minzhu Xie and   
               Jianxin Wang and   
                       Xin Chen   LGH: a Fast and Accurate Algorithm for
                                  Single Individual Haplotyping Based on a
                                  Two-Locus Linkage Graph  . . . . . . . . 1255--1266
           Shotaro Kumozaki and   
                 Kengo Sato and   
            Yasubumi Sakakibara   A Machine Learning Based Approach to de
                                  novo Sequencing of Glycans from Tandem
                                  Mass Spectrometry Spectrum . . . . . . . 1267--1274
               Xiaojing Xie and   
              Shuigeng Zhou and   
                    Jihong Guan   CoGI: Towards Compressing Genomes as an
                                  Image  . . . . . . . . . . . . . . . . . 1275--1285
               Beichen Wang and   
              Xiaodong Chen and   
          Hiroshi Mamitsuka and   
                   Shanfeng Zhu   BMExpert: Mining MEDLINE for Finding
                                  Experts in Biomedical Domains Based on
                                  Language Model . . . . . . . . . . . . . 1286--1294
                     Han Li and   
                    Chun Li and   
                     Jie Hu and   
                    Xiaodan Fan   A Resampling Based Clustering Algorithm
                                  for Replicated Gene Expression Data  . . 1295--1303
 Mohammad Shahrokh Esfahani and   
            Edward R. Dougherty   An Optimization-Based Framework for the
                                  Transformation of Incomplete Biological
                                  Knowledge into a Probabilistic Structure
                                  and Its Application to the Utilization
                                  of Gene/Protein Signaling Pathways in
                                  Discrete Phenotype Classification  . . . 1304--1321
               Kin-On Cheng and   
                   Paula Wu and   
              Ngai-Fong Law and   
                    Wan-Chi Siu   Compression of Multiple DNA Sequences
                                  Using Intra-Sequence and Inter-Sequence
                                  Similarities . . . . . . . . . . . . . . 1322--1332
                 Le Ou-Yang and   
               Dao-Qing Dai and   
                 Xiao-Fei Zhang   Detecting Protein Complexes from Signed
                                  Protein-Protein Interaction Networks . . 1333--1344
       Alexandru I. Tomescu and   
               Travis Gagie and   
             Alexandru Popa and   
                Romeo Rizzi and   
             Anna Kuosmanen and   
                   Veli Makinen   Explaining a Weighted DAG with Few Paths
                                  for Solving Genome-Guided Multi-Assembly 1345--1354
         Chandrabhan Seniya and   
                 Ajay Yadav and   
                 G. J. Khan and   
                    Nand K. Sah   In-silico Studies Show Potent Inhibition
                                  of HIV-1 Reverse Transcriptase Activity
                                  by a Herbal Drug . . . . . . . . . . . . 1355--1364
            Mariano Rubiolo and   
            Diego H. Milone and   
             Georgina Stegmayer   Mining Gene Regulatory Networks by
                                  Neural Modeling of Expression
                                  Time-Series  . . . . . . . . . . . . . . 1365--1373
                    Bo Liao and   
                  Yan Jiang and   
                  Wei Liang and   
                Lihong Peng and   
                    Li Peng and   
       Damien Hanyurwimfura and   
                   Zejun Li and   
                       Min Chen   On Efficient Feature Ranking Methods for
                                  High-Throughput Data Analysis  . . . . . 1374--1384
                     Xin Ma and   
                   Jing Guo and   
                    Ke Xiao and   
                       Xiao Sun   PRBP: Prediction of RNA-Binding Proteins
                                  Using a Random Forest Algorithm Combined
                                  with an RNA-Binding Residue Predictor    1385--1393
      Brijesh K. Sriwastava and   
              Subhadip Basu and   
                  Ujjwal Maulik   Predicting Protein-Protein Interaction
                                  Sites with a Novel Membership Based
                                  Fuzzy SVM Classifier . . . . . . . . . . 1394--1404
                Ehsan Ullah and   
                Mark Walker and   
               Kyongbum Lee and   
                   Soha Hassoun   PreProPath: an Uncertainty-Aware
                                  Algorithm for Identifying Predictable
                                  Profitable Pathways in Biochemical
                                  Networks . . . . . . . . . . . . . . . . 1405--1415
               Ka-Chun Wong and   
              Chengbin Peng and   
                         Yue Li   Probabilistic Inference on Multiple
                                  Normalized Signal Profiles from Next
                                  Generation Sequencing: Transcription
                                  Factor Binding Sites . . . . . . . . . . 1416--1428
                 Alon Raveh and   
                Yoram Zarai and   
          Michael Margaliot and   
                   Tamir Tuller   Ribosome Flow Model on a Ring  . . . . . 1429--1439
       Mohammadreza Sehhati and   
       Alireza Mehridehnavi and   
            Hossein Rabbani and   
              Meraj Pourhossein   Stable Gene Signature Selection for
                                  Prediction of Breast Cancer Recurrence
                                  Using Joint Mutual Information . . . . . 1440--1448
                  Hao Zhang and   
              Xingyuan Wang and   
                    Xiaohui Lin   Synchronization of Asynchronous Switched
                                  Boolean Network  . . . . . . . . . . . . 1449--1456
                T. Sengupta and   
                 M. Bhushan and   
                 P. P. Wangikar   A Computational Approach Using Ratio
                                  Statistics for Identifying Housekeeping
                                  Genes from cDNA Microarray Data  . . . . 1457--1463
             Prachi Pradeep and   
              Craig Struble and   
           Terrence Neumann and   
              Daniel S. Sem and   
             Stephen J. Merrill   A Novel Scoring Based Distributed
                                  Protein Docking Application to Improve
                                  Enrichment . . . . . . . . . . . . . . . 1464--1469
             Babette Dellen and   
               Hanno Scharr and   
                   Carme Torras   Growth Signatures of Rosette Plants from
                                  Time-Lapse Video . . . . . . . . . . . . 1470--1478
                Torbjorn Wigren   Model Order and Identifiability of
                                  Non-Linear Biological Systems in Stable
                                  Oscillation  . . . . . . . . . . . . . . 1479--1484


IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 13, Number 1, January, 2016

            De-Shuang Huang and   
     Vitoantonio Bevilacqua and   
             M. Michael Gromiha   Guest Editorial for Special Section on
                                  the 10th International Conference on
                                  Intelligent Computing (ICIC) . . . . . . 1--3
              Kyungsook Han and   
                  Jeonghoon Lee   GeneNetFinder2: Improved Inference of
                                  Dynamic Gene Regulatory Relations with
                                  Multiple Regulators  . . . . . . . . . . 4--11
     Edmundo Bonilla-Huerta and   
  Alberto Hernandez-Montiel and   
    Roberto-Morales Caporal and   
             Marco Arjona Lopez   Hybrid Framework Using Multiple-Filters
                                  and an Embedded Approach for an
                                  Efficient Selection and Classification
                                  of Microarray Data . . . . . . . . . . . 12--26
               Su-Ping Deng and   
                    Lin Zhu and   
                De-Shuang Huang   Predicting Hub Genes Associated with
                                  Cervical Cancer through Gene
                                  Co-Expression Networks . . . . . . . . . 27--35
                    Xumi Qu and   
                  Dong Wang and   
                Yuehui Chen and   
              Shanping Qiao and   
                      Qing Zhao   Predicting the Subcellular Localization
                                  of Proteins with Multiple Sites Based on
                                  Multiple Features Fusion . . . . . . . . 36--42
             Sun-Yuan Hsieh and   
                   Yu-Chun Chou   A Faster cDNA Microarray Gene Expression
                                  Data Classifier for Diagnosing Diseases  43--54
                    Lin Zhu and   
                 Wei-Li Guo and   
               Su-Ping Deng and   
                De-Shuang Huang   ChIP--PIT: Enhancing the Analysis of
                                  ChIP-Seq Data Using Convex-Relaxed
                                  Pair-Wise Interaction Tensor
                                  Decomposition  . . . . . . . . . . . . . 55--63
              Yu-Ting Hsiao and   
                 Wei-Po Lee and   
                   Wei Yang and   
              Stefan Muller and   
            Christoph Flamm and   
               Ivo Hofacker and   
                 Philipp Kugler   Practical Guidelines for Incorporating
                                  Knowledge-Based and Data-Driven
                                  Strategies into the Inference of Gene
                                  Regulatory Networks  . . . . . . . . . . 64--75
                    Yi Fang and   
               Mengtian Sun and   
                Guoxian Dai and   
                 Karthik Ramain   The Intrinsic Geometric Structure of
                                  Protein-Protein Interaction Networks for
                                  Protein Interaction Prediction . . . . . 76--85
                  Yu-Huei Cheng   A Novel Teaching-Learning-Based
                                  Optimization for Improved Mutagenic
                                  Primer Design in Mismatch PCR-RFLP SNP
                                  Genotyping . . . . . . . . . . . . . . . 86--98
               Indranil Roy and   
                 Srinivas Aluru   Discovering Motifs in Biological
                                  Sequences Using the Micron Automata
                                  Processor  . . . . . . . . . . . . . . . 99--111
                S. Bahlouli and   
                A. Mokaddem and   
                F. Hamdache and   
                   H. Riane and   
                     M. Kameche   Fractal Behavior of the Pancreatic $
                                  \beta $-Cell Near the Percolation
                                  Threshold: Effect of the K$_{\rm ATP}$
                                  Channel On the Electrical Response . . . 112--121
                Ehsan Ullah and   
              Shuchin Aeron and   
                   Soha Hassoun   gEFM: an Algorithm for Computing
                                  Elementary Flux Modes Using Graph
                                  Traversal  . . . . . . . . . . . . . . . 122--134
                 Xian Zhang and   
                  Ligang Wu and   
                     Jiahua Zou   Globally Asymptotic Stability Analysis
                                  for Genetic Regulatory Networks with
                                  Mixed Delays: an $M$-Matrix-Based
                                  Approach . . . . . . . . . . . . . . . . 135--147
     Preethi Ranganarayanan and   
        Narmadha Thanigesan and   
               Vivek Ananth and   
        Valadi K. Jayaraman and   
        Vigneshwar Ramakrishnan   Identification of Glucose-Binding
                                  Pockets in Human Serum Albumin Using
                                  Support Vector Machine and Molecular
                                  Dynamics Simulations . . . . . . . . . . 148--157
Oscar Miguel Rivera-Borroto and   
Jose Manuel Garcia-de la Vega and   
       Yovani Marrero-Ponce and   
                   Ricardo Grau   Relational Agreement Measures for
                                  Similarity Searching of Cheminformatic
                                  Data Sets  . . . . . . . . . . . . . . . 158--167
                      Anonymous   2015 reviewers list  . . . . . . . . . . 168--171
                          Title   2015 Index IEEE/ACM Transactions on
                                  Computational Biology and Bioinformatics
                                  Vol. 12  . . . . . . . . . . . . . . . . 172--195

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 13, Number 2, March, 2016

            Pietro H. Guzzi and   
                     Marco Mina   Guest Editorial for Special Section on
                                  Semantic-Based Approaches for Analysis
                                  of Biological Data . . . . . . . . . . . 196--196
           Giuseppe Agapito and   
            Marianna Milano and   
         Pietro Hiram Guzzi and   
                Mario Cannataro   Extracting Cross-Ontology Weighted
                                  Association Rules from Gene Ontology
                                  Annotations  . . . . . . . . . . . . . . 197--208
            Marco Masseroli and   
             Arif Canakoglu and   
                   Stefano Ceri   Integration and Querying of Genomic and
                                  Proteomic Semantic Annotations for
                                  Biomedical Knowledge Extraction  . . . . 209--219
                 Guoxian Yu and   
               Guangyuan Fu and   
                   Jun Wang and   
                    Hailong Zhu   Predicting Protein Function via Semantic
                                  Integration of Multiple Networks . . . . 220--232
        Javier D. Fernandez and   
         Maurizio Lenzerini and   
            Marco Masseroli and   
            Francesco Venco and   
                   Stefano Ceri   Ontology-Based Search of Genomic
                                  Metadata . . . . . . . . . . . . . . . . 233--247
              Davide Chicco and   
                Marco Masseroli   Ontology-Based Prediction and
                                  Prioritization of Gene Functional
                                  Annotations  . . . . . . . . . . . . . . 248--260
               Ka-Chun Wong and   
                     Yue Li and   
              Chengbin Peng and   
                   Hau-San Wong   A Comparison Study for DNA Motif
                                  Modeling on Protein Binding Microarray   261--271
                  An Nguyen and   
        Adam Prugel-Bennett and   
         Srinandan Dasmahapatra   A Low Dimensional Approximation For
                                  Competence In \bionameBacillus Subtilis  272--280
                   Xumin Ni and   
                    Wei Guo and   
                   Kai Yuan and   
                 Xiong Yang and   
                 Zhiming Ma and   
                  Shuhua Xu and   
                   Shihua Zhang   A Probabilistic Method for Estimating
                                  the Sharing of Identity by Descent for
                                  Populations with Migration . . . . . . . 281--290
                  Yuanqi Hu and   
              Pantelis Georgiou   A Real-Time de novo DNA Sequencing
                                  Assembly Platform Based on an FPGA
                                  Implementation . . . . . . . . . . . . . 291--300
                Nitin Singh and   
        Mathukumalli Vidyasagar   bLARS: an Algorithm to Infer Gene
                                  Regulatory Networks  . . . . . . . . . . 301--314
              Daniel Taliun and   
              Johann Gamper and   
                  Ulf Leser and   
               Cristian Pattaro   Fast Sampling-Based Whole-Genome
                                  Haplotype Block Recognition  . . . . . . 315--325
            Madhu S. Sigdel and   
              Madhav Sigdel and   
                 Semih Dinc and   
                 Imren Dinc and   
              Marc L. Pusey and   
               Ramazan S. Aygun   FocusALL: Focal Stacking of Microscopic
                                  Images Using Modified Harris Corner
                                  Response Measure . . . . . . . . . . . . 326--340
              Tyler A. Land and   
              Perry Fizzano and   
                Robin B. Kodner   Measuring Cluster Stability in a Large
                                  Scale Phylogenetic Analysis of
                                  Functional Genes in Metagenomes Using
                                  \tt pplacer  . . . . . . . . . . . . . . 341--349
            Narayan Ganesan and   
                     Jie Li and   
            Vishakha Sharma and   
                Hanyu Jiang and   
             Adriana Compagnoni   Process Simulation of Complex Biological
                                  Pathways in Physical Reactive Space and
                                  Reformulated for Massively Parallel
                                  Computing Platforms  . . . . . . . . . . 365--379
                  Xudong Tu and   
             Yuanliang Wang and   
               Maolan Zhang and   
                    Jinchuan Wu   Using Formal Concept Analysis to
                                  Identify Negative Correlations in Gene
                                  Expression Data  . . . . . . . . . . . . 380--391
               Jin-Xing Liu and   
                    Yong Xu and   
              Ying-Lian Gao and   
             Chun-Hou Zheng and   
                  Dong Wang and   
                         Qi Zhu   A Class-Information-Based Sparse
                                  Component Analysis Method to Identify
                                  Differentially Expressed Genes on
                                  RNA-Seq Data . . . . . . . . . . . . . . 392--398

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 13, Number 3, May, 2016

   Mehran Mozaffari-Kermani and   
          Reza Azarderakhsh and   
                    Kui Ren and   
               Jean-Luc Beuchat   Introduction to the special section on
                                  emerging security trends for biomedical
                                  computations, devices, and
                                  infrastructures: guest editorial . . . . 399--400
              Ovunc Kocabas and   
               Tolga Soyata and   
                Mehmet K. Aktas   Emerging security mechanisms for medical
                                  cyber physical systems . . . . . . . . . 401--416
                 Cheng Chen and   
             Fengchao Zhang and   
               Jamie Barras and   
           Kaspar Althoefer and   
              Swarup Bhunia and   
               Soumyajit Mandal   Authentication of medicines using
                                  nuclear quadrupole resonance
                                  spectroscopy . . . . . . . . . . . . . . 417--430
                Yanmin Gong and   
               Yuguang Fang and   
                  Yuanxiong Guo   Private data analytics on biomedical
                                  sensing data via distributed computation 431--444
              Sk Subidh Ali and   
            Mohamed Ibrahim and   
            Ozgur Sinanoglu and   
     Krishnendu Chakrabarty and   
                   Ramesh Karri   Security assessment of cyberphysical
                                  digital microfluidic biochips  . . . . . 445--458
              David A. Knox and   
                Robin D. Dowell   A modeling framework for generation of
                                  positional and temporal simulations of
                                  transcriptional regulation . . . . . . . 459--471
                          Xu Gu   A multi-state optimization framework for
                                  parameter estimation in biological
                                  systems  . . . . . . . . . . . . . . . . 472--482
                  Jiang Xie and   
             Chaojuan Xiang and   
                     Jin Ma and   
                    Jun Tan and   
                Tieqiao Wen and   
                 Jinzhi Lei and   
                       Qing Nie   An adaptive hybrid algorithm for global
                                  network alignment  . . . . . . . . . . . 483--493
              Rami Al-Dalky and   
                 Kamal Taha and   
            Dirar Al Homouz and   
                 Murad Qasaimeh   Applying Monte Carlo simulation to
                                  biomedical literature to approximate
                                  genetic network  . . . . . . . . . . . . 494--504
            Antonin Pavelka and   
              Eva Sebestova and   
          Barbora Kozlikova and   
              Jan Brezovsky and   
                Jiri Sochor and   
                 Jiri Damborsky   CAVER: algorithms for analyzing dynamics
                                  of tunnels in macromolecules . . . . . . 505--517
              Zrinka Puljiz and   
                   Haris Vikalo   Decoding genetic variations:
                                  communications-inspired haplotype
                                  assembly . . . . . . . . . . . . . . . . 518--530
                    Cong Li and   
                   Can Yang and   
                Greg Hather and   
                    Ray Liu and   
                    Hongyu Zhao   Efficient drug-pathway association
                                  analysis via integrative penalized
                                  matrix decomposition . . . . . . . . . . 531--540
            Isaac G. Macwan and   
                  Zihe Zhao and   
               Omar T. Sobh and   
             Ishita Mukerji and   
      Bhushan Dharmadhikari and   
                Prabir K. Patra   Residue specific and chirality dependent
                                  interactions between carbon nanotubes
                                  and flagellin  . . . . . . . . . . . . . 541--548
                Cheng Liang and   
                     Yue Li and   
                     Jiawei Luo   A novel method to detect functional
                                  microRNA regulatory modules by bicliques
                                  merging  . . . . . . . . . . . . . . . . 549--556
                   Ben Teng and   
                   Can Yang and   
                 Jiming Liu and   
                Zhipeng Cai and   
                      Xiang Wan   Exploring the genetic patterns of
                                  complex diseases via the integrative
                                  genome-wide approach . . . . . . . . . . 557--564
              Sajad Mirzaei and   
                      Yufeng Wu   Fast construction of near parsimonious
                                  hybridization networks for multiple
                                  phylogenetic trees . . . . . . . . . . . 565--570
               Hai-Peng Ren and   
              Xiao-Na Huang and   
                   Jia-Xuan Hao   Finding robust adaptation gene
                                  regulatory networks using
                                  multi-objective genetic algorithm  . . . 571--577
                     Dan He and   
                 Irina Rish and   
                 David Haws and   
                   Laxmi Parida   MINT: mutual information based
                                  transductive feature selection for
                                  genetic trait prediction . . . . . . . . 578--583
        Catherine Stamoulis and   
            Rebecca A. Betensky   Optimization of signal decomposition
                                  matched filtering (SDMF) for improved
                                  detection of copy-number variations  . . 584--591
               Yongchao Liu and   
             Thomas Hankeln and   
                 Bertil Schmidt   Parallel and space-efficient
                                  construction of Burrows--Wheeler
                                  transform and suffix array for big
                                  genome data  . . . . . . . . . . . . . . 592--598

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 13, Number 4, 2016

                Biing-Feng Wang   A New Efficient Algorithm for the All
                                  Sorting Reversals Problem with No Bad
                                  Components . . . . . . . . . . . . . . . 599--609
                Junzhong Ji and   
                 Jiawei Luo and   
                Cuicui Yang and   
                   Aidong Zhang   Detecting Functional Modules Based on a
                                  Multiple-Grain Model in Large-Scale
                                  Protein-Protein Interaction Networks . . 610--622
             Ngoc Hieu Tran and   
                       Xin Chen   AMAS: Optimizing the Partition and
                                  Filtration of Adaptive Seeds to Speed up
                                  Read Mapping . . . . . . . . . . . . . . 623--633
             Zhenchao Jiang and   
                Lishuang Li and   
                    Degen Huang   An Unsupervised Graph Based Continuous
                                  Word Representation Method for
                                  Biomedical Text Mining . . . . . . . . . 634--642
          Daniele Catanzaro and   
        Stanley E. Shackney and   
 Alejandro A. Schäffer and   
               Russell Schwartz   Classifying the Progression of Ductal
                                  Carcinoma from Single-Cell Sampled Data
                                  via Integer Linear Programming: a Case
                                  Study  . . . . . . . . . . . . . . . . . 643--655
                 Jianing Xi and   
                          Ao Li   Discovering Recurrent Copy Number
                                  Aberrations in Complex Patterns via
                                  Non-Negative Sparse Singular Value
                                  Decomposition  . . . . . . . . . . . . . 656--668
                Lishuang Li and   
               Shanshan Liu and   
                 Meiyue Qin and   
                 Yiwen Wang and   
                    Degen Huang   Extracting Biomedical Event with Dual
                                  Decomposition Integrating Word
                                  Embeddings . . . . . . . . . . . . . . . 669--677
           Benjamin X. Guan and   
                  Bir Bhanu and   
                Prue Talbot and   
              Nikki Jo-Hao Weng   Extraction of Blebs in Human Embryonic
                                  Stem Cell Videos . . . . . . . . . . . . 678--688
            Ahed Elmsallati and   
               Connor Clark and   
                   Jugal Kalita   Global Alignment of Protein-Protein
                                  Interaction Networks: a Survey . . . . . 689--705
                Shibiao Wan and   
                Man-Wai Mak and   
                  Sun-Yuan Kung   Mem-mEN: Predicting Multi-Functional
                                  Types of Membrane Proteins by
                                  Interpretable Elastic Nets . . . . . . . 706--718
                 Lori A. Dalton   Optimal ROC-Based Classification and
                                  Performance Analysis under Bayesian
                                  Uncertainty Models . . . . . . . . . . . 719--729
            Shun-ichi Azuma and   
              Katsuya Owaki and   
         Nobuhiro Shinohara and   
                Toshiharu Sugie   Performance Analysis of Chemotaxis
                                  Controllers: Which has Better Chemotaxis
                                  Controller, \bionameEscherichia coli or
                                  \bionameParamecium caudatum? . . . . . . 730--741
            Sajid A. Marhon and   
               Stefan C. Kremer   Prediction of Protein Coding Regions
                                  Using a Wide-Range Wavelet Window Method 742--753
                Yun-Bo Zhao and   
                    J. Krishnan   Probabilistic Boolean Network Modelling
                                  and Analysis Framework for mRNA
                                  Translation  . . . . . . . . . . . . . . 754--766
           Young Hwan Chang and   
                 Roel Dobbe and   
              Palak Bhushan and   
                Joe W. Gray and   
               Claire J. Tomlin   Reconstruction of Gene Regulatory
                                  Networks Based on Repairing Sparse
                                  Low-Rank Matrices  . . . . . . . . . . . 767--777
                  Yang Tang and   
                 Huijun Gao and   
                     Wei Du and   
                Jianquan Lu and   
    Athanasios V. Vasilakos and   
             Jürgen Kurths   Robust Multiobjective Controllability of
                                  Complex Neuronal Networks  . . . . . . . 778--791
                  Yifeng Li and   
                Haifen Chen and   
                  Jie Zheng and   
                   Alioune Ngom   The Max-Min High-Order Dynamic Bayesian
                                  Network for Learning Gene Regulatory
                                  Networks with Time-Delayed Regulations   792--803
                  Ling Jian and   
              Zhonghang Xia and   
                 Xinnan Niu and   
                Xijun Liang and   
              Parimal Samir and   
                 Andrew J. Link   $ \ell_2 $ Multiple Kernel Fuzzy
                                  SVM-Based Data Fusion for Improving
                                  Peptide Identification . . . . . . . . . 804--809

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 13, Number 5, September, 2016

                  Chao Wang and   
                    Hong Yu and   
                  Aili Wang and   
                        Kai Xia   Guest Editorial for Special Section on
                                  Big Data Computing and Processing in
                                  Computational Biology and Bioinformatics 810--811
         Erin Jessica Moore and   
             Thirmachos Bourlai   Expectation Maximization of Frequent
                                  Patterns, a Specific, Local,
                                  Pattern-Based Biclustering Algorithm for
                                  Biological Datasets  . . . . . . . . . . 812--824
                   Ya Zhang and   
                      Ao Li and   
                  Chen Peng and   
                   Minghui Wang   Improve Glioblastoma Multiforme
                                  Prognosis Prediction by Using Feature
                                  Selection and Multiple Kernel Learning   825--835
                  Xiaoyi Xu and   
                   Minghui Wang   Inferring Disease Associated
                                  Phosphorylation Sites via Random Walk on
                                  Multi-Layer Heterogeneous Network  . . . 836--844
                 Cheng Ling and   
            Tsuyoshi Hamada and   
               Jingyang Gao and   
              Guoguang Zhao and   
               Donghong Sun and   
                    Weifeng Shi   MrBayes tgMC 3++: a High Performance and
                                  Resource-Efficient GPU-Oriented
                                  Phylogenetic Analysis Method . . . . . . 845--854
             Jingsong Zhang and   
               Yinglin Wang and   
                 Chao Zhang and   
                   Yongyong Shi   Mining Contiguous Sequential Generators
                                  in Biological Sequences  . . . . . . . . 855--867
                   Keru Hua and   
                     Qin Yu and   
                  Ruiming Zhang   A Guaranteed Similarity Metric Learning
                                  Framework for Biological Sequence
                                  Comparison . . . . . . . . . . . . . . . 868--877
            Steinar Thorvaldsen   A Mutation Model from First Principles
                                  of the Genetic Code  . . . . . . . . . . 878--886
                Xiao-Hu Hao and   
              Gui-Jun Zhang and   
              Xiao-Gen Zhou and   
                     Xu-Feng Yu   A Novel Method Using Abstract Convex
                                  Underestimation in Ab-Initio Protein
                                  Structure Prediction for Guiding Search
                                  in Conformational Feature Space  . . . . 887--900
                  Peng Chen and   
                ShanShan Hu and   
                  Jun Zhang and   
                    Xin Gao and   
                  Jinyan Li and   
                Junfeng Xia and   
                      Bing Wang   A Sequence-Based Dynamic Ensemble
                                  Learning System for Protein
                                  Ligand-Binding Site Prediction . . . . . 901--912
            Filippo Disanto and   
              Noah A. Rosenberg   Asymptotic Properties of the Number of
                                  Matching Coalescent Histories for
                                  Caterpillar-Like Families of Species
                                  Trees  . . . . . . . . . . . . . . . . . 913--925
             David Nogueira and   
                Pedro Tomas and   
                      Nuno Roma   BowMapCL: Burrows--Wheeler Mapping on
                                  Multiple Heterogeneous Accelerators  . . 926--938
                    Yan Shi and   
               Jinglong Niu and   
                 Zhixin Cao and   
                 Maolin Cai and   
                   Jian Zhu and   
                     Weiqing Xu   Online Estimation Method for Respiratory
                                  Parameters Based on a Pneumatic Model    939--946
                    Liqi Li and   
                  Jinhui Li and   
               Weidong Xiao and   
               Yongsheng Li and   
                 Yufang Qin and   
                Shiwen Zhou and   
                       Hua Yang   Prediction the Substrate Specificities
                                  of Membrane Transport Proteins Based on
                                  Support Vector Machine and Hybrid
                                  Features . . . . . . . . . . . . . . . . 947--953
      Apostolos Axenopoulos and   
       Dimitrios Rafailidis and   
      Georgios Papadopoulos and   
           Elias N. Houstis and   
                   Petros Daras   Similarity Search of Flexible $3$D
                                  Molecules Combining Local and Global
                                  Shape Descriptors  . . . . . . . . . . . 954--970
               Jun Chin Ang and   
               Andri Mirzal and   
           Habibollah Haron and   
        Haza Nuzly Abdull Hamed   Supervised, Unsupervised, and
                                  Semi-Supervised Feature Selection: a
                                  Review on Gene Selection . . . . . . . . 971--989
               Yuanning Liu and   
                    Qi Zhao and   
                  Hao Zhang and   
                     Rui Xu and   
                    Yang Li and   
                      Liyan Wei   A New Method to Predict RNA Secondary
                                  Structure Based on RNA Folding
                                  Simulation . . . . . . . . . . . . . . . 990--995
             Yung-Keun Kwon and   
                  Junil Kim and   
                 Kwang-Hyun Cho   Dynamical Robustness against Multiple
                                  Mutations in Signaling Networks  . . . . 996--1002

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 13, Number 6, November, 2016

                 Xing-Ming Zhao   Data Mining in Systems Biology . . . . . 1003--1003
                  Jian Tang and   
                  Shuigeng Zhou   A New Approach for Feature Selection
                                  from Microarray Data Based on Mutual
                                  Information  . . . . . . . . . . . . . . 1004--1015
                     Xi Yin and   
               Ying-Ying Xu and   
                  Hong-Bin Shen   Enhancing the Prediction of
                                  Transmembrane $ \beta $-Barrel Segments
                                  with Chain Learning and Feature Sparse
                                  Representation . . . . . . . . . . . . . 1016--1026
                Gui-Min Qin and   
                  Rui-Yi Li and   
                 Xing-Ming Zhao   Identifying Disease Associated miRNAs
                                  Based on Protein Domains . . . . . . . . 1027--1035
                     Hao Wu and   
                    Lin Gao and   
              Nikola K. Kasabov   Network-Based Method for Inferring
                                  Cancer Progression at the Pathway Level
                                  from Cross-Sectional Mutation Data . . . 1036--1044
               Fabio Fabris and   
            Alex A. Freitas and   
          Jennifer M. A. Tullet   An Extensive Empirical Comparison of
                                  Probabilistic Hierarchical Classifiers
                                  in Datasets of Ageing-Related Genes  . . 1045--1058
                  Dong Wang and   
               Jin-Xing Liu and   
              Ying-Lian Gao and   
             Chun-Hou Zheng and   
                        Yong Xu   Characteristic Gene Selection Based on
                                  Robust Graph Regularized Non-Negative
                                  Matrix Factorization . . . . . . . . . . 1059--1067
          Adriano N. Raposo and   
               Abel J. P. Gomes   Computational $3$D Assembling Methods
                                  for DNA: a Survey  . . . . . . . . . . . 1068--1085
                Sumanta Ray and   
      Sanghamitra Bandyopadhyay   Discovering Condition Specific
                                  Topological Pattern Changes in
                                  Coexpression Network: an Application to
                                  HIV-1 Progression  . . . . . . . . . . . 1086--1099
      Natalia Vilor-Tejedor and   
           Juan R. Gonzalez and   
                   M. Luz Calle   Efficient and Powerful Method for
                                  Combining $P$-Values in Genome-Wide
                                  Association Studies  . . . . . . . . . . 1100--1106
             Xiaoqing Cheng and   
                Tomoya Mori and   
                 Yushan Qiu and   
               Wai-Ki Ching and   
                 Tatsuya Akutsu   Exact Identification of the Structure of
                                  a Probabilistic Boolean Network from
                                  Samples  . . . . . . . . . . . . . . . . 1107--1116
                Maoguo Gong and   
              Zhenglin Peng and   
                   Lijia Ma and   
                 Jiaxiang Huang   Global Biological Network Alignment by
                                  Using Efficient Memetic Algorithm  . . . 1117--1129
               Meredith Ray and   
                  Jian Kang and   
                  Hongmei Zhang   Identifying Activation Centers with
                                  Spatial Cox Point Processes Using fMRI
                                  Data . . . . . . . . . . . . . . . . . . 1130--1141
                  Hong Wang and   
               Xicheng Wang and   
                   Zheng Li and   
                       Keqiu Li   Kriging-Based Parameter Estimation
                                  Algorithm for Metabolic Networks
                                  Combined with Single-Dimensional
                                  Optimization and Dynamic Coordinate
                                  Perturbation . . . . . . . . . . . . . . 1142--1154
                Guanyun Wei and   
                  Sheng Qin and   
                 Wenjuan Li and   
                Liming Chen and   
                         Fei Ma   MDTE DB: a Database for MicroRNAs
                                  Derived from Transposable Element  . . . 1155--1160
               Shuang Cheng and   
                  Maozu Guo and   
                Chunyu Wang and   
                Xiaoyan Liu and   
                   Yang Liu and   
                     Xuejian Wu   MiRTDL: a Deep Learning Approach for
                                  miRNA Target Prediction  . . . . . . . . 1161--1169
                      Yi Qi and   
                     Jiawei Luo   Prediction of Essential Proteins Based
                                  on Local Interaction Density . . . . . . 1170--1182
           Sergiy Ancherbak and   
          Ercan E. Kuruoglu and   
                 Martin Vingron   Time-Dependent Gene Network Modelling by
                                  Sequential Monte Carlo . . . . . . . . . 1183--1193
                   Yang Liu and   
                   Bowen Li and   
                    Jungang Lou   Disturbance Decoupling of Singular
                                  Boolean Control Networks . . . . . . . . 1194--1200


IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 14, Number 1, January, 2017

                   Ying Tan and   
                      Yuhui Shi   Editorial: Special Section on
                                  Bio-Inspired Swarm Computing and
                                  Engineering  . . . . . . . . . . . . . . 1--3
                    Ben Niu and   
                Huali Huang and   
                 Lijing Tan and   
                      Qiqi Duan   Symbiosis-Based Alternative Learning
                                  Multi-Swarm Particle Swarm Optimization  4--14
                 Hongwei Mo and   
                   Lili Liu and   
                      Jiao Zhao   A New Magnetotactic Bacteria
                                  Optimization Algorithm Based on Moment
                                  Migration  . . . . . . . . . . . . . . . 15--26
              Shaoqiu Zheng and   
                  Junzhi Li and   
            Andreas Janecek and   
                       Ying Tan   A Cooperative Framework for Fireworks
                                  Algorithm  . . . . . . . . . . . . . . . 27--41
                  Bei Zhang and   
               Yu-Jun Zheng and   
              Min-Xia Zhang and   
                Sheng-Yong Chen   Fireworks Algorithm with Enhanced
                                  Fireworks Interaction  . . . . . . . . . 42--55
                 Shan Cheng and   
             Long-Long Zhao and   
                  Xiao-Yu Jiang   An Effective Application of Bacteria
                                  Quorum Sensing and Circular Elimination
                                  in MOPSO . . . . . . . . . . . . . . . . 56--63
                 Yong Zhang and   
               Dun-wei Gong and   
                     Jian Cheng   Multi-Objective Particle Swarm
                                  Optimization Approach for Cost-Based
                                  Feature Selection in Classification  . . 64--75
                Qingjian Ni and   
               Qianqian Pan and   
                  Huimin Du and   
                    Cen Cao and   
                    Yuqing Zhai   A Novel Cluster Head Selection Algorithm
                                  Based on Fuzzy Clustering and Particle
                                  Swarm Optimization . . . . . . . . . . . 76--84
                    Fei Han and   
                  Chun Yang and   
                   Ya-Qi Wu and   
             Jian-Sheng Zhu and   
              Qing-Hua Ling and   
               Yu-Qing Song and   
                De-Shuang Huang   A Gene Selection Method for Microarray
                                  Data Based on Binary PSO Encoding
                                  Gene-to-Class Sensitivity Information    85--96
                   Bo Zhang and   
                    Haibin Duan   Three-Dimensional Path Planning for
                                  Uninhabited Combat Aerial Vehicle Based
                                  on Predator-Prey Pigeon-Inspired
                                  Optimization in Dynamic Environment  . . 97--107
                  Yuxin Liu and   
                   Chao Gao and   
                 Zili Zhang and   
                  Yuxiao Lu and   
                   Shi Chen and   
              Mingxin Liang and   
                         Li Tao   Solving NP-Hard Problems with
                                  \bionamePhysarum-Based Ant Colony System 108--120
             Elena Czeizler and   
              Tommi Hirvola and   
                    Kalle Karhu   A Graph-Theoretical Approach for Motif
                                  Discovery in Protein Sequences . . . . . 121--130
                 Hasan M. Jamil   A Visual Interface for Querying
                                  Heterogeneous Phylogenetic Databases . . 131--144
                  Lin Zhang and   
                    Hui Liu and   
                Yufei Huang and   
               Xuesong Wang and   
                Yidong Chen and   
                       Jia Meng   Cancer Progression Prediction Using Gene
                                  Interaction Regularized Elastic Net  . . 145--154
                     Lun Hu and   
               Keith C. C. Chan   Extracting Coevolutionary Features from
                                  Protein Sequences for Predicting
                                  Protein--Protein Interactions  . . . . . 155--166
          Mehrdad J. Gangeh and   
               Hadi Zarkoob and   
                     Ali Ghodsi   Fast and Scalable Feature Selection for
                                  Gene Expression Data Using
                                  Hilbert--Schmidt Independence Criterion  167--181
                 Hailong Hu and   
                   Zhong Li and   
               Hongwei Dong and   
                    Tianhe Zhou   Graphical Representation and Similarity
                                  Analysis of Protein Sequences Based on
                                  Fractal Interpolation  . . . . . . . . . 182--192
           Vincenzo Bonnici and   
                 Rosalba Giugno   On the Variable Ordering in Subgraph
                                  Isomorphism Algorithms . . . . . . . . . 193--203
         Arvind Kumar Sinha and   
              Pradeep Singh and   
              Anand Prakash and   
                  Dharm Pal and   
              Anuradha Dube and   
                  Awanish Kumar   Putative Drug and Vaccine Target
                                  Identification in \bionameLeishmania
                                  donovani Membrane Proteins Using
                                  Na\"\ive Bayes Probabilistic Classifier  204--211
                Shibiao Wan and   
                Man-Wai Mak and   
                  Sun-Yuan Kung   Transductive Learning for Multi-Label
                                  Protein Subchloroplast Localization
                                  Prediction . . . . . . . . . . . . . . . 212--224
                Kuize Zhang and   
                Lijun Zhang and   
                  Shaoshuai Mou   An Application of Invertibility of
                                  Boolean Control Networks to the Control
                                  of the Mammalian Cell Cycle  . . . . . . 225--229

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 14, Number 2, March, 2017

                   Aidong Zhang   Editorial from the New Editor-in-Chief   251--251
                 Illhoi Yoo and   
                   Amarda Shehu   Guest Editorial for Special Section on
                                  BIBM 2014  . . . . . . . . . . . . . . . 252--253
         En-Shiun Annie Lee and   
      Ho-Yin Antonio Sze-To and   
               Man-Hon Wong and   
            Kwong-Sak Leung and   
      Terrence Chi-Kong Lau and   
              Andrew K. C. Wong   Discovering Protein-DNA Binding Cores by
                                  Aligned Pattern Clustering . . . . . . . 254--263
                 Yong Zhang and   
                 Xiaohua Hu and   
                 Xingpeng Jiang   Multi-View Clustering of Microbiome
                                  Samples by Robust Similarity Network
                                  Fusion and Spectral Clustering . . . . . 264--271
                Ilona Kifer and   
              Rui M. Branca and   
               Amir Ben-Dor and   
                Linhui Zhai and   
                    Ping Xu and   
               Janne Lehtio and   
                  Zohar Yakhini   Optimizing Analytical Depth and Cost
                                  Efficiency of IEF-LC/MS Proteomics . . . 272--281
                Huiru Zheng and   
              Chaoyang Wang and   
                   Haiying Wang   Analysis of Organization of the
                                  Interactome Using Dominating Sets: a
                                  Case Study on Cell Cycle Interaction
                                  Networks . . . . . . . . . . . . . . . . 282--289
            Matthias Becker and   
        Nadia Magnenat-Thalmann   Muscle Tissue Labeling of Human Lower
                                  Limb in Multi-Channel mDixon MR Imaging:
                                  Concepts and Applications  . . . . . . . 290--299
              Daniel Veltri and   
                Uday Kamath and   
                   Amarda Shehu   Improving Recognition of Antimicrobial
                                  Peptides and Target Selectivity through
                                  Machine Learning and Genetic Programming 300--313
                 Mitra Basu and   
                     Yi Pan and   
                   Jianxin Wang   Guest Editors Introduction to the
                                  Special Section on ISBRA 2014  . . . . . 314--315
                   Fa Zhang and   
                    Yu Chen and   
                    Fei Ren and   
                  Xuan Wang and   
                Zhiyong Liu and   
                    Xiaohua Wan   A Two-Phase Improved Correlation Method
                                  for Automatic Particle Selection in
                                  Cryo-EM  . . . . . . . . . . . . . . . . 316--325
                     Yi Liu and   
                     Bin Ma and   
             Kaizhong Zhang and   
                  Gilles Lajoie   An Approach for Peptide Identification
                                  by De Novo Sequencing of Mixture Spectra 326--336
                        Yan and   
         Anthony J. Kusalik and   
                  Fang-Xiang Wu   NovoExD: De novo Peptide Sequencing for
                                  ETD/ECD Spectra  . . . . . . . . . . . . 337--344
                    Lin Zhu and   
               Su-Ping Deng and   
               Zhu-Hong You and   
                De-Shuang Huang   Identifying Spurious Interactions in the
                                  Protein-Protein Interaction Networks
                                  Using Local Similarity Preserving
                                  Embedding  . . . . . . . . . . . . . . . 345--352
             Xingpeng Jiang and   
                 Xiaohua Hu and   
                      Weiwei Xu   Microbiome Data Representation by Joint
                                  Nonnegative Matrix Factorization with
                                  Laplacian Regularization . . . . . . . . 353--359
                   Wei Peng and   
                     Min Li and   
                    Lu Chen and   
                   Lusheng Wang   Predicting Protein Functions by Using
                                  Unbalanced Random Walk Algorithm on
                                  Three Biological Networks  . . . . . . . 360--369
                     Min Li and   
                      Yu Lu and   
                 Zhibei Niu and   
                  Fang-Xiang Wu   United Complex Centrality for
                                  Identification of Essential Proteins
                                  from PPI Networks  . . . . . . . . . . . 370--380
            Behrang Mahjani and   
                Salman Toor and   
            Carl Nettelblad and   
               Sverker Holmgren   A Flexible Computational Framework Using
                                  $R$ and Map-Reduce for Permutation Tests
                                  of Massive Genetic Analysis of Complex
                                  Traits . . . . . . . . . . . . . . . . . 381--392
             Van-Nui Nguyen and   
              Kai-Yao Huang and   
           Chien-Hsun Huang and   
              K. Robert Lai and   
                   Tzong-Yi Lee   A New Scheme to Characterize and
                                  Identify Protein Ubiquitination Sites    393--403
             Julia Matsieva and   
                Steven Kelk and   
         Celine Scornavacca and   
              Chris Whidden and   
                   Dan Gusfield   A Resolution of the Static Formulation
                                  Question for the Problem of Computing
                                  the History Bound  . . . . . . . . . . . 404--417
            Ashok Rajaraman and   
 Joao Paulo Pereira Zanetti and   
                 Jan Manuch and   
                  Cedric Chauve   Algorithms and Complexity Results for
                                  Genome Mapping Problems  . . . . . . . . 418--430
               Kieran Alden and   
                 Jon Timmis and   
            Paul S. Andrews and   
   Henrique Veiga-Fernandes and   
                     Mark Coles   Extending and Applying Spartan to
                                  Perform Temporal Sensitivity Analyses
                                  for Predicting Changes in Influential
                                  Biological Pathways in Computational
                                  Models . . . . . . . . . . . . . . . . . 431--442
                 Oscar Dias and   
               Daniel Gomes and   
               Paulo Vilaca and   
               Joao Cardoso and   
               Miguel Rocha and   
        Eugenio C. Ferreira and   
                   Isabel Rocha   Genome-Wide Semi-Automated Annotation of
                                  Transporter Systems  . . . . . . . . . . 443--456
            Katya Mkrtchyan and   
        Anirban Chakraborty and   
          Amit K. Roy-Chowdhury   Optimal Landmark Selection for
                                  Registration of $4$D Confocal Image
                                  Stacks in \bionameArabidopsis  . . . . . 457--467
            Momoko Hayamizu and   
               Hiroshi Endo and   
                 Kenji Fukumizu   A Characterization of Minimum Spanning
                                  Tree-Like Metric Spaces  . . . . . . . . 468--471
               Olivier Boes and   
            Mareike Fischer and   
                    Steven Kelk   A Linear Bound on the Number of States
                                  in Optimal Convex Characters for Maximum
                                  Parsimony Distance . . . . . . . . . . . 472--477
     Thao Thi Phuong Nguyen and   
                 Vinh Sy Le and   
                Hai Bich Ho and   
                    Quang Si Le   Building Ancestral Recombination Graphs
                                  for Whole Genomes  . . . . . . . . . . . 478--483
     Emmanouil Athanasiadis and   
         Marilena Bourdakou and   
                  George Spyrou   D-Map: Random Walking on Gene Network
                                  Inference Maps Towards differential
                                  Avenue Discovery . . . . . . . . . . . . 484--490
          Stephane Mottelet and   
               Gil Gaullier and   
                 Georges Sadaka   Metabolic Flux Analysis in Isotope
                                  Labeling Experiments Using the Adjoint
                                  Approach . . . . . . . . . . . . . . . . 491--497
            Scott Goldweber and   
             Jamal Theodore and   
    John Torcivia-Rodriguez and   
             Vahan Simonyan and   
                  Raja Mazumder   Pubcast and Genecast: Browsing and
                                  Exploring Publications and Associated
                                  Curated Content in Biology Through
                                  Mobile Devices . . . . . . . . . . . . . 498--500

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 14, Number 3, May, 2017

                   Fei Wang and   
                 Xiao-Li Li and   
           Jason T. L. Wang and   
                   See-Kiong Ng   Guest Editorial: Special Section on
                                  Biological Data Mining and Its
                                  Applications in Healthcare . . . . . . . 501--502
                   Hua Wang and   
                    Lin Yan and   
                 Heng Huang and   
                     Chris Ding   From Protein Sequence to Protein
                                  Function via Multi-Label Linear
                                  Discriminant Analysis  . . . . . . . . . 503--513
               Jianqiang Li and   
                       Fei Wang   Towards Unsupervised Gene Selection: a
                                  Matrix Factorization Framework . . . . . 514--521
          Chelsea J. -T. Ju and   
            Zhuangtian Zhao and   
                       Wei Wang   Efficient Approach to Correct Read
                                  Alignment for Pseudogene Abundance
                                  Estimates  . . . . . . . . . . . . . . . 522--533
            Peter B. Walker and   
            Jacob N. Norris and   
         Anna E. Tschiffely and   
        Melissa L. Mehalick and   
        Craig A. Cunningham and   
                Ian N. Davidson   Applications of Transductive Spectral
                                  Clustering Methods in a Military Medical
                                  Concussion Database  . . . . . . . . . . 534--544
          Jelena Stojanovic and   
       Djordje Gligorijevic and   
       Vladan Radosavljevic and   
             Nemanja Djuric and   
            Mihajlo Grbovic and   
                Zoran Obradovic   Modeling Healthcare Quality via Compact
                                  Representations of Electronic Health
                                  Records  . . . . . . . . . . . . . . . . 545--554
          Robert Moskovitch and   
                Hyunmi Choi and   
            George Hripcsak and   
             Nicholas Tatonetti   Prognosis of Clinical Outcomes with
                                  Temporal Patterns and Experiences with
                                  One Class Feature Selection  . . . . . . 555--563
                   Xin Wang and   
                       Jinbo Bi   Bi-convex Optimization to Learn
                                  Classifiers from Multiple Biomedical
                                  Annotations  . . . . . . . . . . . . . . 564--575
         Robert W. Harrison and   
             Ion I. Mandoiu and   
           Alexander Zelikovsky   Guest Editors' Introduction to the
                                  Special Section on Bioinformatics
                                  Research and Applications  . . . . . . . 576--577
            Abhishek Biswas and   
                Desh Ranjan and   
            Mohammad Zubair and   
             Stephanie Zeil and   
              Kamal Al Nasr and   
                        Jing He   An Effective Computational Method
                                  Incorporating Multiple Secondary
                                  Structure Predictions in Topology
                                  Determination for Cryo-EM Images . . . . 578--586
               Misagh Kordi and   
                Mukul S. Bansal   On the Complexity of
                                  Duplication-Transfer-Loss Reconciliation
                                  with Non-Binary Gene Trees . . . . . . . 587--599
                   Xuan Guo and   
                 Jing Zhang and   
                Zhipeng Cai and   
                Ding-Zhu Du and   
                         Yi Pan   Searching Genome-Wide Multi-Locus
                                  Associations for Multiple Diseases Based
                                  on Bayesian Inference  . . . . . . . . . 600--610
                     Hao Ji and   
                 Yaohang Li and   
               Seth H. Weinberg   Calcium Ion Fluctuations Alter Channel
                                  Gating in a Stochastic Luminal Calcium
                                  Release Site Model . . . . . . . . . . . 611--619
   Gustavo Rodrigues Galvao and   
           Christian Baudet and   
                    Zanoni Dias   Sorting Circular Permutations by Super
                                  Short Reversals  . . . . . . . . . . . . 620--633
               Weihua Zheng and   
                   Kenli Li and   
                   Keqin Li and   
                 Hing Cheung So   A Modified Multiple Alignment Fast
                                  Fourier Transform with Higher Efficiency 634--645
                  Ali Ezzat and   
                Peilin Zhao and   
                     Min Wu and   
                 Xiao-Li Li and   
                Chee-Keong Kwoh   Drug-Target Interaction Prediction with
                                  Graph Regularized Matrix Factorization   646--656
              Vo Hong Thanh and   
             Roberto Zunino and   
                 Corrado Priami   Efficient Constant-Time Complexity
                                  Algorithm for Stochastic Simulation of
                                  Large Reaction Networks  . . . . . . . . 657--667
                James Arram and   
              Thomas Kaplan and   
                  Wayne Luk and   
                  Peiyong Jiang   Leveraging FPGAs for Accelerating Short
                                  Read Alignment . . . . . . . . . . . . . 668--677
                    Feng He and   
               Guanghui Zhu and   
              Yin-Ying Wang and   
             Xing-Ming Zhao and   
                De-Shuang Huang   PCID: a Novel Approach for Predicting
                                  Disease Comorbidity by Integrating
                                  Multi-Scale Data . . . . . . . . . . . . 678--686
            Xiangxiang Zeng and   
                Yuanlu Liao and   
              Yuansheng Liu and   
                       Quan Zou   Prediction and Validation of Disease
                                  Genes Using HeteSim Scores . . . . . . . 687--695
              Boris Shabash and   
                   Kay C. Wiese   RNA Visualization: Relevance and the
                                  Current State-of-the-Art Focusing on
                                  Pseudoknots  . . . . . . . . . . . . . . 696--712
                  Chen Peng and   
                          Ao Li   A Heterogeneous Network Based Method for
                                  Identifying GBM-Related Genes by
                                  Integrating Multi-Dimensional Data . . . 713--720
   Anastasiia Vasylchenkova and   
                  Miha Mraz and   
              Nikolaj Zimic and   
                    Miha Moskon   Classical Mechanics Approach Applied to
                                  Analysis of Genetic Oscillators  . . . . 721--727
           Poly H. da Silva and   
            Raphael Machado and   
              Simone Dantas and   
            Marilia D. V. Braga   Genomic Distance with High Indel Costs   728--732
                     Min Wu and   
                 Le Ou-Yang and   
                     Xiao-Li Li   Protein Complex Detection via Effective
                                  Integration of Base Clustering Solutions
                                  and Co-Complex Affinity Scores . . . . . 733--739
                 Fangfei Li and   
                      Yang Tang   Robust Reachability of Boolean Control
                                  Networks . . . . . . . . . . . . . . . . 740--745
              Zhangming Yan and   
                     Ke Liu and   
              Shunian Xiang and   
                    Zhirong Sun   txCoords: a Novel Web Application for
                                  Transcriptomic Peak Re-Mapping . . . . . 746--748

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 14, Number 4, July, 2017

                Manjari Jha and   
            Raunaq Malhotra and   
                    Raj Acharya   A Generalized Lattice Based
                                  Probabilistic Approach for Metagenomic
                                  Clustering . . . . . . . . . . . . . . . 749--761
  Sanghamitra Bandyopadhyay and   
                Koushik Mallick   A New Feature Vector Based on Gene
                                  Ontology Terms for Protein--Protein
                                  Interaction Prediction . . . . . . . . . 762--770
                Heewon Park and   
           Yuichi Shiraishi and   
                Seiya Imoto and   
                  Satoru Miyano   A Novel Adaptive Penalized Logistic
                                  Regression for Uncovering Biomarker
                                  Associated with Anti-Cancer Drug
                                  Sensitivity  . . . . . . . . . . . . . . 771--782
                  Chao Wang and   
                   Dong Dai and   
                      Xi Li and   
                  Aili Wang and   
                    Xuehai Zhou   SuperMIC: Analyzing Large Biological
                                  Datasets in Bioinformatics with Maximal
                                  Information Coefficient  . . . . . . . . 783--795
   Rao Muhammad Adeel Nawab and   
             Mark Stevenson and   
                    Paul Clough   An IR-Based Approach Utilizing Query
                                  Expansion for Plagiarism Detection in
                                  MEDLINE  . . . . . . . . . . . . . . . . 796--804
         Sugeerth Murugesan and   
        Kristopher Bouchard and   
             Jesse A. Brown and   
               Bernd Hamann and   
          William W. Seeley and   
            Andrew Trujillo and   
               Gunther H. Weber   Brain Modulyzer: Interactive Visual
                                  Analysis of Functional Brain
                                  Connectivity . . . . . . . . . . . . . . 805--818
            Sandra Barragan and   
             Cristina Rueda and   
            Miguel A. Fernandez   Circular Order Aggregation and Its
                                  Application to Cell-Cycle Genes
                                  Expressions  . . . . . . . . . . . . . . 819--829
                 Jing Zhang and   
                   Hao Wang and   
                   Wu-chun Feng   cuBLASTP: Fine-Grained Parallelization
                                  of Protein Sequence Search on CPU + GPU  830--843
                     Lu Xie and   
           Gregory R. Smith and   
               Russell Schwartz   Derivative-Free Optimization of Rate
                                  Parameters of Capsid Assembly Models
                                  from Bulk in Vitro Data  . . . . . . . . 844--855
                  Yue Zhang and   
            Yiu-ming Cheung and   
                      Bo Xu and   
                     Weifeng Su   Detection Copy Number Variants from NGS
                                  with Sparse and Smooth Constraints . . . 856--867
                Xiaofei Fan and   
                 Xian Zhang and   
                  Ligang Wu and   
                    Michael Shi   Finite-Time Stability Analysis of
                                  Reaction-Diffusion Genetic Regulatory
                                  Networks with Time-Varying Delays  . . . 868--879
       Maziyar Baran Pouyan and   
                Mehrdad Nourani   Identifying Cell Populations in Flow
                                  Cytometry Data Using Phenotypic
                                  Signatures . . . . . . . . . . . . . . . 880--891
       Anne Florence Keller and   
             Nicolas Ambert and   
            Arnaud Legendre and   
              Mathieu Bedez and   
      Jean-Marie Bouteiller and   
             Serge Bischoff and   
              Michel Baudry and   
               Saliha Moussaoui   Impact of Synaptic Localization and
                                  Subunit Composition of Ionotropic
                                  Glutamate Receptors on Synaptic
                                  Function: Modeling and Simulation
                                  Studies  . . . . . . . . . . . . . . . . 892--904
              Yuansheng Liu and   
            Xiangxiang Zeng and   
                 Zengyou He and   
                       Quan Zou   Inferring MicroRNA-Disease Associations
                                  by Random Walk on a Heterogeneous
                                  Network with Multiple Data Sources . . . 905--915
                     Min Li and   
            Zhongxiang Liao and   
                  Yiming He and   
               Jianxin Wang and   
                 Junwei Luo and   
                         Yi Pan   ISEA: Iterative Seed-Extension Algorithm
                                  for De Novo Assembly Using Paired-End
                                  Information and Insert Size Distribution 916--925
                  Tianle Ma and   
                   Aidong Zhang   Omics Informatics: From Scattered
                                  Individual Software Tools to Integrated
                                  Workflow Management Systems  . . . . . . 926--946
              Jianhua Zhang and   
                  Zhong Yin and   
                     Rubin Wang   Pattern Classification of Instantaneous
                                  Cognitive Task-load Through GMM
                                  Clustering, Laplacian Eigenmap, and
                                  Ensemble SVMs  . . . . . . . . . . . . . 947--965
                   Liang Yu and   
                  Ruidan Su and   
                Bingbo Wang and   
                 Long Zhang and   
                 Yapeng Zou and   
                 Jing Zhang and   
                        Lin Gao   Prediction of Novel Drugs for
                                  Hepatocellular Carcinoma Based on
                                  Multi-Source Random Walk . . . . . . . . 966--977
           Egils Stalidzans and   
                Ivars Mozga and   
              Jurijs Sulins and   
               Peteris Zikmanis   Search for a Minimal Set of Parameters
                                  by Assessing the Total Optimization
                                  Potential for a Dynamic Model of a
                                  Biochemical Network  . . . . . . . . . . 978--985
                 Imren Dinc and   
                 Semih Dinc and   
              Madhav Sigdel and   
            Madhu S. Sigdel and   
              Marc L. Pusey and   
               Ramazan S. Aygun   Super-Thresholding: Supervised
                                  Thresholding of Protein Crystal Images   986--998

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 14, Number 5, September, 2017

             Umit V. Catalyurek   Guest Editor's Introduction: Selected
                                  Papers from ACM-BCB 2014 . . . . . . . . 1000--1001
        Pawel Pawel Gorecki and   
            Jaroslaw Paszek and   
              Oliver Eulenstein   Unconstrained Diameters for Deep
                                  Coalescence  . . . . . . . . . . . . . . 1002--1012
               Zhiyong Wang and   
                Benika Hall and   
                   Jinbo Xu and   
                    Xinghua Shi   A Sparse Learning Framework for Joint
                                  Effect Analysis of Copy Number Variants  1013--1027
               Dan DeBlasio and   
                John Kececioglu   Learning Parameter-Advising Sets for
                                  Multiple Sequence Alignment  . . . . . . 1028--1041
                  Anna Ritz and   
              Brendan Avent and   
                   T. M. Murali   Pathway Analysis with Signaling
                                  Hypergraphs  . . . . . . . . . . . . . . 1042--1055
                Boyoung Yoo and   
         Fazle Elahi Faisal and   
                 Huili Chen and   
              Tijana Milenkovic   Improving Identification of Key Players
                                  in Aging via Network De-Noising and Core
                                  Inference  . . . . . . . . . . . . . . . 1056--1069
         Joseph G. Azofeifa and   
              Mary A. Allen and   
          Manuel E. Lladser and   
                Robin D. Dowell   An Annotation Agnostic Algorithm for
                                  Detecting Nascent RNA Transcripts in
                                  GRO-Seq  . . . . . . . . . . . . . . . . 1070--1081
            Norman Goodacre and   
             Nathan Edwards and   
             Mark Danielsen and   
                 Peter Uetz and   
                       Cathy Wu   Predicting nsSNPs that Disrupt
                                  Protein-Protein Interactions Using
                                  Docking  . . . . . . . . . . . . . . . . 1082--1093
                     Dan He and   
              Zhanyong Wang and   
               Laxmi Parida and   
                  Eleazar Eskin   IPED2: Inheritance Path Based Pedigree
                                  Reconstruction Algorithm for Complicated
                                  Pedigrees  . . . . . . . . . . . . . . . 1094--1103
            De-Shuang Huang and   
     Vitoantonio Bevilacqua and   
             M. Michael Gromiha   Guest Editorial for Special Section on
                                  the 11th International Conference on
                                  Intelligent Computing ICIC . . . . . . . 1104--1105
                 Hongjie Wu and   
                   Kun Wang and   
                   Liyao Lu and   
                     Yu Xue and   
                  Qiang Lyu and   
                      Min Jiang   Deep Conditional Random Field Approach
                                  to Transmembrane Topology Prediction and
                                  Application to GPCR Three-Dimensional
                                  Structure Modeling . . . . . . . . . . . 1106--1114
               Shu-Guang Ge and   
                Junfeng Xia and   
                    Wen Sha and   
                 Chun-Hou Zheng   Cancer Subtype Discovery Based on
                                  Integrative Model of Multigenomic Data   1115--1121
               Wenzheng Bao and   
                  Dong Wang and   
                    Yuehui Chen   Classification of Protein Structure
                                  Classes on Flexible Neutral Tree . . . . 1122--1133
              Qingfeng Chen and   
               Chaowang Lan and   
               Baoshan Chen and   
               Lusheng Wang and   
                  Jinyan Li and   
                  Chengqi Zhang   Exploring Consensus RNA Substructural
                                  Patterns Using Subgraph Mining . . . . . 1134--1146
               Su-Ping Deng and   
               Shaolong Cao and   
            De-Shuang Huang and   
                   Yu-Ping Wang   Identifying Stages of Kidney Renal Cell
                                  Carcinoma by Combining Gene Expression
                                  and DNA Methylation Data . . . . . . . . 1147--1153
                   Lin Yuan and   
                    Lin Zhu and   
                 Wei-Li Guo and   
                Xiaobo Zhou and   
               Youhua Zhang and   
              Zhenhua Huang and   
                De-Shuang Huang   Nonconvex Penalty Based Low-Rank
                                  Representation and Sparse Regression for
                                  eQTL Mapping . . . . . . . . . . . . . . 1154--1164
              Jian-Qiang Li and   
               Zhu-Hong You and   
                    Xiao Li and   
                 Zhong Ming and   
                      Xing Chen   PSPEL: In Silico Prediction of
                                  Self-Interacting Proteins from Amino
                                  Acids Sequences Using Ensemble Learning  1165--1172
                    Pu Wang and   
                 Ruiquan Ge and   
                  Xuan Xiao and   
                 Manli Zhou and   
                  Fengfeng Zhou   hMuLab: a Biomedical Hybrid MUlti-LABel
                                  Classifier Based on Multiple Linear
                                  Regression . . . . . . . . . . . . . . . 1173--1180
           Tuomo Muki-Marttunen   An Algorithm for Motif-Based Network
                                  Design . . . . . . . . . . . . . . . . . 1181--1186
                  Lichun Ma and   
              Debby D. Wang and   
                    Bin Zou and   
                       Hong Yan   An Eigen-Binding Site Based Method for
                                  the Analysis of Anti-EGFR Drug
                                  Resistance in Lung Cancer Treatment  . . 1187--1194
               Antonio dAcierno   IsAProteinDB: an Indexed Database of
                                  Trypsinized Proteins for Fast Peptide
                                  Mass Fingerprinting  . . . . . . . . . . 1195--1201

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 14, Number 6, November, 2017

             Ahmad Al Kawam and   
               Sunil Khatri and   
                Aniruddha Datta   A Survey of Software and Hardware
                                  Approaches to Performing Read Alignment
                                  in Next Generation Sequencing  . . . . . 1202--1213
                 Utku Sirin and   
                Faruk Polat and   
                    Reda Alhajj   Batch Mode TD$ \lambda $ for Controlling
                                  Partially Observable Gene Regulatory
                                  Networks . . . . . . . . . . . . . . . . 1214--1227
                 Biji C. L. and   
           Achuthsankar S. Nair   Benchmark Dataset for Whole Genome
                                  Sequence Compression . . . . . . . . . . 1228--1236
    Francisco do Nascimento and   
             Katia S. Guimaraes   Copy Number Variations Detection:
                                  Unravelling the Problem in Tangible
                                  Aspects  . . . . . . . . . . . . . . . . 1237--1250
               Stefano Ceri and   
        Abdulrahman Kaitoua and   
            Marco Masseroli and   
              Pietro Pinoli and   
                Francesco Venco   Data Management for Heterogeneous
                                  Genomic Datasets . . . . . . . . . . . . 1251--1264
            Amin Ahmadi Adl and   
              Hye-Seung Lee and   
                  Xiaoning Qian   Detecting Pairwise Interactive Effects
                                  of Continuous Random Variables for
                                  Biomarker Identification with Small
                                  Sample Size  . . . . . . . . . . . . . . 1265--1275
               Nivit Grewal and   
           Shailendra Singh and   
                   Trilok Chand   Effect of Aggregation Operators on
                                  Network-Based Disease Gene
                                  Prioritization: a Case Study on Blood
                                  Disorders  . . . . . . . . . . . . . . . 1276--1287
              Gui-Jun Zhang and   
              Xiao-Gen Zhou and   
                 Xu-Feng Yu and   
                Xiao-Hu Hao and   
                          Li Yu   Enhancing Protein Conformational Space
                                  Sampling Using Distance Profile-Guided
                                  Differential Evolution . . . . . . . . . 1288--1301
             David Aparicio and   
              Pedro Ribeiro and   
                 Fernando Silva   Extending the Applicability of Graphlets
                                  to Directed Networks . . . . . . . . . . 1302--1315
         Georgina Stegmayer and   
             Cristian Yones and   
           Laura Kamenetzky and   
                Diego H. Milone   High Class-Imbalance in pre-miRNA
                                  Prediction: a Novel Approach Based on
                                  deepSOM  . . . . . . . . . . . . . . . . 1316--1326
               Abbas Akkasi and   
                  Ekrem Varoglu   Improving Biochemical Named Entity
                                  Recognition Using PSO Classifier
                                  Selection and Bayesian Combination
                                  Methods  . . . . . . . . . . . . . . . . 1327--1338
             Arne T. Bittig and   
          Adelinde M. Uhrmacher   ML-Space: Hybrid Spatial Gillespie and
                                  Particle Simulation of Multi-Level
                                  Rule-Based Models in Cell Biology  . . . 1339--1349
                Mingon Kang and   
               Juyoung Park and   
              Dong-Chul Kim and   
            Ashis K. Biswas and   
                 Chunyu Liu and   
                       Jean Gao   Multi-Block Bipartite Graph for
                                  Integrative Genomic Analysis . . . . . . 1350--1358
            Grady Weyenberg and   
             Ruriko Yoshida and   
                    Daniel Howe   Normalizing Kernels in the
                                  Billera--Holmes--Vogtmann Treespace  . . 1359--1365
                Yuchun Ding and   
     Marie Christine Pardon and   
        Alessandra Agostini and   
                Henryk Faas and   
               Jinming Duan and   
             Wil O. C. Ward and   
            Felicity Easton and   
              Dorothee Auer and   
                         Li Bai   Novel Methods for Microglia
                                  Segmentation, Feature Extraction, and
                                  Classification . . . . . . . . . . . . . 1366--1377
               Daniel Savel and   
         Thomas LaFramboise and   
               Ananth Grama and   
                Mehmet Koyuturk   Pluribus --- Exploring the Limits of
                                  Error Correction Using a Suffix Tree . . 1378--1388
                     Jun Hu and   
                    Yang Li and   
                 Ming Zhang and   
                 Xibei Yang and   
              Hong-Bin Shen and   
                    Dong-Jun Yu   Predicting Protein-DNA Binding Residues
                                  by Weightedly Combining Sequence-Based
                                  Features and Boosting Multiple SVMs  . . 1389--1398
            Jiancheng Zhong and   
              Jianxing Wang and   
               Xiaojun Ding and   
                 Zhen Zhang and   
                     Min Li and   
              Fang-Xiang Wu and   
                         Yi Pan   Protein Inference from the Integration
                                  of Tandem MS Data and Interactome
                                  Networks . . . . . . . . . . . . . . . . 1399--1409
                  Deqing Gu and   
              Xingxing Jian and   
                Cheng Zhang and   
                      Qiang Hua   Reframed Genome-Scale Metabolic Model to
                                  Facilitate Genetic Design and
                                  Integration with Expression Data . . . . 1410--1418
              Pradipta Maji and   
                      Ekta Shah   Significance and Functional Similarity
                                  for Identification of Disease Genes  . . 1419--1433
                    Zhen Qi and   
               Eberhard O. Voit   Strategies for Comparing Metabolic
                                  Profiles: Implications for the Inference
                                  of Biochemical Mechanisms from
                                  Metabolomics Data  . . . . . . . . . . . 1434--1445
           Shahin Mohammadi and   
            David F. Gleich and   
            Tamara G. Kolda and   
                   Ananth Grama   Triangular Alignment TAME: a
                                  Tensor-Based Approach for Higher-Order
                                  Network Alignment  . . . . . . . . . . . 1446--1458
                    Yun Liu and   
                    Tao Hou and   
                  Bing Kang and   
                         Fu Liu   Unsupervised Binning of Metagenomic
                                  Assembled Contigs Using Improved Fuzzy
                                  C-Means Method . . . . . . . . . . . . . 1459--1467
                 Jiawei Luo and   
              Pingjian Ding and   
                Cheng Liang and   
                  Buwen Cao and   
                  Xiangtao Chen   Collective Prediction of
                                  Disease-Associated miRNAs Based on
                                  Transduction Learning  . . . . . . . . . 1468--1475
              Maxime Dureau and   
          Angelo Alessandri and   
         Patrizia Bagnerini and   
               Stephane Vincent   Modeling and Identification of
                                  Amnioserosa Cell Mechanical Behavior by
                                  Using Mass-Spring Lattices . . . . . . . 1476--1481
              Pietro Lovato and   
             Marco Cristani and   
                 Manuele Bicego   Soft Ngram Representation and Modeling
                                  for Protein Remote Homology Detection    1482--1488


IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 15, Number 1, January, 2018

                 Yanbo Wang and   
               Weikang Qian and   
                        Bo Yuan   A Graphical Model of Smoking-Induced
                                  Global Instability in Lung Cancer  . . . 1--14
             Jesper Jansson and   
              Ramesh Rajaby and   
               Chuanqi Shen and   
                  Wing-Kin Sung   Algorithms for the Majority Rule +
                                  Consensus Tree and the Frequency
                                  Difference Consensus Tree  . . . . . . . 15--26
                  Renu Vyas and   
               Sanket Bapat and   
                 Purva Goel and   
Muthukumarasamy Karthikeyan and   
           Sanjeev S. Tambe and   
            Bhaskar D. Kulkarni   Application of Genetic Programming GP
                                  Formalism for Building Disease
                                  Predictive Models from Protein--Protein
                                  Interactions PPI Data  . . . . . . . . . 27--37
                     Bin Hu and   
                 Xiaowei Li and   
                Shuting Sun and   
               Martyn Ratcliffe   Attention Recognition in EEG-Based
                                  Affective Learning Research Using CFS +
                                  KNN Algorithm  . . . . . . . . . . . . . 38--45
           Anton V. Ushakov and   
           Xenia Klimentova and   
                  Igor Vasilyev   Bi-level and Bi-objective $p$-Median
                                  Type Problems for Integrative
                                  Clustering: Application to Analysis of
                                  Cancer Gene-Expression and Drug-Response
                                  Data . . . . . . . . . . . . . . . . . . 46--59
         Narayanan C. Viswanath   Calculating the Expected Time to
                                  Eradicate HIV-1 Using a Markov Chain . . 60--67
     Alireza Karbalayghareh and   
         Ulisses Braga-Neto and   
               Jianping Hua and   
       Edward Russell Dougherty   Classification of State Trajectories in
                                  Gene Regulatory Networks . . . . . . . . 68--82
               Tom Hartmann and   
              An-Chiang Chu and   
          Martin Middendorf and   
                 Matthias Bernt   Combinatorics of Tandem Duplication
                                  Random Loss Mutations on Circular
                                  Genomes  . . . . . . . . . . . . . . . . 83--95
          Ademir Hujdurovic and   
                 Ursa Kacar and   
             Martin Milanic and   
               Bernard Ries and   
           Alexandru I. Tomescu   Complexity and Algorithms for Finding a
                                  Perfect Phylogeny from Mixed Tumor
                                  Samples  . . . . . . . . . . . . . . . . 96--108
                  Wei Zhang and   
                     Jia Xu and   
                Yuanyuan Li and   
                     Xiufen Zou   Detecting Essential Proteins Based on
                                  Network Topology, Gene Expression Data,
                                  and Gene Ontology Information  . . . . . 109--116
               Cinzia Pizzi and   
           Mattia Ornamenti and   
            Simone Spangaro and   
            Simona E. Rombo and   
                   Laxmi Parida   Efficient Algorithms for Sequence
                                  Analysis with Entropic Profiles  . . . . 117--128
                Hyunjin Kim and   
              Sang-Min Choi and   
                  Sanghyun Park   GSEH: a Novel Approach to Select
                                  Prostate Cancer-Associated Genes Using
                                  Gene Expression Heterogeneity  . . . . . 129--146
                 Jian Zhang and   
               Haiting Chai and   
                     Bo Gao and   
                 Guifu Yang and   
                    Zhiqiang Ma   HEMEsPred: Structure-Based
                                  Ligand-Specific Heme Binding Residues
                                  Prediction by Using Fast-Adaptive
                                  Ensemble Learning Scheme . . . . . . . . 147--156
                     Kamal Taha   Inferring the Functions of Proteins from
                                  the Interrelationships between
                                  Functional Categories  . . . . . . . . . 157--167
            Guillermo Leale and   
          Ariel Emilio Baya and   
            Diego H. Milone and   
          Pablo M. Granitto and   
             Georgina Stegmayer   Inferring Unknown Biological Function by
                                  Integration of GO Annotations and Gene
                                  Expression Data  . . . . . . . . . . . . 168--180
      Nikolaos-Kosmas Chlis and   
           Ekaterini S. Bei and   
              Michalis Zervakis   Introducing a Stable Bootstrap
                                  Validation Framework for Reliable
                                  Genomic Signature Extraction . . . . . . 181--190
             Eddie Y. T. Ma and   
      Sujeevan Ratnasingham and   
               Stefan C. Kremer   Machine Learned Replacement of
                                  $N$-Labels for Basecalled Sequences in
                                  DNA Barcoding  . . . . . . . . . . . . . 191--204
               Laura Jetten and   
                 Leo van Iersel   Nonbinary Tree-Based Phylogenetic
                                  Networks . . . . . . . . . . . . . . . . 205--217
     Daniel N. Mohsenizadeh and   
      Roozbeh Dehghannasiri and   
            Edward R. Dougherty   Optimal Objective-Based Experimental
                                  Design for Uncertain Dynamical Gene
                                  Networks with Experimental Error . . . . 218--230
           Behnam Behinaein and   
                Karen Rudie and   
                 Waheed Sangrar   Petri Net Siphon Analysis and Graph
                                  Theoretic Measures for Identifying
                                  Combination Therapies in Cancer  . . . . 231--243
               Shujaat Khan and   
               Imran Naseem and   
            Roberto Togneri and   
             Mohammed Bennamoun   RAFP-Pred: Robust Prediction of
                                  Antifreeze Proteins Using Localized
                                  Analysis of $n$-Peptide Compositions . . 244--250
                   Roman Czapla   Random Sets of Stadiums in Square and
                                  Collective Behavior of Bacteria  . . . . 251--256
      Vinicius R. P. Borges and   
Maria Cristina F. de Oliveira and   
         Thais Garcia Silva and   
Armando Augusto Henriques Vieira and   
                   Bernd Hamann   Region Growing for Segmenting Green
                                  Microalgae Images  . . . . . . . . . . . 257--270
                M. Syed Ali and   
             N. Gunasekaran and   
               Choon Ki Ahn and   
                       Peng Shi   Sampled-Data Stabilization for Fuzzy
                                  Genetic Regulatory Networks with Leakage
                                  Delays . . . . . . . . . . . . . . . . . 271--285
      Chendra Hadi Suryanto and   
               Hiroto Saigo and   
                 Kazuhiro Fukui   Structural Class Classification of $3$D
                                  Protein Structure Based on Multi-View
                                  $2$D Images  . . . . . . . . . . . . . . 286--299
                Gerd Anders and   
           Ulrich Hassiepen and   
           Stephan Theisgen and   
            Stephan Heymann and   
              Lionel Muller and   
             Tania Panigada and   
              Daniel Huster and   
             Sergey A. Samsonov   The Intrinsic Pepsin Resistance of
                                  Interleukin-8 Can Be Explained from a
                                  Combined Bioinformatical and
                                  Experimental Approach  . . . . . . . . . 300--308
                 Jiawei Luo and   
                  Wei Huang and   
                      Buwen Cao   A Novel Approach to Identify the
                                  miRNA--mRNA Causal Regulatory Modules in
                                  Cancer . . . . . . . . . . . . . . . . . 309--315
                   Feng Bao and   
                   Yue Deng and   
                   Qionghai Dai   ACID: Association Correction for
                                  Imbalanced Data in GWAS  . . . . . . . . 316--322
               Hongmei Jiao and   
                Michael Shi and   
                 Qikun Shen and   
                  Junwu Zhu and   
                       Peng Shi   Filter Design with Adaptation to
                                  Time-Delay Parameters for Genetic
                                  Regulatory Networks  . . . . . . . . . . 323--329
            Ahed Elmsallati and   
         Abdulghani Msalati and   
                   Jugal Kalita   Index-Based Network Aligner of
                                  Protein--Protein Interaction Networks    330--336
        Elizabeth S. Allman and   
            James H. Degnan and   
                 John A. Rhodes   Species Tree Inference from Gene Splits
                                  by Unrooted STAR Methods . . . . . . . . 337--342
        Frederick A. Matsen and   
             Sara C. Billey and   
                 Arnold Kas and   
              Matjaz Konvalinka   Tanglegrams: a Reduction Tool for
                                  Mathematical Phylogenetics . . . . . . . 343--349

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 15, Number 2, March, 2018

     Thiago da Silva Arruda and   
               Ulisses Dias and   
                    Zanoni Dias   A GRASP-Based Heuristic for the Sorting
                                  by Length-Weighted Inversions Problem    352--363
               Congping Lin and   
         Laurent Lemarchand and   
            Reinhardt Euler and   
                 Imogen Sparkes   Modeling the Geometry and Dynamics of
                                  the Endoplasmic Reticulum Network  . . . 377--386
           Noushin Ghaffari and   
            Osama A. Arshad and   
              Hyundoo Jeong and   
              John Thiltges and   
    Michael F. Criscitiello and   
             Byung-Jun Yoon and   
            Aniruddha Datta and   
             Charles D. Johnson   Examining De Novo Transcriptome
                                  Assemblies via a Quality Assessment
                                  Pipeline . . . . . . . . . . . . . . . . 494--505
                Mansuck Kim and   
                 Huan Zhang and   
           Charles Woloshuk and   
                Won-Bo Shim and   
                 Byung-Jun Yoon   Computational Prediction of Pathogenic
                                  Network Modules in Fusarium
                                  verticillioides  . . . . . . . . . . . . 506--515
     Arghavan Bahadorinejad and   
          Ulisses M. Braga-Neto   Optimal Fault Detection and Diagnosis in
                                  Transcriptional Circuits Using
                                  Next-Generation Sequencing . . . . . . . 516--525
               Xiaodong Cui and   
                  Lin Zhang and   
                   Jia Meng and   
             Manjeet K. Rao and   
                Yidong Chen and   
                    Yufei Huang   MeTDiff: a Novel Differential RNA
                                  Methylation Analysis for MeRIP-Seq Data  526--534
                  Yize Zhao and   
                  Jian Kang and   
                        Qi Long   Bayesian Multiresolution Variable
                                  Selection for Ultra-High Dimensional
                                  Neuroimaging Data  . . . . . . . . . . . 537--550
                   Lin Yuan and   
               Fanglin Chen and   
               Ling-Li Zeng and   
                 Lubin Wang and   
                       Dewen Hu   Gender Identification of Human Brain
                                  Image with a Novel $3$D Descriptor . . . 551--561
                    Meng Hu and   
                      Wu Li and   
                   Hualou Liang   A Copula-Based Granger Causality Measure
                                  for the Analysis of Neural Spike Train
                                  Data . . . . . . . . . . . . . . . . . . 562--569
                Lijun Zhang and   
                  Ming Wang and   
       Nicholas W. Sterling and   
              Eun-Young Lee and   
           Paul J. Eslinger and   
             Daymond Wagner and   
                Guangwei Du and   
          Mechelle M. Lewis and   
               Young Truong and   
           F. DuBois Bowman and   
                   Xuemei Huang   Cortical Thinning and Cognitive
                                  Impairment in Parkinson's Disease
                                  without Dementia . . . . . . . . . . . . 570--580
          Joao Ricardo Sato and   
        Maciel Calebe Vidal and   
  Suzana de Siqueira Santos and   
     Katlin Brauer Massirer and   
                   Andre Fujita   Complex Network Measures in Autism
                                  Spectrum Disorders . . . . . . . . . . . 581--587

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 15, Number 3, May, 2018

                   J. Handl and   
                   A. Shehu and   
              Jose Santos Reyes   Advances in the Application and
                                  Development of Non-Linear Global
                                  Optimization Techniques in Computational
                                  Structural Biology . . . . . . . . . . . 688--689
            Leonardo Correa and   
            Bruno Borguesan and   
              Camilo Farfan and   
      Mario Inostroza-Ponta and   
                    Marcio Dorn   A Memetic Algorithm for $3$D Protein
                                  Structure Prediction Problem . . . . . . 690--704
             Jiaxiang Huang and   
                Maoguo Gong and   
                       Lijia Ma   A Global Network Alignment Method Using
                                  Discrete Particle Swarm Optimization . . 705--718
             Emmanuel Sapin and   
         Kenneth A. De Jong and   
                   Amarda Shehu   From Optimization to Mapping: an
                                  Evolutionary Algorithm for Protein
                                  Energy Landscapes  . . . . . . . . . . . 719--731
            Jakub Rydzewski and   
           Rafal Jakubowski and   
           Giuseppe Nicosia and   
                  Wieslaw Nowak   Conformational Sampling of a
                                  Biomolecular Rugged Energy Landscape . . 732--739
         Matthias Leinweber and   
               Thomas Fober and   
               Bernd Freisleben   GPU-Based Point Cloud Superpositioning
                                  for Structural Comparisons of Protein
                                  Binding Sites  . . . . . . . . . . . . . 740--752
                   Jie Zhou and   
                  Yuan-Yuan Shi   A Bipartite Network and Resource
                                  Transfer-Based Approach to Infer
                                  lncRNA-Environmental Factor Associations 753--759
              Maiju Pesonen and   
          Jaakko Nevalainen and   
              Steven Potter and   
              Somnath Datta and   
                  Susmita Datta   A Combined PLS and Negative Binomial
                                  Regression Model for Inferring
                                  Association Networks from
                                  Next-Generation Sequencing Count Data    760--773
                Xiangtao Li and   
                   Ka-Chun Wong   A Comparative Study for Identifying the
                                  Chromosome-Wide Spatial Clusters from
                                  High-Throughput Chromatin Conformation
                                  Capture Data . . . . . . . . . . . . . . 774--787
                   Xin Peng and   
                  Yang Tang and   
                  Wangli He and   
                   Wenli Du and   
                      Feng Qian   A Just-in-Time Learning Based Monitoring
                                  and Classification Method for
                                  Hyper/Hypocalcemia Diagnosis . . . . . . 788--801
               Xichuan Zhou and   
                   Fan Yang and   
                 Yujie Feng and   
                     Qin Li and   
                  Fang Tang and   
               Shengdong Hu and   
                    Zhi Lin and   
                      Lei Zhang   A Spatial-Temporal Method to Detect
                                  Global Influenza Epidemics Using
                                  Heterogeneous Data Collected from the
                                  Internet . . . . . . . . . . . . . . . . 802--812
              Neslihan Avcu and   
             Nihal Pekergin and   
            Ferhan Pekergin and   
                 Cuneyt Guzelis   Aggregation for Computing Multi-Modal
                                  Stationary Distributions in $1$-D Gene
                                  Regulatory Networks  . . . . . . . . . . 813--827
                   Wei Shao and   
                Mingxia Liu and   
               Ying-Ying Xu and   
              Hong-Bin Shen and   
                 Daoqiang Zhang   An Organelle Correlation-Guided Feature
                                  Selection Approach for Classifying
                                  Multi-Label Subcellular Bio-Images . . . 828--838
               Pritha Dutta and   
              Subhadip Basu and   
               Mahantapas Kundu   Assessment of Semantic Similarity
                                  between Proteins Using Information
                                  Content and Topological Properties of
                                  the Gene Ontology Graph  . . . . . . . . 839--849
            Aurelie Pirayre and   
            Camille Couprie and   
              Laurent Duval and   
        Jean-Christophe Pesquet   BRANE Clust: Cluster-Assisted Gene
                                  Regulatory Network Inference Refinement  850--860
              Somaya Hashem and   
                Gamal Esmat and   
               Wafaa Elakel and   
            Shahira Habashy and   
          Safaa Abdel Raouf and   
          Mohamed Elhefnawi and   
            Mohamed Eladawy and   
              Mahmoud ElHefnawi   Comparison of Machine Learning
                                  Approaches for Prediction of Advanced
                                  Liver Fibrosis in Chronic Hepatitis C
                                  Patients . . . . . . . . . . . . . . . . 861--868
                Sumanta Ray and   
                  Ujjwal Maulik   Discovering Perturbation of Modular
                                  Structure in HIV Progression by
                                  Integrating Multiple Data Sources
                                  Through Non-Negative Matrix
                                  Factorization  . . . . . . . . . . . . . 869--877
                Aseel Awdeh and   
              Hilary Phenix and   
                  Mads Karn and   
            Theodore J. Perkins   Dynamics in Epistasis Analysis . . . . . 878--891
                Tiantian He and   
               Keith C. C. Chan   Evolutionary Graph Clustering for
                                  Protein Complex Identification . . . . . 892--904
               Najmul Ikram and   
       Muhammad Abdul Qadir and   
          Muhammad Tanvir Afzal   Investigating Correlation between
                                  Protein Sequence Similarity and Semantic
                                  Similarity Using Gene Ontology
                                  Annotations  . . . . . . . . . . . . . . 905--912
                    Lin Zhu and   
              Hong-Bo Zhang and   
                De-Shuang Huang   LMMO: a Large Margin Approach for
                                  Refining Regulatory Motifs . . . . . . . 913--925
                Pedro Alves and   
                 Shuang Liu and   
               Daifeng Wang and   
                  Mark Gerstein   Multiple-Swarm Ensembles: Improving the
                                  Predictive Power and Robustness of
                                  Predictive Models and Its Use in
                                  Computational Biology  . . . . . . . . . 926--933
  Samira Fotoohifiroozabadi and   
        Mohd Saberi Mohamad and   
                   Safaai Deris   NAHAL-Flex: a Numerical and Alphabetical
                                  Hinge Detection Algorithm for Flexible
                                  Protein Structure Alignment  . . . . . . 934--943
                 Wenwen Min and   
                   Juan Liu and   
                   Shihua Zhang   Network-Regularized Sparse Logistic
                                  Regression Models for Clinical Risk
                                  Prediction and Biomarker Discovery . . . 944--953
              Davide Chicco and   
          Fernando Palluzzi and   
                Marco Masseroli   Novelty Indicator for Enhanced
                                  Prioritization of Predicted Gene
                                  Ontology Annotations . . . . . . . . . . 954--965
                Zoya Khalid and   
            Osman Ugur Sezerman   Prediction of HIV Drug Resistance by
                                  Combining Sequence and Structural
                                  Properties . . . . . . . . . . . . . . . 966--973
               Jin-Xing Liu and   
                  Dong Wang and   
              Ying-Lian Gao and   
             Chun-Hou Zheng and   
                    Yong Xu and   
                       Jiguo Yu   Regularized Non-Negative Matrix
                                  Factorization for Identifying
                                  Differentially Expressed Genes and
                                  Clustering Samples: a Survey . . . . . . 974--987
               Junhua Zhang and   
                   Shihua Zhang   The Discovery of Mutated Driver Pathways
                                  in Cancer: Models and Algorithms . . . . 988--998
                   Bin Wang and   
              Xuedong Zheng and   
                Shihua Zhou and   
              Changjun Zhou and   
               Xiaopeng Wei and   
                Qiang Zhang and   
                       Ziqi Wei   Constructing DNA Barcode Sets Based on
                                  Particle Swarm Optimization  . . . . . . 999--1002
               Carl Poirier and   
            Benoit Gosselin and   
                   Paul Fortier   DNA Assembly with de Bruijn Graphs Using
                                  an FPGA Platform . . . . . . . . . . . . 1003--1009
              Ruth Davidson and   
              MaLyn Lawhorn and   
             Joseph Rusinko and   
                     Noah Weber   Efficient Quartet Representations of
                                  Trees and Applications to Supertree and
                                  Summary Methods  . . . . . . . . . . . . 1010--1015
             Xianpeng Liang and   
                    Lin Zhu and   
                De-Shuang Huang   Optimization of Gene Set Annotations
                                  Using Robust Trace-Norm Multitask
                                  Learning . . . . . . . . . . . . . . . . 1016--1021
                Chengyu Liu and   
            Rainer Lehtonen and   
              Sampsa Hautaniemi   PerPAS: Topology-Based Single Sample
                                  Pathway Analysis Method  . . . . . . . . 1022--1027
Abolfazl Doostparast Torshizi and   
                  Linda Petzold   Sparse Pathway-Induced Dynamic Network
                                  Biomarker Discovery for Early Warning
                                  Signal Detection in Complex Diseases . . 1028--1034
                  Wei Zhang and   
                     Jia Xu and   
                Yuanyuan Li and   
                     Xiufen Zou   Correction to ``Detecting Essential
                                  Proteins Based on Network Topology, Gene
                                  Expression Data, and Gene Ontology
                                  Information''  . . . . . . . . . . . . . 1035--1035

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 15, Number 4, July, 2018

                   T. M. Murali   Guest Editorial  . . . . . . . . . . . . 1036--1036
              Asish Ghoshal and   
                Jinyi Zhang and   
            Michael A. Roth and   
           Kevin Muyuan Xia and   
            Ananth Y. Grama and   
                Somali Chaterji   A Distributed Classifier for MicroRNA
                                  Target Prediction with Validation
                                  Through TCGA Expression Data . . . . . . 1037--1051
                   Shi Qiao and   
       Mehmet Koyutürk and   
      Meral Z. Özsoyo\uglu   Querying of Disparate Association and
                                  Interaction Data in Biomedical
                                  Applications . . . . . . . . . . . . . . 1052--1065
            Alexej Gossmann and   
               Shaolong Cao and   
             Damian Brzyski and   
              Lan-Juan Zhao and   
              Hong-Wen Deng and   
                   Yu-Ping Wang   A Sparse Regression Method for
                                  Group-Wise Feature Selection with False
                                  Discovery Rate Control . . . . . . . . . 1066--1078
              Md Abdul Alim and   
                   Ahmet Ay and   
          Md Mahmudul Hasan and   
                 My T. Thai and   
                  Tamer Kahveci   Construction of Signaling Pathways with
                                  RNAi Data and Multiple Reference
                                  Networks . . . . . . . . . . . . . . . . 1079--1091
                Xiaodan Fan and   
                 Xinglai Ji and   
                      Rui Jiang   Guest Editorial for Special Section on
                                  the Sixth National Conference on
                                  Bioinformatics and System Biology of
                                  China  . . . . . . . . . . . . . . . . . 1092--1092
          Mahdi Zamanighomi and   
           Mostafa Zamanian and   
             Michael Kimber and   
                  Zhengdao Wang   Gene Regulatory Network Inference from
                                  Perturbed Time-Series Expression Data
                                  via Ordered Dynamical Expansion of
                                  Non-Steady State Actors  . . . . . . . . 1093--1106
                     Ke Liu and   
                    Sha Hou and   
                Junbiao Dai and   
                    Zhirong Sun   PyMut: a Web Tool for Overlapping Gene
                                  Loss-of-Function Mutation Design . . . . 1107--1110
             Xiangfei Cheng and   
                    Yue Hou and   
                  Yumin Nie and   
                 Yiru Zhang and   
                 Huan Huang and   
                 Hongde Liu and   
                       Xiao Sun   Nucleosome Positioning of Intronless
                                  Genes in the Human Genome  . . . . . . . 1111--1121
              Ezio Bartocci and   
                 Pietro Lio and   
                Nicola Paoletti   Guest Editors' Introduction to the
                                  Special Section on the 14th
                                  International Conference on
                                  Computational Methods in Systems Biology
                                  CMSB 2016  . . . . . . . . . . . . . . . 1122--1123
               Jerome Feret and   
                   Kim Quyen Ly   Local Traces: an Over-Approximation of
                                  the Behavior of the Proteins in
                                  Rule-Based Models  . . . . . . . . . . . 1124--1137
      François Fages and   
           Thierry Martinez and   
       David A. Rosenblueth and   
                Sylvain Soliman   Influence Networks Compared with
                                  Reaction Networks: Semantics,
                                  Expressivity and Attractors  . . . . . . 1138--1151
                 Chunyan Mu and   
             Peter Dittrich and   
               David Parker and   
               Jonathan E. Rowe   Organisation-Oriented Coarse Graining
                                  and Refinement of Stochastic Reaction
                                  Networks . . . . . . . . . . . . . . . . 1152--1166
                   Loic Pauleve   Reduction of Qualitative Models of
                                  Biological Networks for Transient
                                  Dynamics Analysis  . . . . . . . . . . . 1167--1179
       Michael Backenkohler and   
            Luca Bortolussi and   
                    Verena Wolf   Moment-Based Parameter Estimation for
                                  Stochastic Reaction Networks in
                                  Equilibrium  . . . . . . . . . . . . . . 1180--1192
    Alejandro F. Villaverde and   
               Kolja Becker and   
                 Julio R. Banga   PREMER: a Tool to Infer Biological
                                  Networks . . . . . . . . . . . . . . . . 1193--1202
             Andrzej Mizera and   
                   Jun Pang and   
                     Cui Su and   
                     Qixia Yuan   \sf ASSA-PBN: a Toolbox for
                                  Probabilistic Boolean Networks . . . . . 1203--1216
             Eugen Czeizler and   
                Kai-Chiu Wu and   
            Cristian Gratie and   
           Krishna Kanhaiya and   
                      Ion Petre   Structural Target Controllability of
                                  Linear Networks  . . . . . . . . . . . . 1217--1228
          Tijana Milenkovic and   
           Sarath Chandra Janga   Great Lakes Bioinformatics Conference
                                  GLBIO 2015 Special Section Editorial . . 1229--1230
             James B. Pease and   
         Benjamin K. Rosenzweig   Encoding Data Using Biological
                                  Principles: The Multisample Variant
                                  Format for Phylogenomics and Population
                                  Genomics . . . . . . . . . . . . . . . . 1231--1238
                  Adam Roth and   
        Sandeep Subramanian and   
       Madhavi K. Ganapathiraju   Towards Extracting Supporting
                                  Information About Predicted
                                  Protein-Protein Interactions . . . . . . 1239--1246
            Satwica Yerneni and   
             Ishita K. Khan and   
                   Qing Wei and   
                 Daisuke Kihara   IAS: Interaction Specific GO Term
                                  Associations for Predicting
                                  Protein-Protein Interaction Networks . . 1247--1258
   Seyedsasan Hashemikhabir and   
                    Ran Xia and   
                 Yang Xiang and   
           Sarath Chandra Janga   A Framework for Identifying Genotypic
                                  Information from Clinical Records:
                                  Exploiting Integrated Ontology
                                  Structures to Transfer Annotations
                                  between ICD Codes and Gene Ontologies    1259--1269
              Pranjal Patra and   
               Tatsuo Izawa and   
          Lourdes Pena-Castillo   REPA: Applying Pathway Analysis to
                                  Genome-Wide Transcription Factor Binding
                                  Data . . . . . . . . . . . . . . . . . . 1270--1283
         Rodrigo F. Ramalho and   
                   Sujun Li and   
          Predrag Radivojac and   
                Matthew W. Hahn   Proteomic Evidence for In-Frame and
                                  Out-of-Frame Alternatively Spliced
                                  Isoforms in Human and Mouse  . . . . . . 1284--1289
              Rami Al-Ouran and   
             Robert Schmidt and   
               Ashwini Naik and   
              Jeffrey Jones and   
                Frank Drews and   
               David Juedes and   
             Laura Elnitski and   
                   Lonnie Welch   Discovering Gene Regulatory Elements
                                  Using Coverage-Based Heuristics  . . . . 1290--1300
              Liliana Ironi and   
               Ettore Lanzarone   A Model-Based Tool for the Analysis and
                                  Design of Gene Regulatory Networks . . . 1301--1314
               Chun-Qiu Xia and   
                     Ke Han and   
                    Yong Qi and   
                 Yang Zhang and   
                    Dong-Jun Yu   A Self-Training Subspace Clustering
                                  Algorithm under Low-Rank Representation
                                  for Cancer Classification on Gene
                                  Expression Data  . . . . . . . . . . . . 1315--1324
                   Xinyu He and   
                Lishuang Li and   
                   Yang Liu and   
                Xiaoming Yu and   
                       Jun Meng   A Two-Stage Biomedical Event Trigger
                                  Detection Method Integrating Feature
                                  Selection and Word Embeddings  . . . . . 1325--1332
               Iman Deznabi and   
           Mohammad Mobayen and   
             Nazanin Jafari and   
               Oznur Tastan and   
                    Erman Ayday   An Inference Attack on Genomic Data
                                  Using Kinship, Complex Correlations, and
                                  Phenotype Information  . . . . . . . . . 1333--1343
                   Qian Xie and   
                 Xiaoyan He and   
                Fangji Yang and   
                 Xuling Liu and   
                    Ying Li and   
                 Yujing Liu and   
             ZhengMeng Yang and   
                 Jianhai Yu and   
                  Bao Zhang and   
                       Wei Zhao   Analysis of the Genome Sequence and
                                  Prediction of B-Cell Epitopes of the
                                  Envelope Protein of Middle East
                                  Respiratory Syndrome-Coronavirus . . . . 1344--1350
                Yoram Zarai and   
          Michael Margaliot and   
          Eduardo D. Sontag and   
                   Tamir Tuller   Controllability Analysis and Control
                                  Synthesis for the Ribosome Flow Model    1351--1364
                Shangce Gao and   
             Shuangbao Song and   
               Jiujun Cheng and   
                  Yuki Todo and   
                   MengChu Zhou   Incorporation of Solvent Effect into
                                  Multi-Objective Evolutionary Algorithm
                                  for Improved Protein Structure
                                  Prediction . . . . . . . . . . . . . . . 1365--1378
       Karlene Nicole Meyer and   
              Michelle R. Lacey   Modeling Methylation Patterns with Long
                                  Read Sequencing Data . . . . . . . . . . 1379--1389
                 Guoxian Yu and   
               Guangyuan Fu and   
                   Jun Wang and   
                   Yingwen Zhao   NewGOA: Predicting New GO Annotations of
                                  Proteins by Bi-Random Walks on a Hybrid
                                  Graph  . . . . . . . . . . . . . . . . . 1390--1402

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 15, Number 5, September, 2018

                Erman Ayday and   
             Xiaoqian Jiang and   
                  Bradley Malin   GenoPri'16: International Workshop on
                                  Genome Privacy and Security  . . . . . . 1403--1404
             Michael Backes and   
             Pascal Berrang and   
            Mathias Humbert and   
                Xiaoyu Shen and   
                    Verena Wolf   Simulating the Large-Scale Erosion of
                                  Genomic Privacy Over Time  . . . . . . . 1405--1412
         Jean Louis Raisaro and   
              Gwangbae Choi and   
         Sylvain Pradervand and   
           Raphael Colsenet and   
        Nathalie Jacquemont and   
              Nicolas Rosat and   
             Vincent Mooser and   
             Jean-Pierre Hubaux   Protecting Privacy and Security of
                                  Genomic Data in i2b2 with Homomorphic
                                  Encryption and Differential Privacy  . . 1413--1426
               Dan Bogdanov and   
                 Liina Kamm and   
                  Sven Laur and   
                     Ville Sokk   Implementation and Evaluation of an
                                  Algorithm for Cryptographically Private
                                  Principal Component Analysis on Genomic
                                  Data . . . . . . . . . . . . . . . . . . 1427--1432
            De-Shuang Huang and   
     Vitoantonio Bevilacqua and   
             M. Michael Gromiha   Guest Editorial for Special Section on
                                  the 12th International Conference on
                                  Intelligent Computing ICIC . . . . . . . 1433--1435
            A. Kulandaisamy and   
           Ambuj Srivastava and   
              Pradeep Kumar and   
               R. Nagarajan and   
             S. Binny Priya and   
             M. Michael Gromiha   Identification and Analysis of Key
                                  Residues in Protein-RNA Complexes  . . . 1436--1444
                 Hongjie Wu and   
              Chengyuan Cao and   
                Xiaoyan Xia and   
                       Qiang Lu   Unified Deep Learning Architecture for
                                  Modeling Biology Sequence  . . . . . . . 1445--1452
               Wenzheng Bao and   
              Chang-An Yuan and   
               Youhua Zhang and   
              Kyungsook Han and   
             Asoke K. Nandi and   
                Barry Honig and   
                De-Shuang Huang   Mutli-Features Prediction of Protein
                                  Translational Modification Sites . . . . 1453--1460
                   Wook Lee and   
              Byungkyu Park and   
                  Kyungsook Han   Sequence-Based Prediction of Putative
                                  Transcription Factor Binding Sites in
                                  DNA Sequences of Any Length  . . . . . . 1461--1469
                 Xiaoli Lin and   
                 Xiaolong Zhang   Prediction of Hot Regions in PPIs Based
                                  on Improved Local Community Structure
                                  Detecting  . . . . . . . . . . . . . . . 1470--1479
               Su-Ping Deng and   
                 Wenxing Hu and   
           Vince D. Calhoun and   
                   Yu-Ping Wang   Integrating Imaging Genomic Data in the
                                  Quest for Biomarkers of Schizophrenia
                                  Disease  . . . . . . . . . . . . . . . . 1480--1491
               Giulia Russo and   
             Marzio Pennisi and   
          Roberta Boscarino and   
           Francesco Pappalardo   Continuous Petri Nets and microRNA
                                  Analysis in Melanoma . . . . . . . . . . 1492--1499
                   Jian Liu and   
                 Yuhu Cheng and   
               Xuesong Wang and   
                Xiaoluo Cui and   
                    Yi Kong and   
                     Junping Du   Low Rank Subspace Clustering via
                                  Discrete Constraint and Hypergraph
                                  Regularization for Tumor Molecular
                                  Pattern Discovery  . . . . . . . . . . . 1500--1512
               Lusheng Wang and   
             Shuai Cheng Li and   
            Yi-Ping Phoebe Chen   Guest Editorial for the 15th Asia
                                  Pacific Bioinformatics Conference  . . . 1513--1514
            Jaroslaw Paszek and   
                  Pawel Gorecki   Efficient Algorithms for Genomic
                                  Duplication Models . . . . . . . . . . . 1515--1524
             Andrzej Mizera and   
                   Jun Pang and   
                     Qixia Yuan   Reviving the Two-State Markov Chain
                                  Approach . . . . . . . . . . . . . . . . 1525--1537
                   Shuai An and   
                   Jun Wang and   
                     Jinmao Wei   Local-Nearest-Neighbors-Based Feature
                                  Weighting for Gene Selection . . . . . . 1538--1548
                  Nan Jiang and   
                 Wenge Rong and   
                  Yifan Nie and   
                Yikang Shen and   
                    Zhang Xiong   Biological Event Trigger Identification
                                  with Noise Contrastive Estimation  . . . 1549--1559
              Manuel Lafond and   
              Cedric Chauve and   
           Nadia El-Mabrouk and   
                Aida Ouangraoua   Gene Tree Construction and Correction
                                  Using SuperTree and Reconciliation . . . 1560--1570
       Agnieszka Mykowiecka and   
             Pawel Szczesny and   
                  Pawel Gorecki   Inferring Gene-Species Assignments in
                                  the Presence of Horizontal Gene Transfer 1571--1578
                  Yue Zhang and   
             Chunfang Zheng and   
                  David Sankoff   Evolutionary Model for the Statistical
                                  Divergence of Paralogous and Orthologous
                                  Gene Pairs Generated by Whole Genome
                                  Duplication and Speciation . . . . . . . 1579--1584
               Tom Hartmann and   
            Nicolas Wieseke and   
               Roded Sharan and   
          Martin Middendorf and   
                 Matthias Bernt   Genome Rearrangement with ILP  . . . . . 1585--1593
           Nafiseh Sedaghat and   
              Mahmood Fathy and   
Mohammad Hossein Modarressi and   
                    Ali Shojaie   Combining Supervised and Unsupervised
                                  Learning for Improved miRNA Target
                                  Prediction . . . . . . . . . . . . . . . 1594--1604
               Safwat Hamad and   
              Ahmed Elhadad and   
                   Amal Khalifa   DNA Watermarking Using Codon Postfix
                                  Technique  . . . . . . . . . . . . . . . 1605--1610
    Jorge E. Duarte-Sanchez and   
       Jaime Velasco-Medina and   
                Pedro A. Moreno   Hardware Accelerator for the
                                  Multifractal Analysis of DNA Sequences   1611--1624
                 Nha Nguyen and   
                      An Vo and   
                 Haibin Sun and   
                     Heng Huang   Heavy-Tailed Noise Suppression and
                                  Derivative Wavelet Scalogram for
                                  Detecting DNA Copy Number Aberrations    1625--1635
                  Xiaoke Ma and   
               Penggang Sun and   
                     Guimin Qin   Identifying Condition-Specific Modules
                                  by Clustering Multiple Networks  . . . . 1636--1648
                    Jin Liu and   
               Jianxin Wang and   
               Zhenjun Tang and   
                     Bin Hu and   
              Fang-Xiang Wu and   
                         Yi Pan   Improving Alzheimer's Disease
                                  Classification by Combining Multiple
                                  Measures . . . . . . . . . . . . . . . . 1649--1659
                  Shuai Ren and   
                    Yan Shi and   
                 Maolin Cai and   
                     Weiqing Xu   Influence of Airway Secretion on Airflow
                                  Dynamics of Mechanical Ventilated
                                  Respiratory System . . . . . . . . . . . 1660--1668
              Vipin Vijayan and   
              Tijana Milenkovic   Multiple Network Alignment via
                                  MultiMAGNA++ . . . . . . . . . . . . . . 1669--1682
               Chunjiang Yu and   
                  Wentao Wu and   
                  Jing Wang and   
                  Yuxin Lin and   
                       Yang and   
                Jiajia Chen and   
                    Fei Zhu and   
                   Bairong Shen   NGS-FC: a Next-Generation Sequencing
                                  Data Format Converter  . . . . . . . . . 1683--1691
                 Hasan M. Jamil   Optimizing Phylogenetic Queries for
                                  Performance  . . . . . . . . . . . . . . 1692--1705
                    Min Liu and   
                     Yue He and   
                 Weili Qian and   
                Yangliu Wei and   
                    Xiaoyan Liu   Cell Population Tracking in a Honeycomb
                                  Structure Using an IMM Filter Based $3$D
                                  Local Graph Matching Model . . . . . . . 1706--1717
                 Shifu Chen and   
                   Ming Liu and   
               Xiaoni Zhang and   
                Renwen Long and   
                Yixing Wang and   
                    Yue Han and   
               Shiwei Zhang and   
                 Mingyan Xu and   
                         Jia Gu   A Study of Cell-Free DNA Fragmentation
                                  Pattern and Its Application in DNA
                                  Sample Type Classification . . . . . . . 1718--1722
              Pawel Gorecki and   
              Oliver Eulenstein   Bijective Diameters of Gene Tree
                                  Parsimony Costs  . . . . . . . . . . . . 1723--1727
                 Youyuan Li and   
                Yingping Zhuang   fmpRPMF: a Web Implementation for
                                  Protein Identification by Robust Peptide
                                  Mass Fingerprinting  . . . . . . . . . . 1728--1731
   Jorge Gonzalez-Dominguez and   
                Maria J. Martin   MPIGeneNet: Parallel Calculation of Gene
                                  Co-Expression Networks on Multicore
                                  Clusters . . . . . . . . . . . . . . . . 1732--1737
         Shubhanshu Shekhar and   
             Sebastien Roch and   
                Siavash Mirarab   Species Tree Estimation Using ASTRAL:
                                  How Many Genes Are Enough? . . . . . . . 1738--1747

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 15, Number 6, November, 2018

               Tianhai Tian and   
                 Jingshan Huang   Guest Editorial for Special Section on
                                  BIBM 2015  . . . . . . . . . . . . . . . 1752--1753
              Yu-Chiao Chiu and   
             Tzu-Hung Hsiao and   
                 Li-Ju Wang and   
                Yidong Chen and   
                 Eric Y. Chuang   Analyzing Differential Regulatory
                                  Networks Modulated by Continuous-State
                                  Genomic Features in Glioblastoma
                                  Multiforme . . . . . . . . . . . . . . . 1754--1764
                     Bin Hu and   
              Yongqiang Dai and   
                     Yun Su and   
               Philip Moore and   
              Xiaowei Zhang and   
             Chengsheng Mao and   
                  Jing Chen and   
                       Lixin Xu   Feature Selection for Optimized
                                  High-Dimensional Biomedical Data Using
                                  an Improved Shuffled Frog Leaping
                                  Algorithm  . . . . . . . . . . . . . . . 1765--1773
                    Wei Lan and   
               Jianxin Wang and   
                     Min Li and   
                    Jin Liu and   
              Fang-Xiang Wu and   
                         Yi Pan   Predicting MicroRNA-Disease Associations
                                  Based on Improved MicroRNA and Disease
                                  Similarities . . . . . . . . . . . . . . 1774--1782
           Tatiana Maximova and   
                Erion Plaku and   
                   Amarda Shehu   Structure-Guided Protein Transition
                                  Modeling with a Probabilistic Roadmap
                                  Algorithm  . . . . . . . . . . . . . . . 1783--1796
                      Bo Xu and   
                Hongfei Lin and   
                   Yuan Lin and   
                 Yunlong Ma and   
                 Liang Yang and   
                  Jian Wang and   
                    Zhihao Yang   Improve Biomedical Information Retrieval
                                  Using Modified Learning to Rank Methods  1797--1809
               Hongbo Zhang and   
                    Lin Zhu and   
                De-Shuang Huang   DiscMLA: an Efficient Discriminative
                                  Motif Learning Algorithm over
                                  High-Throughput Datasets . . . . . . . . 1810--1820
                        Sun Kim   Editorial for Selected Papers of a Joint
                                  Conferences, Genome Informatics
                                  Workshop/International Conference on
                                  Bioinformatics GIW/InCoB 2015  . . . . . 1821--1821
               Osamu Hirose and   
          Shotaro Kawaguchi and   
          Terumasa Tokunaga and   
               Yu Toyoshima and   
          Takayuki Teramoto and   
                Sayuri Kuge and   
           Takeshi Ishihara and   
                Yuichi Iino and   
                    Ryo Yoshida   SPF-CellTracker: Tracking Multiple Cells
                                  with Strongly-Correlated Moves Using a
                                  Spatial Particle Filter  . . . . . . . . 1822--1831
             Zhanzhan Cheng and   
              Shuigeng Zhou and   
                  Yang Wang and   
                    Hui Liu and   
                Jihong Guan and   
            Yi-Ping Phoebe Chen   Effectively Identifying Compound-Protein
                                  Interactions by Learning from Positive
                                  and Unlabeled Examples . . . . . . . . . 1832--1843
            Hamid D. Ismail and   
               Hiroto Saigo and   
                    Dukka B. KC   RF-NR: Random Forest Based Approach for
                                  Improved Classification of Nuclear
                                  Receptors  . . . . . . . . . . . . . . . 1844--1852
            Takeyuki Tamura and   
                     Wei Lu and   
             Jiangning Song and   
                 Tatsuya Akutsu   Computing Minimum Reaction Modifications
                                  in a Boolean Metabolic Network . . . . . 1853--1862
                   Ying Tan and   
                      Yuhui Shi   Special Section on Swarm-Based
                                  Algorithms and Applications in
                                  Computational Biology and Bioinformatics 1863--1864
                    Ben Niu and   
                   Jing Liu and   
                  Teresa Wu and   
               Xianghua Chu and   
               Zhengxu Wang and   
                     Yanmin Liu   Coevolutionary
                                  Structure-Redesigned-Based Bacterial
                                  Foraging Optimization  . . . . . . . . . 1865--1876
                    Biao Xu and   
                 Yong Zhang and   
                Dunwei Gong and   
                  Yinan Guo and   
                      Miao Rong   Environment Sensitivity-Based
                                  Cooperative Co-Evolutionary Algorithms
                                  for Dynamic Multi-Objective Optimization 1877--1890
                 Yi-Nan Guo and   
                 Jian Cheng and   
                    Sha Luo and   
                Dunwei Gong and   
                         Yu Xue   Robust Dynamic Multi-Objective Vehicle
                                  Routing Optimization Method  . . . . . . 1891--1903
                  Weian Guo and   
               Chengyong Si and   
                     Yu Xue and   
                 Yanfen Mao and   
                   Lei Wang and   
                        Qidi Wu   A Grouping Particle Swarm Optimizer with
                                  Personal-Best-Position Guidance for
                                  Large Scale Optimization . . . . . . . . 1904--1915
                   Chao Gao and   
              Mingxin Liang and   
                Xianghua Li and   
                 Zili Zhang and   
                  Zhen Wang and   
                     Zhili Zhou   Network Community Detection Based on the
                                  Physarum-Inspired Computational
                                  Framework  . . . . . . . . . . . . . . . 1916--1928
            Andres Iglesias and   
               Akemi Galvez and   
                 Andreina Avila   Immunological Approach for Full NURBS
                                  Reconstruction of Outline Curves from
                                  Noisy Data Points in Medical Imaging . . 1929--1942
                Qirong Tang and   
                    Lu Ding and   
                Fangchao Yu and   
                 Yuan Zhang and   
                 Yinghao Li and   
                       Haibo Tu   Swarm Robots Search for Multiple Targets
                                  Based on an Improved Grouping Strategy   1943--1950
                    Xin Gao and   
               Jake Y. Chen and   
               Mohammed J. Zaki   Multiscale and Multimodal Analysis for
                                  Computational Biology  . . . . . . . . . 1951--1952
            Miguel Monteiro and   
       Ana Catarina Fonseca and   
         Ana Teresa Freitas and   
        Teresa Pinho e Melo and   
     Alexandre P. Francisco and   
              Jose M. Ferro and   
            Arlindo L. Oliveira   Using Machine Learning to Improve the
                                  Prediction of Functional Outcome in
                                  Ischemic Stroke Patients . . . . . . . . 1953--1959
                 Annie Wang and   
                Hansaim Lim and   
             Shu-Yuan Cheng and   
                        Lei Xie   ANTENNA, a Multi-Rank, Multi-Layered
                                  Recommender System for Inferring
                                  Reliable Drug-Gene-Disease Associations:
                                  Repurposing Diazoxide as a Targeted
                                  Anti-Cancer Therapy  . . . . . . . . . . 1960--1967
              Haishuai Wang and   
               Zhicheng Cui and   
                 Yixin Chen and   
             Michael Avidan and   
          Arbi Ben Abdallah and   
              Alexander Kronzer   Predicting Hospital Readmission via
                                  Cost-Sensitive Deep Learning . . . . . . 1968--1978
              Ahmed Halioui and   
             Petko Valtchev and   
        Abdoulaye Banire Diallo   Bioinformatic Workflow Extraction from
                                  Scientific Texts based on Word Sense
                                  Disambiguation . . . . . . . . . . . . . 1979--1990
              Zongliang Yue and   
          Michael T. Neylon and   
               Thanh Nguyen and   
            Timothy Ratliff and   
                   Jake Y. Chen   ``Super Gene Set'' Causal Relationship
                                  Discovery from Functional Genomics Data  1991--1998
             Meshari Alazmi and   
                Ahmed Abbas and   
               Xianrong Guo and   
                   Ming Fan and   
                   Lihua Li and   
                        Xin Gao   A Slice-based $^{13}$C-detected NMR Spin
                                  System Forming and Resonance Assignment
                                  Method . . . . . . . . . . . . . . . . . 1999--2008
             Kavitha Mukund and   
             Samuel R. Ward and   
          Richard L. Lieber and   
            Shankar Subramaniam   Co-Expression Network Approach to
                                  Studying the Effects of Botulinum
                                  Neurotoxin-A . . . . . . . . . . . . . . 2009--2016
          Daniel P. Martins and   
     Michael Taynnan Barros and   
      Massimiliano Pierobon and   
Meenakshisundaram Kandhavelu and   
                Pietro Lio' and   
     Sasitharan Balasubramaniam   Computational Models for Trapping Ebola
                                  Virus Using Engineered Bacteria  . . . . 2017--2027
                  Juntao Li and   
               Wenpeng Dong and   
                    Deyuan Meng   Grouped Gene Selection of Cancer via
                                  Adaptive Sparse Group Lasso Based on
                                  Conditional Mutual Information . . . . . 2028--2038
                 Ho-Chun Wu and   
               Xi-Guang Wei and   
                Shing-Chow Chan   Novel Consensus Gene Selection Criteria
                                  for Distributed GPU Partial Least
                                  Squares-Based Gene Microarray Analysis
                                  in Diffused Large B Cell Lymphoma DLBCL
                                  and Related Findings . . . . . . . . . . 2039--2052
              Surama Biswas and   
             Sriyankar Acharyya   A Bi-Objective RNN Model to Reconstruct
                                  Gene Regulatory Network: a Modified
                                  Multi-Objective Simulated Annealing
                                  Approach . . . . . . . . . . . . . . . . 2053--2059
       Warith Eddine Djeddi and   
            Sadok Ben Yahia and   
         Engelbert Mephu Nguifo   A Novel Computational Approach for
                                  Global Alignment for Multiple Biological
                                  Networks . . . . . . . . . . . . . . . . 2060--2066
            Martin C. Frith and   
           Anish M. S. Shrestha   A Simplified Description of Child Tables
                                  for Sequence Similarity Search . . . . . 2067--2073
                    Xizhe Zhang   Altering Indispensable Proteins in
                                  Controlling Directed Human Protein
                                  Interaction Network  . . . . . . . . . . 2074--2078
                    Ting Xu and   
                 Le Ou-Yang and   
                 Xiaohua Hu and   
                 Xiao-Fei Zhang   Identifying Gene Network Rewiring by
                                  Integrating Gene Expression and Gene
                                  Network Data . . . . . . . . . . . . . . 2079--2085
               Hongmei Jiao and   
               Liping Zhang and   
                 Qikun Shen and   
                  Junwu Zhu and   
                       Peng Shi   Robust Gene Circuit Control Design for
                                  Time-Delayed Genetic Regulatory Networks
                                  Without SUM Regulatory Logic . . . . . . 2086--2093
               Nina Luhmann and   
              Cedric Chauve and   
                 Jens Stoye and   
                 Roland Wittler   Scaffolding of Ancient Contigs and
                                  Ancestral Reconstruction in a
                                  Phylogenetic Framework . . . . . . . . . 2094--2100


IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 16, Number 1, January, 2019

        Yoshihiro Yamanishi and   
        Yasubumi Sakakibara and   
            Yi-Ping Phoebe Chen   Guest Editorial for the 16th Asia
                                  Pacific Bioinformatics Conference  . . . 1--2
             Kouichi Kimura and   
                    Asako Koike   Parallel Computation of the
                                  Burrows--Wheeler Transform of Short
                                  Reads Using Prefix Parallelism . . . . . 3--13
               Jordan Haack and   
                  Eli Zupke and   
             Andrew Ramirez and   
                Yi-Chieh Wu and   
            Ran Libeskind-Hadas   Computing the Diameter of the Space of
                                  Maximum Parsimony Reconciliations in the
                                  Duplication--Transfer--Loss Model  . . . 14--22
                Romeo Rizzi and   
              Massimo Cairo and   
               Veli Makinen and   
       Alexandru I. Tomescu and   
              Daniel Valenzuela   Hardness of Covering Alignment: Phase
                                  Transition in Post-Sequence Genomics . . 23--30
             Andrzej Mizera and   
                   Jun Pang and   
                Hongyang Qu and   
                     Qixia Yuan   Taming Asynchrony for Attractor
                                  Detection in Large Boolean Networks  . . 31--42
              Tiancong Wang and   
                         Bin Ma   Adjacent Y-Ion Ratio Distributions and
                                  Its Application in Peptide Sequencing    43--51
               Tom Hartmann and   
             Matthias Bernt and   
              Martin Middendorf   An Exact Algorithm for Sorting by
                                  Weighted Preserving Genome
                                  Rearrangements . . . . . . . . . . . . . 52--62
                     Lei Li and   
                Mukul S. Bansal   An Integrated Reconciliation Framework
                                  for Domain, Gene, and Species Level
                                  Evolution  . . . . . . . . . . . . . . . 63--76
            Yuhei Nishiyama and   
      Aleksandar Shurbevski and   
          Hiroshi Nagamochi and   
                 Tatsuya Akutsu   Resource Cut, a New Bounding Procedure
                                  to Algorithms for Enumerating Tree-Like
                                  Chemical Graphs  . . . . . . . . . . . . 77--90
               Bairong Shen and   
             Xiaoqian Jiang and   
                  Xingming Zhao   Modeling and Simulation Studies of
                                  Complex Biological Systems for Precision
                                  Medicine and Healthcare  . . . . . . . . 91--92
            Md Nazmus Sadat and   
           Md Momin Al Aziz and   
             Noman Mohammed and   
                  Feng Chen and   
             Xiaoqian Jiang and   
                    Shuang Wang   SAFETY: Secure gwAs in Federated
                                  Environment through a hYbrid Solution    93--102
             Chengsheng Mao and   
                  Yuan Zhao and   
                Mengxin Sun and   
                       Yuan Luo   Are My EHRs Private Enough? Event-Level
                                  Privacy Protection . . . . . . . . . . . 103--112
               Yichen Jiang and   
                Jenny Hamer and   
             Chenghong Wang and   
             Xiaoqian Jiang and   
                  Miran Kim and   
               Yongsoo Song and   
                  Yuhou Xia and   
             Noman Mohammed and   
            Md Nazmus Sadat and   
                    Shuang Wang   SecureLR: Secure Logistic Regression
                                  Model via a Hybrid Cryptographic
                                  Protocol . . . . . . . . . . . . . . . . 113--123
               Mengmeng Sun and   
                   Tao Ding and   
               Xu-Qing Tang and   
                      Yu Keming   An Efficient Mixed-Model for Screening
                                  Differentially Expressed Genes of Breast
                                  Cancer Based on LR--RF . . . . . . . . . 124--130
               Wenliang Zhu and   
                Xiaohe Chen and   
                   Yan Wang and   
                    Lirong Wang   Arrhythmia Recognition and
                                  Classification Using ECG Morphology and
                                  Segment Feature Analysis . . . . . . . . 131--138
                Zexian Zeng and   
                    Yu Deng and   
                  Xiaoyu Li and   
            Tristan Naumann and   
                       Yuan Luo   Natural Language Processing for
                                  EHR-Based Computational Phenotyping  . . 139--153
              Yin-Ying Wang and   
               Chunfeng Cui and   
                   Liqun Qi and   
                   Hong Yan and   
                 Xing-Ming Zhao   DrPOCS: Drug Repositioning Based on
                                  Projection Onto Convex Sets  . . . . . . 154--162
                  Dewu Ding and   
                       Xiao Sun   A Comparative Study of Network Motifs in
                                  the Integrated Transcriptional
                                  Regulation and Protein Interaction
                                  Networks of \bionameShewanella . . . . . 163--171
                  Juan Wang and   
               Jin-Xing Liu and   
             Chun-Hou Zheng and   
               Ya-Xuan Wang and   
            Xiang-Zhen Kong and   
                 Chang-Gang Wen   A Mixed-Norm Laplacian Regularized
                                  Low-Rank Representation Method for Tumor
                                  Samples Clustering . . . . . . . . . . . 172--182
              Sushmita Paul and   
                Dhanajit Brahma   An Integrated Approach for
                                  Identification of Functionally Similar
                                  MicroRNAs in Colorectal Cancer . . . . . 183--192
     Alireza Karbalayghareh and   
         Ulisses Braga-Neto and   
            Edward R. Dougherty   Classification of Single-Cell Gene
                                  Expression Trajectories from Incomplete
                                  and Noisy Data . . . . . . . . . . . . . 193--207
               Kin-On Cheng and   
              Ngai-Fong Law and   
                    Wan-Chi Siu   Clustering-Based Compression for
                                  Population DNA Sequences . . . . . . . . 208--221
                   Ping Luo and   
               Li-Ping Tian and   
                Jishou Ruan and   
                  Fang-Xiang Wu   Disease Gene Prediction by Integrating
                                  PPI Networks, Clinical RNA-Seq Data and
                                  OMIM Data  . . . . . . . . . . . . . . . 222--232
                  Cheng Yan and   
               Jianxin Wang and   
                    Peng Ni and   
                    Wei Lan and   
              Fang-Xiang Wu and   
                         Yi Pan   DNRLMF--MDA: Predicting microRNA-Disease
                                  Associations Based on Similarities of
                                  microRNAs and Diseases . . . . . . . . . 233--243
                 Ronghui Ju and   
                 Chenhui Hu and   
                   Pan Zhou and   
                   Quanzheng Li   Early Diagnosis of Alzheimer's Disease
                                  Based on Resting-State Brain Networks
                                  and Deep Learning  . . . . . . . . . . . 244--257
     Paola Pesantez-Cabrera and   
            Ananth Kalyanaraman   Efficient Detection of Communities in
                                  Biological Bipartite Networks  . . . . . 258--271
                Xiangtao Li and   
                   Ka-Chun Wong   Elucidating Genome-Wide Protein-RNA
                                  Interactions Using Differential
                                  Evolution  . . . . . . . . . . . . . . . 272--282
                 Xuan Zhang and   
                   Quan Zou and   
    Alfonso Rodriguez-Paton and   
                Xiangxiang Zeng   Meta-Path Methods for Prioritizing
                                  Candidate Disease miRNAs . . . . . . . . 283--291
                    Bin Liu and   
                Junjie Chen and   
                Mingyue Guo and   
                  Xiaolong Wang   Protein Remote Homology Detection and
                                  Fold Recognition Based on Sequence-Order
                                  Frequency Matrix . . . . . . . . . . . . 292--300
               Minghan Chen and   
            Brandon D. Amos and   
            Layne T. Watson and   
              John J. Tyson and   
                  Young Cao and   
        Clifford A. Shaffer and   
         Michael W. Trosset and   
                 Cihan Oguz and   
                 Gisella Kakoti   Quasi-Newton Stochastic Optimization
                                  Algorithm for Parameter Estimation of a
                                  Stochastic Model of the Budding Yeast
                                  Cell Cycle . . . . . . . . . . . . . . . 301--311
                  Cheng Liu and   
                   Hau San Wong   Structured Penalized Logistic Regression
                                  for Gene Selection in Gene Expression
                                  Data Analysis  . . . . . . . . . . . . . 312--321
     Andres F. Lopez-Lopera and   
            Mauricio A. Alvarez   Switched Latent Force Models for
                                  Reverse-Engineering Transcriptional
                                  Regulation in Gene Expression Data . . . 322--335
                 Jiao Zhang and   
                  Sam Kwong and   
                   Ka-Chun Wong   ToBio: Global Pathway Similarity Search
                                  Based on Topological and Biological
                                  Features . . . . . . . . . . . . . . . . 336--349

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 16, Number 2, March, 2019

              Shuigeng Zhou and   
        Yi-Ping Phoebe Chen and   
              Hiroshi Mamitsuka   Editorial  . . . . . . . . . . . . . . . 350--351
               Xiaojun Chen and   
            Joshua Z. Huang and   
                 Qingyao Wu and   
                       Min Yang   Subspace Weighting Co-Clustering of Gene
                                  Expression Data  . . . . . . . . . . . . 352--364
                    Bo Tian and   
                 Qiong Duan and   
                   Can Zhao and   
                   Ben Teng and   
                     Zengyou He   Reinforce: an Ensemble Approach for
                                  Inferring PPI Network from AP--MS Data   365--376
                     Bin Xu and   
                Jihong Guan and   
                  Yang Wang and   
                     Zewei Wang   Essential Protein Detection by Random
                                  Walk on Weighted Protein--Protein
                                  Interaction Networks . . . . . . . . . . 377--387
                Weiping Sun and   
                     Yi Liu and   
            Gills A. Lajoie and   
                     Bin Ma and   
                 Kaizhong Zhang   An Improved Approach for $N$-Linked
                                  Glycan Structure Identification from HCD
                                  MS/MS Spectra  . . . . . . . . . . . . . 388--395
               Jingpu Zhang and   
               Zuping Zhang and   
               Zhigang Chen and   
                       Lei Deng   Integrating Multiple Heterogeneous
                                  Networks for Novel LncRNA-Disease
                                  Association Inference  . . . . . . . . . 396--406
               Zuping Zhang and   
               Jingpu Zhang and   
                   Chao Fan and   
               Yongjun Tang and   
                       Lei Deng   KATZLGO: Large-Scale Prediction of
                                  LncRNA Functions by Using the KATZ
                                  Measure Based on Multiple Networks . . . 407--416
                     Min Li and   
              Ruiqing Zheng and   
                 Yaohang Li and   
              Fang-Xiang Wu and   
                   Jianxin Wang   MGT--SM: a Method for Constructing
                                  Cellular Signal Transduction Networks    417--424
             Shaoliang Peng and   
                 Yingbo Cui and   
               Shunyun Yang and   
                   Wenhe Su and   
               Xiaoyu Zhang and   
           Tenglilang Zhang and   
                 Weiguo Liu and   
                 Xing-Ming Zhao   A CPU--MIC Collaborated Parallel
                                  Framework for GROMACS on Tianhe-2
                                  Supercomputer  . . . . . . . . . . . . . 425--433
                  Jie Zhang and   
                Zhigen Zhao and   
                  Kai Zhang and   
                        Zhi Wei   A Feature Sampling Strategy for Analysis
                                  of High Dimensional Genomic Data . . . . 434--441
                  Kefei Liu and   
                 Jieping Ye and   
                  Yang Yang and   
                    Li Shen and   
                      Hui Jiang   A Unified Model for Joint Normalization
                                  and Differential Gene Expression
                                  Detection in RNA-Seq Data  . . . . . . . 442--454
                  Wei Zhang and   
                   Shu-Lin Wang   An Integrated Framework for Identifying
                                  Mutated Driver Pathway and Cancer
                                  Progression  . . . . . . . . . . . . . . 455--464
                Tim Michels and   
               Dimitri Berh and   
                   Xiaoyi Jiang   An RJMCMC-Based Method for Tracking and
                                  Resolving Collisions of
                                  \bionameDrosophila Larvae  . . . . . . . 465--474
                   Lu Zhang and   
                Qiuping Pan and   
                   Yue Wang and   
                  Xintao Wu and   
                    Xinghua Shi   Bayesian Network Construction and
                                  Genotype-Phenotype Inference Using GWAS
                                  Statistics . . . . . . . . . . . . . . . 475--489
               Koyel Mandal and   
                Rosy Sarmah and   
     Dhruba Kumar Bhattacharyya   Biomarker Identification for Cancer
                                  Disease Using Biclustering Approach: an
                                  Empirical Study  . . . . . . . . . . . . 490--509
          Jakob L. Andersen and   
            Christoph Flamm and   
              Daniel Merkle and   
               Peter F. Stadler   Chemical Transformation Motifs ---
                                  Modelling Pathways as Integer Hyperflows 510--523
              Shahin Boluki and   
 Mohammad Shahrokh Esfahani and   
              Xiaoning Qian and   
            Edward R. Dougherty   Constructing Pathway-Based Priors within
                                  a Gaussian Mixture Model for Bayesian
                                  Regression and Classification  . . . . . 524--537
               Huanan Zhang and   
                  David Roe and   
                      Rui Kuang   Detecting Population-Differentiation
                                  Copy Number Variants in Human Population
                                  Tree by Sparse Group Selection . . . . . 538--549
             Claudia Caudai and   
           Emanuele Salerno and   
             Monica Zopp\`e and   
                 Anna Tonazzini   Estimation of the Spatial Chromatin
                                  Structure Based on a Multiresolution
                                  Bead-Chain Model . . . . . . . . . . . . 550--559
               Bilal Nizami and   
Elham Mousavinezhad Sarasia and   
         Mehbub I. K. Momin and   
            Bahareh Honarparvar   Estrogenic Active Stilbene Derivatives
                                  as Anti-Cancer Agents: a DFT and QSAR
                                  Study  . . . . . . . . . . . . . . . . . 560--568
            Biing-Feng Wang and   
                     Chih-Yu Li   Fast Algorithms for Computing
                                  Path-Difference Distances  . . . . . . . 569--582
                Mathias Foo and   
                Jongrae Kim and   
                Declan G. Bates   Modelling and Control of Gene Regulatory
                                  Networks for Perturbation Mitigation . . 583--595
              Son P. Nguyen and   
                  Zhaoyu Li and   
                    Dong Xu and   
                       Yi Shang   New Deep Learning Methods for Protein
                                  Loop Modeling  . . . . . . . . . . . . . 596--606
                    Yun Niu and   
                 Hongmei Wu and   
                     Yuwei Wang   Protein-Protein Interaction
                                  Identification Using a
                                  Similarity-Constrained Graph Model . . . 607--616
              Leena Salmela and   
           Alexandru I. Tomescu   Safely Filling Gaps with Partial
                                  Solutions Common to All Solutions  . . . 617--626
Fernando López-Caamal and   
              Heinrich J. Huber   Stable IL-$ 1 \beta 1 \beta $-Activation
                                  in an Inflammasome Signalling Model
                                  Depends on Positive and Negative
                                  Feedbacks and Tight Regulation of
                                  Protein Production . . . . . . . . . . . 627--637
                Amir Najafi and   
         Sepehr Janghorbani and   
    Seyed Abolfazl Motahari and   
               Emad Fatemizadeh   Statistical Association Mapping of
                                  Population-Structured Genetic Data . . . 638--649
                Xiaohui Lin and   
                  Xin Huang and   
                  Lina Zhou and   
                 Weijie Ren and   
                   Jun Zeng and   
                Weihong Yao and   
                  Xingyuan Wang   The Robust Classification Model Based on
                                  Combinatorial Features . . . . . . . . . 650--657
                Mingfu Shao and   
                 Carl Kingsford   Theory and A Heuristic for the Minimum
                                  Path Flow Decomposition Problem  . . . . 658--670
             Florian Kaiser and   
                   Dirk Labudde   Unsupervised Discovery of Geometrically
                                  Common Structural Motifs and Long-Range
                                  Contacts in Protein $3$D Structures  . . 671--680

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 16, Number 3, May, 2019

         Carlos Martin-Vide and   
       Miguel A. Vega-Rodriguez   Algorithms for Computational Biology:
                                  Third Edition  . . . . . . . . . . . . . 701--702
             Syed Ali Ahmed and   
                  Saad Mneimneh   Gibbs/MCMC Sampling for Multiple RNA
                                  Interaction with Sub-Optimal Solutions   703--712
       Agnieszka Mykowiecka and   
                  Pawel Gorecki   Credibility of Evolutionary Events in
                                  Gene Trees . . . . . . . . . . . . . . . 713--726
              David Sankoff and   
             Chunfang Zheng and   
                  Yue Zhang and   
              Joao Meidanis and   
                 Eric Lyons and   
                    Haibao Tang   Models for Similarity Distributions of
                                  Syntenic Homologs and Applications to
                                  Phylogenomics  . . . . . . . . . . . . . 727--737
               Laura Urbini and   
          Blerina Sinaimeri and   
           Catherine Matias and   
             Marie-France Sagot   Exploring the Robustness of the
                                  Parsimonious Reconciliation Method in
                                  Host-Symbiont Cophylogeny  . . . . . . . 738--748
            De-Shuang Huang and   
     Vitoantonio Bevilacqua and   
             M. Michael Gromiha   Guest Editorial for Special Section on
                                  the 13th International Conference on
                                  Intelligent Computing ICIC . . . . . . . 749--750
     Jyotsna Talreja Wassan and   
               Haiying Wang and   
               Fiona Browne and   
                    Huiru Zheng   A Comprehensive Study on Predicting
                                  Functional Role of Metagenomes Using
                                  Machine Learning Methods . . . . . . . . 751--763
                     Min Li and   
                    Li Tang and   
            Zhongxiang Liao and   
                 Junwei Luo and   
              Fang-Xiang Wu and   
                     Yi Pan and   
                   Jianxin Wang   A Novel Scaffolding Algorithm Based on
                                  Contig Error Correction and Path
                                  Extension  . . . . . . . . . . . . . . . 764--773
             Xiaolong Zhang and   
                 Xiaoli Lin and   
                 Jiafu Zhao and   
             Qianqian Huang and   
                         Xin Xu   Efficiently Predicting Hot Spots in PPIs
                                  by Combining Random Forest and Synthetic
                                  Minority Over-Sampling Technique . . . . 774--781
                   Lin Yuan and   
                Le-Hang Guo and   
              Chang-An Yuan and   
               Youhua Zhang and   
              Kyungsook Han and   
             Asoke K. Nandi and   
                Barry Honig and   
                De-Shuang Huang   Integration of Multi-Omics Data for Gene
                                  Regulatory Network Inference and
                                  Application to Breast Cancer . . . . . . 782--791
               Su-Ping Deng and   
                     Wei-Li Guo   Identifying Key Genes of Liver Cancer by
                                  Networking of Multiple Data Sets . . . . 792--800
                    Peng Wu and   
                      Dong Wang   Classification of a DNA Microarray for
                                  Diagnosing Cancer Using a Complex
                                  Network Based Method . . . . . . . . . . 801--808
               Zhu-Hong You and   
             Wen-Zhun Huang and   
              Shanwen Zhang and   
                Yu-An Huang and   
              Chang-Qing Yu and   
                     Li-Ping Li   An Efficient Ensemble Learning Approach
                                  for Predicting Protein-Protein
                                  Interactions by Integrating Protein
                                  Primary Sequence and Evolutionary
                                  Information  . . . . . . . . . . . . . . 809--817
                  Hua Zhong and   
                  Mingzhou Song   A Fast Exact Functional Test for
                                  Directional Association and Cancer
                                  Biology Applications . . . . . . . . . . 818--826
            Sandip Samaddar and   
            Rituparna Sinha and   
                    Rajat K. De   A Model for Distributed Processing and
                                  Analyses of NGS Data under Map-Reduce
                                  Paradigm . . . . . . . . . . . . . . . . 827--840
               Dongdong Sun and   
               Minghui Wang and   
                          Ao Li   A Multimodal Deep Neural Network for
                                  Human Breast Cancer Prognosis Prediction
                                  by Integrating Multi-Dimensional Data    841--850
           Michiel Van Dyck and   
      Xavier Woot de Trixhe and   
               An Vermeulen and   
                   Wim Vanroose   A Robust Simulator for Physiologically
                                  Structured Population Models . . . . . . 851--864
             Maryam Sharifi and   
           Arta A. Jamshidi and   
      Nazanin Namazi Sarvestani   An Adaptive Robust Control Strategy in a
                                  Cancer Tumor-Immune System Under
                                  Uncertainties  . . . . . . . . . . . . . 865--873
                Loris Nanni and   
             Sheryl Brahnam and   
            Stefano Ghidoni and   
              Alessandra Lumini   Bioimage Classification with Handcrafted
                                  and Learned Features . . . . . . . . . . 874--885
                Haoyu Cheng and   
                 Yong Zhang and   
                         Yun Xu   BitMapper2: a GPU-Accelerated All-Mapper
                                  Based on the Sparse $q$-Gram Index . . . 886--897
              Chris Whidden and   
            Frederick A. Matsen   Calculating the Unrooted Subtree
                                  Prune-and-Regraft Distance . . . . . . . 898--911
                   Pei Wang and   
                Daojie Wang and   
                       Jinhu Lu   Controllability Analysis of a Gene
                                  Network for \bionameArabidopsis thaliana
                                  Reveals Characteristics of Functional
                                  Gene Families  . . . . . . . . . . . . . 912--924
                Sven Thiele and   
               Sandra Heise and   
        Wiebke Hessenkemper and   
            Hannes Bongartz and   
             Melissa Fensky and   
               Fred Schaper and   
                  Steffen Klamt   Designing Optimal Experiments to
                                  Discriminate Interaction Graph Models    925--935
               Yi-Yan Zhang and   
                     Qin Li and   
                     Yi Xin and   
                      Wei-Qi Lv   Differentiating Prostate Cancer from
                                  Benign Prostatic Hyperplasia Using PSAD
                                  Based on Machine Learning: Single-Center
                                  Retrospective Study in China . . . . . . 936--941
         Dimitrios Kaloudas and   
            Nikolet Pavlova and   
              Robert Penchovsky   EBWS: Essential Bioinformatics Web
                                  Services for Sequence Analyses . . . . . 942--953
                      Bo Xu and   
                Hongfei Lin and   
                       Yuan Lin   Learning to Refine Expansion Terms for
                                  Biomedical Information Retrieval Using
                                  Semantic Resources . . . . . . . . . . . 954--966
                Tiantian He and   
               Keith C. C. Chan   Measuring Boundedness for Protein
                                  Complex Identification in PPI Networks   967--979
                 Aiguo Wang and   
                    Ye Chen and   
                    Ning An and   
                  Jing Yang and   
                    Lian Li and   
                     Lili Jiang   Microarray Missing Value Imputation: a
                                  Regularized Local Learning Method  . . . 980--993
                   You Song and   
                  Siyu Yang and   
                     Jinzhi Lei   ParaCells: a GPU Architecture for
                                  Cell-Centered Models in Computational
                                  Biology  . . . . . . . . . . . . . . . . 994--1006
Mohammad Nazrul Ishlam Patoary and   
               Carl Tropper and   
         Robert A. McDougal and   
               Zhongwei Lin and   
              William W. Lytton   Parallel Stochastic Discrete Event
                                  Simulation of Calcium Dynamics in Neuron 1007--1019
                  Chao Fang and   
                   Yi Shang and   
                        Dong Xu   Prediction of Protein Backbone Torsion
                                  Angles Using Deep Residual Inception
                                  Neural Networks  . . . . . . . . . . . . 1020--1028
               Gregor Urban and   
                Kevin Bache and   
             Duc T. T. Phan and   
               Agua Sobrino and   
       Alexander K. Shmakov and   
        Stephanie J. Hachey and   
   Christopher C. W. Hughes and   
                   Pierre Baldi   Deep Learning for Drug Discovery and
                                  Cancer Research: Automated Analysis of
                                  Vascularization Images . . . . . . . . . 1029--1035
        Kumar Saurabh Singh and   
      Bartlomiej J. Troczka and   
           Katherine Beadle and   
             Linda M. Field and   
          T. G. Emyr Davies and   
       Martin S. Williamson and   
                 Ralf Nauen and   
                     Chris Bass   Extension of Partial Gene Transcripts by
                                  Iterative Mapping of RNA-Seq Raw Reads   1036--1041
                Jia-Juan Tu and   
                 Le Ou-Yang and   
                 Xiaohua Hu and   
                 Xiao-Fei Zhang   Inferring Gene Network Rewiring by
                                  Combining Gene Expression and Gene
                                  Mutation Data  . . . . . . . . . . . . . 1042--1048

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 16, Number 4, July, 2019

           Aisharjya Sarkar and   
               Yuanfang Ren and   
              Rasha Elhesha and   
                  Tamer Kahveci   A New Algorithm for Counting Independent
                                  Motifs in Probabilistic Networks . . . . 1049--1062
              Alexey Markin and   
              Oliver Eulenstein   Computing Manhattan Path-Difference
                                  Median Trees: a Practical Local Search
                                  Approach . . . . . . . . . . . . . . . . 1063--1076
               Misagh Kordi and   
                Mukul S. Bansal   Exact Algorithms for
                                  Duplication-Transfer-Loss Reconciliation
                                  with Non-Binary Gene Trees . . . . . . . 1077--1090
             Priyanka Ghosh and   
            Ananth Kalyanaraman   FastEtch: a Fast Sketch-Based Assembler
                                  for Genomes  . . . . . . . . . . . . . . 1091--1106
           Olivia Choudhury and   
         Ankush Chakrabarty and   
                Scott J. Emrich   Highly Accurate and Efficient
                                  Data-Driven Methods for Genotype
                                  Imputation . . . . . . . . . . . . . . . 1107--1116
                   Tony Pan and   
              Patrick Flick and   
                Chirag Jain and   
               Yongchao Liu and   
                 Srinivas Aluru   Kmerind: a Flexible Parallel Library for
                                  $K$-mer Indexing of Biological Sequences
                                  on Distributed Memory Systems  . . . . . 1117--1131
            Enrico Siragusa and   
             Niina Haiminen and   
               Filippo Utro and   
                   Laxmi Parida   Linear Time Algorithms to Construct
                                  Populations Fitting Multiple Constraint
                                  Distributions at Genomic Scales  . . . . 1132--1142
              Deeptak Verma and   
           Gevorg Grigoryan and   
           Chris Bailey-Kellogg   Pareto Optimization of Combinatorial
                                  Mutagenesis Libraries  . . . . . . . . . 1143--1153
            Muhibur Rasheed and   
             Nathan Clement and   
          Abhishek Bhowmick and   
            Chandrajit L. Bajaj   Statistical Framework for Uncertainty
                                  Quantification in Computational
                                  Molecular Modeling . . . . . . . . . . . 1154--1167
                 Wenruo Bai and   
             Jeffrey Bilmes and   
               William S. Noble   Submodular Generalized Matching for
                                  Peptide Identification in Tandem Mass
                                  Spectrometry . . . . . . . . . . . . . . 1168--1181
                   Quan Zou and   
                         Qi Liu   Advanced Machine Learning Techniques for
                                  Bioinformatics . . . . . . . . . . . . . 1182--1183
                Qinhu Zhang and   
                    Lin Zhu and   
                De-Shuang Huang   High-Order Convolutional Neural Network
                                  Architecture for Predicting DNA-Protein
                                  Binding Sites  . . . . . . . . . . . . . 1184--1192
                     Min Li and   
                 Zhihui Fei and   
                   Min Zeng and   
              Fang-Xiang Wu and   
                 Yaohang Li and   
                     Yi Pan and   
                   Jianxin Wang   Automated ICD-9 Coding via A Deep
                                  Learning Approach  . . . . . . . . . . . 1193--1202
                    Bin Liu and   
                      Shumin Li   ProtDet-CCH: Protein Remote Homology
                                  Detection by Combining Long Short-Term
                                  Memory and Ranking Methods . . . . . . . 1203--1210
              Bingqiang Liu and   
                   Ling Han and   
              Xiangrong Liu and   
                 Jichang Wu and   
                         Qin Ma   Computational Prediction of Sigma-54
                                  Promoters in Bacterial Genomes by
                                  Integrating Motif Finding and Machine
                                  Learning Strategies  . . . . . . . . . . 1211--1218
                 Hongyu Liu and   
           Qinmin Vivian Hu and   
                       Liang He   Term-Based Personalization for Feature
                                  Selection in Clinical Handover Form
                                  Auto-Filling . . . . . . . . . . . . . . 1219--1230
                     Ran Su and   
                 Huichen Wu and   
                      Bo Xu and   
               Xiaofeng Liu and   
                       Leyi Wei   Developing a Multi-Dose Computational
                                  Model for Drug-Induced Hepatotoxicity
                                  Prediction Based on Toxicogenomics Data  1231--1239
                   Liang Yu and   
                        Lin Gao   Human Pathway-Based Disease Network  . . 1240--1249
                Mahdi Imani and   
          Ulisses M. Braga-Neto   Control of Gene Regulatory Networks
                                  Using Bayesian Inverse Reinforcement
                                  Learning . . . . . . . . . . . . . . . . 1250--1261
              Feng-Biao Guo and   
                 Xinglai Ji and   
                     Jian Huang   Guest Editorial for Special Section on
                                  the 7th National Conference on
                                  Bioinformatics and Systems Biology of
                                  China  . . . . . . . . . . . . . . . . . 1262--1263
                   Leyi Wei and   
               Pengwei Xing and   
                 Gaotao Shi and   
                Zhiliang Ji and   
                       Quan Zou   Fast Prediction of Protein Methylation
                                  Sites Using a Sequence-Based Feature
                                  Selection Technique  . . . . . . . . . . 1264--1273
                    Yan Lin and   
              Fa-Zhan Zhang and   
                    Kai Xue and   
                Yi-Zhou Gao and   
                  Feng-Biao Guo   Identifying Bacterial Essential Genes
                                  Based on a Feature-Integrated Method . . 1274--1279
                    Yan Shi and   
                Bolun Zhang and   
                 Maolin Cai and   
                     Weiqing Xu   Coupling Effect of Double Lungs on a VCV
                                  Ventilator with Automatic Secretion
                                  Clearance Function . . . . . . . . . . . 1280--1287
                    Ying Li and   
                      Ye He and   
                   Siyu Han and   
                  Yanchun Liang   Identification and Functional Inference
                                  for Tumor-Associated Long Non-Coding RNA 1288--1301
             Jun-Ping Zhang and   
                     Yi Liu and   
                    Wei Sun and   
             Xiao-Yang Zhao and   
                      La Ta and   
                  Wei-Sheng Guo   Characteristics of Myosin V Processivity 1302--1308
              Pengmian Feng and   
                Zhenyi Wang and   
                      Xiaoyu Yu   Predicting Antimicrobial Peptides by
                                  Using Increment of Diversity with
                                  Quadratic Discriminant Analysis Method   1309--1312
                Guoshi Chai and   
                     Min Yu and   
                 Lixu Jiang and   
               Yaocong Duan and   
                     Jian Huang   HMMCAS: a Web Tool for the
                                  Identification and Domain Annotations of
                                  CAS Proteins . . . . . . . . . . . . . . 1313--1315
                    Hao Lin and   
             Zhi-Yong Liang and   
                   Hua Tang and   
                       Wei Chen   Identifying Sigma70 Promoters with Novel
                                  Pseudo Nucleotide Composition  . . . . . 1316--1321
                Erman Ayday and   
            Muhammad Naveed and   
                     Haixu Tang   GenoPri'17: International Workshop on
                                  Genome Privacy and Security  . . . . . . 1322--1323
                 Alexander Senf   End-to-End Security for Local and Remote
                                  Human Genetic Data Applications at the
                                  EGA  . . . . . . . . . . . . . . . . . . 1324--1327
         Jean Louis Raisaro and   
Juan Ramon Troncoso-Pastoriza and   
            Mickael Misbach and   
              Joao Sa Sousa and   
         Sylvain Pradervand and   
         Edoardo Missiaglia and   
          Olivier Michielin and   
                 Bryan Ford and   
             Jean-Pierre Hubaux   MedCo: Enabling Secure and
                                  Privacy-Preserving Exploration of
                                  Distributed Clinical and Genomic Data    1328--1341
             Dixie B. Baker and   
         Bartha M. Knoppers and   
              Mark Phillips and   
        David van Enckevort and   
             Petra Kaufmann and   
           Hanns Lochmuller and   
              Domenica Taruscio   Privacy-Preserving Linkage of Genomic
                                  and Clinical Data Sets . . . . . . . . . 1342--1348
               Jake Weidman and   
             William Aurite and   
                Jens Grossklags   On Sharing Intentions, and Personal and
                                  Interdependent Privacy Considerations
                                  for Genetic Data: a Vignette Study . . . 1349--1361
             Ion I. Mandoiu and   
                Pavel Skums and   
           Alexander Zelikovsky   Guest Editors' Introduction to the
                                  Special Section on Bioinformatics
                                  Research and Applications  . . . . . . . 1362--1363
               Nina Luhmann and   
              Manuel Lafond and   
          Annelyse Thevenin and   
            Aida Ouangraoua and   
             Roland Wittler and   
                  Cedric Chauve   The SCJ Small Parsimony Problem for
                                  Weighted Gene Adjacencies  . . . . . . . 1364--1373
              Alexey Markin and   
              Oliver Eulenstein   Efficient Local Search for Euclidean
                                  Path-Difference Median Trees . . . . . . 1374--1385
                     Min Li and   
                    Peng Ni and   
               Xiaopei Chen and   
               Jianxin Wang and   
              Fang-Xiang Wu and   
                         Yi Pan   Construction of Refined Protein
                                  Interaction Network for Predicting
                                  Essential Proteins . . . . . . . . . . . 1386--1397
   Roman Sergeevich Sergeev and   
           Ivan S. Kavaliou and   
   Uladzislau V. Sataneuski and   
          Andrei Gabrielian and   
             Alex Rosenthal and   
        Michael Tartakovsky and   
           Alexander V. Tuzikov   Genome-Wide Analysis of MDR and XDR
                                  Tuberculosis from Belarus:
                                  Machine-Learning Approach  . . . . . . . 1398--1408

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 16, Number 5, September, 2019

               Amarda Shehu and   
             Giuseppe Pozzi and   
                  Tamer Kahveci   Guest Editorial for the ACM
                                  International Conference on
                                  Bioinformatics, Computational Biology,
                                  and Health Informatics . . . . . . . . . 1409--1409
            Paola Bonizzoni and   
          Simone Ciccolella and   
      Gianluca Della Vedova and   
                  Mauricio Soto   Does Relaxing the Infinite Sites
                                  Assumption Give Better Tumor
                                  Phylogenies? An ILP-Based Comparative
                                  Approach . . . . . . . . . . . . . . . . 1410--1423
                Alan Cleary and   
      Thiruvarangan Ramaraj and   
             Indika Kahanda and   
                Joann Mudge and   
                  Brendan Mumey   Exploring Frequented Regions in
                                  Pan-Genomic Graphs . . . . . . . . . . . 1424--1435
              Sunyoung Kwon and   
                   Sungroh Yoon   End-to-End Representation Learning for
                                  Chemical-Chemical Interaction Prediction 1436--1447
               Laraib Malik and   
                      Rob Patro   Rich Chromatin Structure Prediction from
                                  Hi-C Data  . . . . . . . . . . . . . . . 1448--1458
              Alexey Markin and   
              Oliver Eulenstein   Cophenetic Median Trees  . . . . . . . . 1459--1470
                     Lu Zhu and   
             Ralf Hofestadt and   
                   Martin Ester   Tissue-Specific Subcellular Localization
                                  Prediction Using Multi-Label Markov
                                  Random Fields  . . . . . . . . . . . . . 1471--1482
                Thuc Duy Le and   
                  Tao Hoang and   
                 Jiuyong Li and   
                    Lin Liu and   
                 Huawen Liu and   
                         Shu Hu   A Fast PC Algorithm for High Dimensional
                                  Causal Discovery with Multi-Core PCs . . 1483--1495
             Pieter Meysman and   
                 Yvan Saeys and   
            Ehsan Sabaghian and   
           Wout Bittremieux and   
           Yves Van de Peer and   
              Bart Goethals and   
                   Kris Laukens   Mining the Enriched Subgraphs for
                                  Specific Vertices in a Biological Graph  1496--1507
             Neda Jahanshad and   
           Joshua Faskowitz and   
        Gennady Roshchupkin and   
            Derrek P. Hibar and   
            Boris A. Gutman and   
       Nicholas J. Tustison and   
          Hieab H. H. Adams and   
            Wiro J. Niessen and   
          Meike W. Vernooij and   
             M. Arfan Ikram and   
           Marcel P. Zwiers and   
    Alejandro Arias Vasquez and   
             Barbara Franke and   
          Jennifer L. Kroll and   
              Benson Mwangi and   
             Jair C. Soares and   
                   Alex Ing and   
        Sylvane Desrivieres and   
            Gunter Schumann and   
         Narelle K. Hansell and   
      Greig I. de Zubicaray and   
           Katie L. McMahon and   
         Nicholas G. Martin and   
         Margaret J. Wright and   
               Paul M. Thompson   Multi-Site Meta-Analysis of Morphometry  1508--1514
          Shokoufeh Mirzaei and   
                 Tomer Sidi and   
                Chen Keasar and   
                Silvia Crivelli   Purely Structural Protein Scoring
                                  Functions Using Support Vector Machine
                                  and Ensemble Learning  . . . . . . . . . 1515--1523
           Ritambhara Singh and   
            Jack Lanchantin and   
             Gabriel Robins and   
                      Yanjun Qi   Transfer String Kernel for Cross-Context
                                  DNA--Protein Binding Prediction  . . . . 1524--1536
           Tanay Kumar Saha and   
               Ataur Katebi and   
               Wajdi Dhifli and   
              Mohammad Al Hasan   Discovery of Functional Motifs from the
                                  Interface Region of Oligomeric Proteins
                                  Using Frequent Subgraph Mining . . . . . 1537--1549
               Marco Frasca and   
            Nicolo Cesa Bianchi   Multitask Protein Function Prediction
                                  through Task Dissimilarity . . . . . . . 1550--1560
               Jerome Feret and   
                   Heinz Koeppl   Editorial  . . . . . . . . . . . . . . . 1561--1561
                Russ Harmer and   
        Yves-Stan Le Cornec and   
           Sebastien Legare and   
                Eugenia Oshurko   Bio-Curation for Cellular Signalling:
                                  The KAMI Project . . . . . . . . . . . . 1562--1573
                Celia Biane and   
               Franck Delaplace   Causal Reasoning on Boolean Control
                                  Networks Based on Abduction: Theory and
                                  Application to Cancer Drug Discovery . . 1574--1585
              Houssam Abbas and   
            Alena Rodionova and   
      Konstantinos Mamouras and   
              Ezio Bartocci and   
            Scott A. Smolka and   
                     Radu Grosu   Quantitative Regular Expressions for
                                  Arrhythmia Detection . . . . . . . . . . 1586--1597
             Alexander Luck and   
               Pascal Giehr and   
             Karl Nordstrom and   
                Jorn Walter and   
                    Verena Wolf   Hidden Markov Modelling Reveals
                                  Neighborhood Dependence of Dnmt3a and 3b
                                  Activity . . . . . . . . . . . . . . . . 1598--1609
              Hugues Mandon and   
                     Cui Su and   
                   Jun Pang and   
                Soumya Paul and   
                Stefan Haar and   
                   Loic Pauleve   Algorithms for the Sequential
                                  Reprogramming of Boolean Networks  . . . 1610--1619
      Viacheslav Kapilevich and   
               Shigeto Seno and   
              Hideo Matsuda and   
                Yoichi Takenaka   Chromatin $3$D Reconstruction from
                                  Chromosomal Contacts Using a Genetic
                                  Algorithm  . . . . . . . . . . . . . . . 1620--1626
               Jong Ho Jhee and   
                Sunjoo Bang and   
                Dong-gi Lee and   
                  Hyunjung Shin   Comorbidity Scoring with Causal Disease
                                  Networks . . . . . . . . . . . . . . . . 1627--1634
                  Donghe Li and   
                  Wonji Kim and   
               Longfei Wang and   
              Kyong-Ah Yoon and   
               Boyoung Park and   
                Charny Park and   
             Sun-Young Kong and   
             Yongdeuk Hwang and   
               Daehyun Baek and   
               Eun Sook Lee and   
                     Sungho Won   Comparison of INDEL Calling Tools with
                                  Simulation Data and Real Short-Read Data 1635--1644
            Shimpei Nishida and   
              Shun Sakuraba and   
               Kiyoshi Asai and   
                Michiaki Hamada   Estimating Energy Parameters for RNA
                                  Secondary Structure Predictions Using
                                  Both Experimental and Computational Data 1645--1655
               Je-Keun Rhee and   
                Jinseon Yoo and   
              Kyu Ryung Kim and   
                Jeeyoon Kim and   
               Yong-Jae Lee and   
            Byoung Chul Cho and   
                    Tae-Min Kim   Identification of Local Clusters of
                                  Mutation Hotspots in Cancer-Related
                                  Genes and Their Biological Relevance . . 1656--1662
           Shailima Rampogu and   
                Ayoung Baek and   
                 Rohit Bavi and   
                  Minky Son and   
             Guang Ping Cao and   
                  Raj Kumar and   
                Chanin Park and   
                   Amir Zeb and   
         Rabia Mukthar Rana and   
               Seok Ju Park and   
                   Keun Woo Lee   Identification of Novel Scaffolds with
                                  Dual Role as Antiepileptic and
                                  Anti-Breast Cancer . . . . . . . . . . . 1663--1674
                Hiroki Sudo and   
             Masanobu Jimbo and   
                 Koji Nuida and   
                   Kana Shimizu   Secure Wavelet Matrix: Alphabet-Friendly
                                  Privacy-Preserving String Search for
                                  Bioinformatics . . . . . . . . . . . . . 1675--1684
                Man-Sun Kim and   
                Dongsan Kim and   
                  Jeong-Rae Kim   Stage-Dependent Gene Expression
                                  Profiling in Colorectal Cancer . . . . . 1685--1692
            SeongRyeol Moon and   
                 Curt Balch and   
               Sungjin Park and   
                Jinhyuk Lee and   
                Jiyong Sung and   
                  Seungyoon Nam   Systematic Inspection of the Clinical
                                  Relevance of TP53 Missense Mutations in
                                  Gastric Cancer . . . . . . . . . . . . . 1693--1701
               FanChang Hao and   
               Melvin Zhang and   
                  Hon Wai Leong   A $2$-Approximation Scheme for Sorting
                                  Signed Permutations by Reversals,
                                  Transpositions, Transreversals, and
                                  Block-Interchanges . . . . . . . . . . . 1702--1711
                   Limin Li and   
                    Menglan Cai   Drug Target Prediction by Multi-View Low
                                  Rank Embedding . . . . . . . . . . . . . 1712--1721
                Wen-Bin Xie and   
                   Hong Yan and   
                 Xing-Ming Zhao   EmDL: Extracting miRNA--Drug
                                  Interactions from Literature . . . . . . 1722--1728
                 Yanbo Wang and   
                   Quan Liu and   
                 Shan Huang and   
                        Bo Yuan   Learning a Structural and Functional
                                  Representation for Gene Expressions: To
                                  Systematically Dissect Complex Cancer
                                  Phenotypes . . . . . . . . . . . . . . . 1729--1742
                 Yishu Wang and   
               Huaying Fang and   
                 Dejie Yang and   
                Hongyu Zhao and   
                   Minghua Deng   Network Clustering Analysis Using
                                  Mixture Exponential-Family Random Graph
                                  Models and Its Application in Genetic
                                  Interaction Data . . . . . . . . . . . . 1743--1752
                Zhenni Zhao and   
                     Xinqi Gong   Protein--Protein Interaction Interface
                                  Residue Pair Prediction Based on Deep
                                  Learning Architecture  . . . . . . . . . 1753--1759
                    Xi Yang and   
               Guoqiang Han and   
                Hongmin Cai and   
                       Yan Song   Recovering Hidden Diagonal Structures
                                  via Non-Negative Matrix Factorization
                                  with Multiple Constraints  . . . . . . . 1760--1772

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 16, Number 6, November, 2019

          Anup Kumar Halder and   
          Piyali Chatterjee and   
              Mita Nasipuri and   
        Dariusz Plewczynski and   
                  Subhadip Basu   3gClust: Human Protein Cluster Analysis  1773--1784
            Aurpan Majumder and   
          Mrityunjay Sarkar and   
                  Prolay Sharma   A Composite Mode Differential Gene
                                  Regulatory Architecture based on
                                  Temporal Expression Profiles . . . . . . 1785--1793
                 Yujie Feng and   
                   Fan Yang and   
               Xichuan Zhou and   
                  Yanli Guo and   
                  Fang Tang and   
                 Fengbo Ren and   
                 Jishun Guo and   
                    Shuiwang Ji   A Deep Learning Approach for Targeted
                                  Contrast-Enhanced Ultrasound Based
                                  Prostate Cancer Detection  . . . . . . . 1794--1801
             Aida Brankovic and   
            Marjan Hosseini and   
                  Luigi Piroddi   A Distributed Feature Selection
                                  Algorithm Based on Distance Correlation
                                  with an Application to Microarrays . . . 1802--1815
                   Li Zhang and   
                 Ho-Chun Wu and   
               Cheuk-Hei Ho and   
                Shing-Chow Chan   A Multi-Laplacian Prior and Augmented
                                  Lagrangian Approach to the Exploratory
                                  Analysis of Time-Varying Gene and
                                  Transcriptional Regulatory Networks for
                                  Gene Microarray Data . . . . . . . . . . 1816--1829
      Anvita Gupta Malhotra and   
                Sudha Singh and   
                  Mohit Jha and   
            Khushhali M. Pandey   A Parametric Targetability Evaluation
                                  Approach for Vitiligo Proteome Extracted
                                  through Integration of Gene Ontologies
                                  and Protein Interaction Topologies . . . 1830--1842
               Juho Timonen and   
    Henrik Mannerström and   
 Harri Lähdesmäki and   
                Jukka Intosalmi   A Probabilistic Framework for Molecular
                                  Network Structure Inference by Means of
                                  Mechanistic Modeling . . . . . . . . . . 1843--1854
                  Xiaoke Ma and   
               Penggang Sun and   
               Zhong-Yuan Zhang   An Integrative Framework for Protein
                                  Interaction Network and Methylation Data
                                  to Discover Epigenetic Modules . . . . . 1855--1866
             Claudia Caudai and   
           Emanuele Salerno and   
             Monica Zopp\`e and   
               Ivan Merelli and   
                 Anna Tonazzini   ChromStruct 4: a Python Code to Estimate
                                  the Chromatin Structure from Hi-C Data   1867--1878
                Huiwei Zhou and   
               Yunlong Yang and   
               Shixian Ning and   
                 Zhuang Liu and   
              Chengkun Lang and   
                 Yingyu Lin and   
                    Degen Huang   Combining Context and Knowledge
                                  Representations for Chemical-Disease
                                  Relation Extraction  . . . . . . . . . . 1879--1889
                 Huimin Luo and   
               Jianxin Wang and   
                     Min Li and   
                 Junwei Luo and   
                    Peng Ni and   
                Kaijie Zhao and   
              Fang-Xiang Wu and   
                         Yi Pan   Computational Drug Repositioning with
                                  Random Walk on a Heterogeneous Network   1890--1900
             Sabrina Stella and   
           Roberto Chignola and   
                Edoardo Milotti   Dynamical Detection of Boundaries and
                                  Cavities in Biophysical Cell-Based
                                  Simulations of Growing Tumor Tissues . . 1901--1911
                 Xingyu Cai and   
          Abdullah-Al Mamun and   
        Sanguthevar Rajasekaran   Efficient Algorithms for Finding the
                                  Closest $ \ell 1$-Mers in Biological
                                  Data . . . . . . . . . . . . . . . . . . 1912--1921
                     Lun Hu and   
               Xiaohui Yuan and   
                   Xing Liu and   
              Shengwu Xiong and   
                        Xin Luo   Efficiently Detecting Protein Complexes
                                  from Protein Interaction Networks via
                                  Alternating Direction Method of
                                  Multipliers  . . . . . . . . . . . . . . 1922--1935
            Toktam Dehghani and   
        Mahmoud Naghibzadeh and   
                    Javad Sadri   Enhancement of Protein $ \beta $-Sheet
                                  Topology Prediction Using Maximum Weight
                                  Disjoint Path Cover  . . . . . . . . . . 1936--1947
                  Xue Jiang and   
                  Han Zhang and   
                 Zhao Zhang and   
                  Xiongwen Quan   Flexible Non-Negative Matrix
                                  Factorization to Unravel Disease-Related
                                  Genes  . . . . . . . . . . . . . . . . . 1948--1957
            Marianna Milano and   
         Pietro Hiram Guzzi and   
                Mario Cannataro   GLAlign: a Novel Algorithm for Local
                                  Network Alignment  . . . . . . . . . . . 1958--1969
                  Amit Paul and   
                       Jaya Sil   Identification of Differentially
                                  Expressed Genes to Establish New
                                  Biomarker for Cancer Prediction  . . . . 1970--1985
                 Xiaoke Hao and   
                Xiaohui Yao and   
        Shannon L. Risacher and   
           Andrew J. Saykin and   
                  Jintai Yu and   
                 Huifu Wang and   
                    Lan Tan and   
                    Li Shen and   
                 Daoqiang Zhang   Identifying Candidate Genetic
                                  Associations with MRI-Derived AD-Related
                                  ROI via Tree-Guided Sparse Learning  . . 1986--1996
                 Anjing Fan and   
                Haitao Wang and   
                  Hua Xiang and   
                     Xiufen Zou   Inferring Large-Scale Gene Regulatory
                                  Networks Using a Randomized Algorithm
                                  Based on Singular Value Decomposition    1997--2008
             Ayan Chaudhury and   
           Christopher Ward and   
                Ali Talasaz and   
        Alexander G. Ivanov and   
                Mark Brophy and   
         Bernard Grodzinski and   
    Norman P. A. Hüner and   
         Rajnikant V. Patel and   
                 John L. Barron   Machine Vision System for $3$D Plant
                                  Phenotyping  . . . . . . . . . . . . . . 2009--2022
        O. Ufuk Nalbantoglu and   
                  Khalid Sayood   MIMOSA: Algorithms for Microbial
                                  Profiling  . . . . . . . . . . . . . . . 2023--2034
Michail-Antisthenis Tsompanas and   
           Andrew Adamatzky and   
         Ioannis Ieropoulos and   
      Neil William Phillips and   
    Georgios Ch. Sirakoulis and   
                  John Greenman   Modelling Microbial Fuel Cells Using
                                  Lattice Boltzmann Methods  . . . . . . . 2035--2045
                Runtao Yang and   
             Chengjin Zhang and   
                    Rui Gao and   
                 Lina Zhang and   
                      Qing Song   Predicting FAD Interacting Residues with
                                  Feature Selection and Comprehensive
                                  Sequence Descriptors . . . . . . . . . . 2046--2056
             MD Aksam V. K. and   
       V. M. Chandrasekaran and   
      Sundaramurthy Pandurangan   Protein Domain Level Cancer Drug Targets
                                  in the Network of MAPK Pathways  . . . . 2057--2065
         Ashis Kumer Biswas and   
              Dong-Chul Kim and   
                Mingon Kang and   
                    Jean X. Gao   Robust Inductive Matrix Completion
                                  Strategy to Explore Associations Between
                                  LincRNAs and Human Disease Phenotypes    2066--2077
         Benjamin Wingfield and   
              Sonya Coleman and   
               TM McGinnity and   
                    AJ Bjourson   Robust Microbial Markers for
                                  Non-Invasive Inflammatory Bowel Disease
                                  Identification . . . . . . . . . . . . . 2078--2088
          Rahul K. Sevakula and   
                Vikas Singh and   
          Nishchal K. Verma and   
              Chandan Kumar and   
                        Yan Cui   Transfer Learning for Molecular Cancer
                                  Classification Using Deep Neural
                                  Networks . . . . . . . . . . . . . . . . 2089--2100


IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 17, Number 1, January, 2020

  Carlos Martín-Vide and   
Miguel A. Vega-Rodríguez   Algorithms for Computational Biology:
                                  Fifth Edition  . . . . . . . . . . . . . 1--1
        Klairton Lima Brito and   
   Andre Rodrigues Oliveira and   
               Ulisses Dias and   
                    Zanoni Dias   Heuristics for the Reversal and
                                  Transposition Distance Problem . . . . . 2--13
             Leo van Iersel and   
              Remie Janssen and   
                 Mark Jones and   
          Yukihiro Murakami and   
                    Norbert Zeh   Polynomial-Time Algorithms for
                                  Phylogenetic Inference Problems
                                  Involving Duplication and Reticulation   14--26
   Atsuko Miyawaki-Kuwakado and   
            Soichiro Komori and   
             Fumihide Shiraishi   A Promising Method for Calculating True
                                  Steady-State Metabolite Concentrations
                                  in Large-Scale Metabolic Reaction
                                  Network Models . . . . . . . . . . . . . 27--36
          Ranjan Kumar Maji and   
            Sunirmal Khatua and   
                   Zhumur Ghosh   A Supervised Ensemble Approach for
                                  Sensitive microRNA Target Prediction . . 37--46
               Mehmet Kocak and   
                Khyobeni Mozhui   An Application of the Bayesian
                                  Periodicity Test to Identify Diurnal
                                  Rhythm Genes in the Brain  . . . . . . . 47--55
          Syed Sazzad Ahmed and   
                 Swarup Roy and   
                   Jugal Kalita   Assessing the Effectiveness of Causality
                                  Inference Methods for Gene Regulatory
                                  Networks . . . . . . . . . . . . . . . . 56--70
            Cheng-Hong Yang and   
                  Yu-Da Lin and   
                  Li-Yeh Chuang   Class Balanced Multifactor
                                  Dimensionality Reduction to Detect
                                  Gene--Gene Interactions  . . . . . . . . 71--81
               Jing wei Tan and   
             Siow-Wee Chang and   
        Sameem Abdul-Kareem and   
                Hwa Jen Yap and   
                 Kien-Thai Yong   Deep Learning for Plant Species
                                  Classification Using Leaf Vein
                                  Morphometric . . . . . . . . . . . . . . 82--90
               Yangqin Feng and   
                  Lei Zhang and   
                        Juan Mo   Deep Manifold Preserving Autoencoder for
                                  Classifying Breast Cancer
                                  Histopathological Images . . . . . . . . 91--101
              Mahnaz Habibi and   
                 Pegah Khosravi   Disruption of Protein Complexes from
                                  Weighted Complex Networks  . . . . . . . 102--109
                 Yicheng He and   
                Junfeng Liu and   
                       Xia Ning   Drug Selection via Joint Push and
                                  Learning to Rank . . . . . . . . . . . . 110--123
                 Jiyun Zhou and   
                     Qin Lu and   
                 Ruifeng Xu and   
                    Lin Gui and   
                  Hongpeng Wang   EL\_LSTM: Prediction of DNA-Binding
                                  Residue from Protein Sequence by
                                  Combining Long Short-Term Memory and
                                  Ensemble Learning  . . . . . . . . . . . 124--135
                   Tony Pan and   
             Rahul Nihalani and   
                 Srinivas Aluru   Fast de Bruijn Graph Compaction in
                                  Distributed Memory Environments  . . . . 136--148
             Michal Marczyk and   
               Roman Jaksik and   
           Andrzej Polanski and   
                Joanna Polanska   GaMRed-Adaptive Filtering of
                                  High-Throughput Biological Data  . . . . 149--157
           Joan Carles Pons and   
         Celine Scornavacca and   
                Gabriel Cardona   Generation of Level-$k$ k LGT Networks   158--164
                 Jiulun Cai and   
                Hongmin Cai and   
               Jiazhou Chen and   
                        Xi Yang   Identifying ``Many-to--Many''
                                  Relationships between Gene-Expression
                                  Data and Drug-Response Data via Sparse
                                  Binary Matching  . . . . . . . . . . . . 165--176
                Xingyu Liao and   
                     Min Li and   
                 Junwei Luo and   
                    You Zou and   
              Fang-Xiang Wu and   
                     Yi Pan and   
                   Feng Luo and   
                   Jianxin Wang   Improving de novo Assembly Based on
                                  Read Classification  . . . . . . . . . . 177--188
               Tianyi Zhang and   
               Minghui Wang and   
                 Jianing Xi and   
                          Ao Li   LPGNMF: Predicting Long Non-Coding RNA
                                  and Protein Interaction Using Graph
                                  Regularized Nonnegative Matrix
                                  Factorization  . . . . . . . . . . . . . 189--197
Patricia Carvajal-López and   
    Fernando D. Von Borstel and   
               Amada Torres and   
          Gabriella Rustici and   
Joaquín Gutiérrez and   
           Eduardo Romero-Vivas   Microarray-Based Quality Assessment as a
                                  Supporting Criterion for de novo
                                  Transcriptome Assembly Selection . . . . 198--206
            Sudipta Acharya and   
              Sriparna Saha and   
               Prasanna Pradhan   Multi-Factored Gene-Gene Proximity
                                  Measures Exploiting Biological Knowledge
                                  Extracted from Gene Ontology:
                                  Application in Gene Clustering . . . . . 207--219
                     Tao Li and   
              Xiankai Zhang and   
                   Feng Luo and   
              Fang-Xiang Wu and   
                   Jianxin Wang   MultiMotifMaker: a Multi-Thread Tool for
                                  Identifying DNA Methylation Motifs from
                                  Pacbio Reads . . . . . . . . . . . . . . 220--225
                Xiangtao Li and   
             Shixiong Zhang and   
                   Ka-Chun Wong   Nature-Inspired Multiobjective Epistasis
                                  Elucidation from Genome-Wide Association
                                  Studies  . . . . . . . . . . . . . . . . 226--237
                 Guoxian Yu and   
                 Keyao Wang and   
               Guangyuan Fu and   
                  Maozu Guo and   
                       Jun Wang   NMFGO: Gene Function Prediction via
                                  Nonnegative Matrix Factorization with
                                  Gene Ontology  . . . . . . . . . . . . . 238--249
          Ali Foroughi pour and   
                 Lori A. Dalton   Optimal Bayesian Filtering for Biomarker
                                  Discovery: Performance and Robustness    250--263
           Sepideh Mazrouee and   
                       Wei Wang   PolyCluster: Minimum Fragment
                                  Disagreement Clustering for Polyploid
                                  Phasing  . . . . . . . . . . . . . . . . 264--277
             Saptarshi Pyne and   
          Alok Ranjan Kumar and   
                   Ashish Anand   Rapid Reconstruction of Time-Varying
                                  Gene Regulatory Networks . . . . . . . . 278--291
    Ramón A. Delgado and   
               Zhiyong Chen and   
           Richard H. Middleton   Stepwise Tikhonov Regularisation:
                                  Application to the Prediction of HIV-1
                                  Drug Resistance  . . . . . . . . . . . . 292--301
               Kieran Alden and   
             Jason Cosgrove and   
                 Mark Coles and   
                     Jon Timmis   Using Emulation to Engineer and
                                  Understand Simulations of Biological
                                  Systems  . . . . . . . . . . . . . . . . 302--315
                  Dor Ganor and   
              Ron Y. Pinter and   
                  Meirav Zehavi   A Note on GRegNetSim: a Tool for the
                                  Discrete Simulation and Analysis of
                                  Genetic Regulatory Networks  . . . . . . 316--320

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 17, Number 2, March, 2020

                 Ziwei Chen and   
                Xiangqi Bai and   
                   Liang Ma and   
                Xiawei Wang and   
                 Xiuqin Liu and   
                 Yuting Liu and   
                Luonan Chen and   
                        Lin Wan   A Branch Point on Differentiation
                                  Trajectory is the Bifurcating Event
                                  Revealed by Dynamical Network Biomarker
                                  Analysis of Single-Cell Data . . . . . . 366--375
                Lihua Zhang and   
                   Shihua Zhang   Comparison of Computational Methods for
                                  Imputing Single-Cell RNA-Sequencing Data 376--389
                    Feng Li and   
                    Lin Gao and   
                    Bingbo Wang   Detection of Driver Modules with Rarely
                                  Mutated Genes in Cancers . . . . . . . . 390--401
                  Hao Jiang and   
                 Yushan Qiu and   
                 Wenpin Hou and   
             Xiaoqing Cheng and   
                 Man Yi Yim and   
                   Wai-Ki Ching   Drug Side-Effect Profiles Prediction:
                                  From Empirical to Structural Risk
                                  Minimization . . . . . . . . . . . . . . 402--410
             Zhan-Ying Feng and   
                      Yong Wang   ELF: Extract Landmark Features By
                                  Optimizing Topology Maintenance,
                                  Redundancy, and Specificity  . . . . . . 411--421
                 Jianing Xi and   
                      Ao Li and   
                   Minghui Wang   HetRCNA: a Novel Method to Identify
                                  Recurrent Copy Number Alternations from
                                  Heterogeneous Tumor Samples Based on
                                  Matrix Decomposition Framework . . . . . 422--434
                     Ye Liu and   
              Michael K. Ng and   
                     Stephen Wu   Multi-Domain Networks Association for
                                  Biological Data Using Block Signed Graph
                                  Clustering . . . . . . . . . . . . . . . 435--448
                  Jifan Shi and   
                  Juan Zhao and   
               Xiaoping Liu and   
                Luonan Chen and   
                      Tiejun Li   Quantifying Direct Dependencies in
                                  Biological Networks by Multiscale
                                  Association Analysis . . . . . . . . . . 449--458
               Rajan Kapoor and   
            Aniruddha Datta and   
                  Chao Sima and   
               Jianping Hua and   
               Rosana Lopes and   
             Michael L. Bittner   A Gaussian Mixture-Model Exploiting
                                  Pathway Knowledge for Dissecting Cancer
                                  Heterogeneity  . . . . . . . . . . . . . 459--468
                Paola Lecca and   
                      Angela Re   A Reaction-Based Model of the State
                                  Space of Chemical Reaction Systems
                                  Enables Efficient Simulations  . . . . . 469--482
              Kaspar Riesen and   
              Miquel Ferrer and   
                    Horst Bunke   Approximate Graph Edit Distance in
                                  Quadratic Time . . . . . . . . . . . . . 483--494
                Xiujuan Lei and   
               Xiaoqin Yang and   
                  Fang-Xiang Wu   Artificial Fish Swarm Optimization Based
                                  Method to Identify Essential Proteins    495--505
                Rishika Sen and   
             Somnath Tagore and   
                    Rajat K. De   ASAPP: Architectural Similarity-Based
                                  Automated Pathway Prediction System and
                                  Its Application in Host-Pathogen
                                  Interactions . . . . . . . . . . . . . . 506--515
                Haifen Chen and   
         D. A. K. Maduranga and   
      Piyushkumar A. Mundra and   
                      Jie Zheng   Bayesian Data Fusion of Gene Expression
                                  and Histone Modification Profiles for
                                  Inference of Gene Regulatory Network . . 516--525
            Hossein Yazdani and   
               Leo L. Cheng and   
        David C. Christiani and   
                   Azam Yazdani   Bounded Fuzzy Possibilistic Method
                                  Reveals Information about Lung Cancer
                                  through Analysis of Metabolomics . . . . 526--535
                   Yujie Li and   
                 Heng Huang and   
                 Hanbo Chen and   
                   Tianming Liu   Deep Neural Networks for \em In Situ
                                  Hybridization Grid Completion and
                                  Clustering . . . . . . . . . . . . . . . 536--546
           Abazar Arabameri and   
              Davud Asemani and   
              Pegah Teymourpour   Detection of Colorectal Carcinoma Based
                                  on Microbiota Analysis Using Generalized
                                  Regression Neural Networks and Nonlinear
                                  Feature Selection  . . . . . . . . . . . 547--557
             Shengping Yang and   
        Mitchell S. Wachtel and   
                   Jiangrong Wu   DFseq: Distribution-Free Method to
                                  Detect Differential Gene Expression for
                                  RNA-Sequencing Data  . . . . . . . . . . 558--565
    Hussain Ahmed Chowdhury and   
 Dhruba Kumar Bhattacharyya and   
             Jugal Kumar Kalita   Differential Expression Analysis of
                                  RNA-seq Reads: Overview, Taxonomy, and
                                  Tools  . . . . . . . . . . . . . . . . . 566--586
                  Hang Wang and   
                 Jianing Xi and   
               Minghui Wang and   
                          Ao Li   Dual-Layer Strengthened Collaborative
                                  Topic Regression Modeling for Predicting
                                  Drug Sensitivity . . . . . . . . . . . . 587--598
                Lishuang Li and   
                   Yang Liu and   
                     Meiyue Qin   Extracting Biomedical Events with
                                  Parallel Multi-Pooling Convolutional
                                  Neural Networks  . . . . . . . . . . . . 599--607
            Aydin Saribudak and   
          Adarsha A. Subick and   
                Na Hyun Kim and   
            Joshua A. Rutta and   
              M. Ümit Uyar   Gene Expressions, Hippocampal Volume
                                  Loss, and MMSE Scores in Computation of
                                  Progression and Pharmacologic Therapy
                                  Effects for Alzheimer's Disease  . . . . 608--622
                   Qiu Xiao and   
                 Jiawei Luo and   
                Cheng Liang and   
                Guanghui Li and   
                    Jie Cai and   
              Pingjian Ding and   
                       Ying Liu   Identifying lncRNA and mRNA
                                  Co-Expression Modules from Matched
                                  Expression Data in Ovarian Cancer  . . . 623--634
            Ali Karimnezhad and   
                David R. Bickel   Incorporating Prior Knowledge about
                                  Genetic Variants into the Analysis of
                                  Genetic Association Data: an Empirical
                                  Bayes Approach . . . . . . . . . . . . . 635--646
             Rongrong Zhang and   
                    Ming Hu and   
                     Yu Zhu and   
                Zhaohui Qin and   
                    Ke Deng and   
                     Jun S. Liu   Inferring Spatial Organization of
                                  Individual Topologically Associated
                                  Domains via Piecewise Helical Model  . . 647--656
                   Zhen Cao and   
                   Shihua Zhang   Probe Efficient Feature Representation
                                  of Gapped $K$-mer Frequency Vectors from
                                  Sequences Using Deep Neural Networks . . 657--667
                Paul Fergus and   
Casimiro Curbelo Montañez and   
           Basma Abdulaimma and   
               Paulo Lisboa and   
              Carl Chalmers and   
                   Beth Pineles   Utilizing Deep Learning and Genome Wide
                                  Association Studies for Epistatic-Driven
                                  Preterm Birth Classification in
                                  African--American Women  . . . . . . . . 668--678
                Qinhu Zhang and   
                    Lin Zhu and   
               Wenzheng Bao and   
                De-Shuang Huang   Weakly-Supervised Convolutional Neural
                                  Network Architecture for Predicting
                                  Protein--DNA Binding . . . . . . . . . . 679--689
              Saurav Mallik and   
      Sanghamitra Bandyopadhyay   WeCoMXP: Weighted Connectivity Measure
                                  Integrating Co-Methylation,
                                  Co-Expression and Protein-Protein
                                  Interactions for Gene-Module Detection   690--703
             Samah J. Fodeh and   
                  Taihua Li and   
                 Haya Jarad and   
                  Basmah Safdar   Classification of Patients with Coronary
                                  Microvascular Dysfunction  . . . . . . . 704--711

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 17, Number 3, May, 2020

                  Jie Zheng and   
                  Jinyan Li and   
                      Yun Zheng   Guest Editorial for the 29th
                                  International Conference on Genome
                                  Informatics (GIW 2018) . . . . . . . . . 726--727
                Xingyu Liao and   
                     Min Li and   
                    You Zou and   
              Fang-Xiang Wu and   
                     Yi Pan and   
                   Jianxin Wang   An Efficient Trimming Algorithm based on
                                  Multi-Feature Fusion Scoring Model for
                                  NGS Data . . . . . . . . . . . . . . . . 728--738
              Shunfang Wang and   
                Zicheng Cao and   
                Mingyuan Li and   
                    Yaoting Yue   G-DipC: an Improved Feature
                                  Representation Method for Short
                                  Sequences to Predict the Type of Cargo
                                  in Cell-Penetrating Peptides . . . . . . 739--747
                   Yong Liu and   
                     Min Wu and   
               Chenghao Liu and   
                 Xiao-Li Li and   
                      Jie Zheng   SL$^2$MF: Predicting Synthetic Lethality
                                  in Human Cancers via Logistic Matrix
                                  Factorization  . . . . . . . . . . . . . 748--757
               Junrong Song and   
                   Wei Peng and   
                      Feng Wang   An Entropy-Based Method for Identifying
                                  Mutual Exclusive Driver Genes in Cancer  758--768
                Jiajie Peng and   
                Linjiao Zhu and   
                Yadong Wang and   
                       Jin Chen   Mining Relationships among Multiple
                                  Entities in Biological Networks  . . . . 769--776
                   Heng Yao and   
                 Yunjia Shi and   
                Jihong Guan and   
                  Shuigeng Zhou   Accurately Detecting Protein Complexes
                                  by Graph Embedding and Combining
                                  Functions with Interactions  . . . . . . 777--787
                Yuanyuan Ma and   
                 Xiaohua Hu and   
                Tingting He and   
                 Xingpeng Jiang   Clustering and Integrating of
                                  Heterogeneous Microbiome Data by Joint
                                  Symmetric Nonnegative Matrix
                                  Factorization with Laplacian
                                  Regularization . . . . . . . . . . . . . 788--795
                 Renjie Tan and   
                Jixuan Wang and   
               Xiaoliang Wu and   
                 Liran Juan and   
             Tianjiao Zhang and   
                     Rui Ma and   
                  Qing Zhan and   
                   Tao Wang and   
                Shuilin Jin and   
              Qinghua Jiang and   
                    Yadong Wang   ERDS-Exome: a Hybrid Approach for Copy
                                  Number Variant Detection from
                                  Whole-Exome Sequencing Data  . . . . . . 796--803
             Shaoliang Peng and   
               Xiaoyu Zhang and   
                   Wenhe Su and   
                  Dong Dong and   
                  Yutong Lu and   
               Xiangke Liao and   
                     Kai Lu and   
                Canqun Yang and   
                    Jie Liu and   
               Weiliang Zhu and   
                   Dongqing Wei   High-Scalable Collaborated Parallel
                                  Framework for Large-Scale Molecular
                                  Dynamic Simulation on Tianhe-2
                                  Supercomputer  . . . . . . . . . . . . . 804--816
                     Min Li and   
              Xiangmao Meng and   
              Ruiqing Zheng and   
              Fang-Xiang Wu and   
                 Yaohang Li and   
                     Yi Pan and   
                   Jianxin Wang   Identification of Protein Complexes by
                                  Using a Spatial and Temporal Active
                                  Protein Interaction Network  . . . . . . 817--827
     Mohammad Arifur Rahman and   
            Nathan LaPierre and   
                Huzefa Rangwala   Phenotype Prediction from Metagenomic
                                  Data Using Clustering and Assembly with
                                  Multiple Instance Learning (CAMIL) . . . 828--840
                Lishuang Li and   
                    Yuxin Jiang   Integrating Language Model and Reading
                                  Control Gate in BLSTM-CRF for Biomedical
                                  Named Entity Recognition . . . . . . . . 841--846
                  Binbin Wu and   
                     Min Li and   
                Xingyu Liao and   
                 Junwei Luo and   
              Fang-Xiang Wu and   
                     Yi Pan and   
                   Jianxin Wang   MEC: Misassembly Error Correction in
                                  Contigs based on Distribution of
                                  Paired-End Reads and Statistics of
                                  GC-contents  . . . . . . . . . . . . . . 847--857
                Huiru Zheng and   
               Haiying Wang and   
        Richard J. Dewhurst and   
                   Rainer Roehe   Improving the Inference of Co-Occurrence
                                  Networks in the Bovine Rumen Microbiome  858--867
                Fatima Zare and   
              Sardar Ansari and   
            Kayvan Najarian and   
                  Sheida Nabavi   Preprocessing Sequence Coverage Data for
                                  More Precise Detection of Copy Number
                                  Variations . . . . . . . . . . . . . . . 868--876
                 Junwei Luo and   
               Jianxin Wang and   
                 Juan Shang and   
                 Huimin Luo and   
                     Min Li and   
              Fang-Xiang Wu and   
                         Yi Pan   GapReduce: a Gap Filling Algorithm Based
                                  on Partitioned Read Sets . . . . . . . . 877--886
                  Haigen Hu and   
                   Qiu Guan and   
             Shengyong Chen and   
                  Zhiwei Ji and   
                        Yao Lin   Detection and Recognition for Life State
                                  of Cell Cancer Using Two-Stage Cascade
                                  CNNs . . . . . . . . . . . . . . . . . . 887--898
              Yuansheng Liu and   
               Chaowang Lan and   
        Michael Blumenstein and   
                      Jinyan Li   Bi-Level Error Correction for PacBio
                                  Long Reads . . . . . . . . . . . . . . . 899--905
                    Peng Ni and   
               Jianxin Wang and   
                 Ping Zhong and   
                 Yaohang Li and   
              Fang-Xiang Wu and   
                         Yi Pan   Constructing Disease Similarity Networks
                                  Based on Disease Module Theory . . . . . 906--915
             Zhi-Zhong Chen and   
               Youta Harada and   
              Yuna Nakamura and   
                   Lusheng Wang   Faster Exact Computation of rSPR
                                  Distance via Better Approximation  . . . 916--929
                   Zaobo He and   
                   Jiguo Yu and   
                      Ji Li and   
                 Qilong Han and   
              Guangchun Luo and   
                     Yingshu Li   Inference Attacks and Controls on
                                  Genotypes and Phenotypes for Individual
                                  Genomic Data . . . . . . . . . . . . . . 930--937
                   Jin Zhao and   
                 Haodi Feng and   
                 Daming Zhu and   
                  Chi Zhang and   
                        Ying Xu   IsoTree: a New Framework for de novo
                                  Transcriptome Assembly from RNA-seq
                                  Reads  . . . . . . . . . . . . . . . . . 938--948
             Jingsong Zhang and   
                Jianmei Guo and   
                 Ming Zhang and   
               Xiangtian Yu and   
                Xiaoqing Yu and   
                Weifeng Guo and   
                   Tao Zeng and   
                    Luonan Chen   Efficient Mining Multi-Mers in a Variety
                                  of Biological Sequences  . . . . . . . . 949--958
             Fatima Boukari and   
          Sokratis Makrogiannis   Automated Cell Tracking Using Motion
                                  Prediction-Based Matching and Event
                                  Handling . . . . . . . . . . . . . . . . 959--971
                   Lei Wang and   
               Zhu-Hong You and   
            De-Shuang Huang and   
                  Fengfeng Zhou   Combining High Speed ELM Learning with a
                                  Deep Convolutional Neural Network
                                  Feature Encoding for Predicting
                                  Protein-RNA Interactions . . . . . . . . 972--980
                 Qiwen Kang and   
                 Neil Moore and   
     Christopher L. Schardl and   
                 Ruriko Yoshida   CURatio: Genome-Wide Phylogenomic
                                  Analysis Method Using Ratios of Total
                                  Branch Lengths . . . . . . . . . . . . . 981--989
            Sarawoot Som-In and   
             Warangkhana Kimpan   Enhancing of Particle Swarm Optimization
                                  Based Method for Multiple Motifs
                                  Detection in DNA Sequences Collections   990--998
            Somayeh Bakhteh and   
  Alireza Ghaffari-Hadigheh and   
              Nader Chaparzadeh   Identification of Minimum Set of Master
                                  Regulatory Genes in Gene Regulatory
                                  Networks . . . . . . . . . . . . . . . . 999--1009
        Haswanth Vundavilli and   
            Aniruddha Datta and   
                  Chao Sima and   
               Jianping Hua and   
               Rosana Lopes and   
                Michael Bittner   In Silico Design and Experimental
                                  Validation of Combination Therapy for
                                  Pancreatic Cancer  . . . . . . . . . . . 1010--1018

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 17, Number 5, September, 2020

            De-Shuang Huang and   
     Vitoantonio Bevilacqua and   
                Michael Gromiha   Guest Editorial for Special Section on
                                  the 14th International Conference on
                                  Intelligent Computing (ICIC) . . . . . . 1474--1475
                   Wook Lee and   
                  Kyungsook Han   Constructive Prediction of Potential RNA
                                  Aptamers for a Protein Target  . . . . . 1476--1482
                  Zhen Shen and   
               Su-Ping Deng and   
                De-Shuang Huang   Capsule Network for Predicting
                                  RNA--Protein Binding Preferences Using
                                  Hybrid Feature . . . . . . . . . . . . . 1483--1492
               Huiqiang Jia and   
                Haichao Wei and   
                 Daming Zhu and   
                Jingjing Ma and   
                   Hai Yang and   
                Ruizhi Wang and   
                 Xianzhong Feng   PASA: Identifying More Credible
                                  Structural Variants of Hedou12 . . . . . 1493--1503
                   Jian Liu and   
                     Zhi Qu and   
                    Mo Yang and   
               Jialiang Sun and   
                  Shuhui Su and   
                      Lei Zhang   Jointly Integrating VCF-Based Variants
                                  and OWL-Based Biomedical Ontologies in
                                  MongoDB  . . . . . . . . . . . . . . . . 1504--1515
                 Pengwei Hu and   
                Yu-An Huang and   
           Keith C. C. Chan and   
                   Zhu-Hong You   Learning Multimodal Networks From
                                  Heterogeneous Data for Prediction of
                                  lncRNA--miRNA Interactions . . . . . . . 1516--1524
                 Xiaoli Lin and   
             Xiaolong Zhang and   
                         Xin Xu   Efficient Classification of Hot Spots
                                  and Hub Protein Interfaces by Recursive
                                  Feature Elimination and Gradient
                                  Boosting . . . . . . . . . . . . . . . . 1525--1534
                  Jade Hind and   
               Paulo Lisboa and   
            Abir J. Hussain and   
               Dhiya Al-Jumeily   A Novel Approach to Detecting Epistasis
                                  using Random Sampling Regularisation . . 1535--1545
               Jianqiang Li and   
               Xiaofeng Shi and   
               Zhu-Hong You and   
               Hai-Cheng Yi and   
          Zhuangzhuang Chen and   
                Qiuzhen Lin and   
                       Min Fang   Using Weighted Extreme Learning Machine
                                  Combined With Scale-Invariant Feature
                                  Transform to Predict Protein-Protein
                                  Interactions From Protein Evolutionary
                                  Information  . . . . . . . . . . . . . . 1546--1554
           Maryam Shahdoust and   
             Hossein Mahjub and   
              Hamid Pezeshk and   
                  Mehdi Sadeghi   A Network-Based Comparison Between
                                  Molecular Apocrine Breast Cancer Tumor
                                  and Basal and Luminal Tumors by Joint
                                  Graphical Lasso  . . . . . . . . . . . . 1555--1562
                   Qian Guo and   
               Tianhong Pan and   
                  Shan Chen and   
                 Xiaobo Zou and   
               Dorothy Yu Huang   A Novel Edge Effect Detection Method for
                                  Real-Time Cellular Analyzer Using
                                  Functional Principal Component Analysis  1563--1572
             Nirmala Sharma and   
              Harish Sharma and   
                    Ajay Sharma   An Effective Solution for Large Scale
                                  Single Machine Total Weighted Tardiness
                                  Problem using Lunar Cycle Inspired
                                  Artificial Bee Colony Algorithm  . . . . 1573--1581
           Aisharjya Sarkar and   
                Yilmaz Atay and   
    Alana Lorraine Erickson and   
                 Ivan Arisi and   
             Cesare Saltini and   
                  Tamer Kahveci   An Efficient Algorithm for Identifying
                                  Mutated Subnetworks Associated with
                                  Survival in Cancer . . . . . . . . . . . 1582--1594
                  Cheng Yan and   
                Guihua Duan and   
              Fang-Xiang Wu and   
                     Yi Pan and   
                   Jianxin Wang   BRWMDA:Predicting Microbe-Disease
                                  Associations Based on Similarities and
                                  Bi-Random Walk on Disease and Microbe
                                  Networks . . . . . . . . . . . . . . . . 1595--1604
                  Chen Peng and   
                 Yang Zheng and   
                De-Shuang Huang   Capsule Network Based Modeling of
                                  Multi-omics Data for Discovery of Breast
                                  Cancer-Related Genes . . . . . . . . . . 1605--1612
      Pourya Naderi Yeganeh and   
             M. Taghi Mostafavi   Causal Disturbance Analysis: a Novel
                                  Graph Centrality Based Method for
                                  Pathway Enrichment Analysis  . . . . . . 1613--1624
      Jirí Filipovic and   
        Ondrej Vávra and   
           Jan Plhák and   
        David Bednár and   
   Sérgio M. Marques and   
       Jan Brezovský and   
              Ludek Matyska and   
   Jirí Damborský   CaverDock: a Novel Method for the Fast
                                  Analysis of Ligand Transport . . . . . . 1625--1638
            Xiangxiang Zeng and   
                Yinglai Lin and   
                  Yuying He and   
            Linyuan Lü and   
               Xiaoping Min and   
Alfonso Rodríguez-Patón   Deep Collaborative Filtering for
                                  Prediction of Disease Genes  . . . . . . 1639--1647
              Ashish Ranjan and   
              Md Shah Fahad and   
David Fernández-Baca and   
              Akshay Deepak and   
              Sudhakar Tripathi   Deep Robust Framework for Protein
                                  Function Prediction Using
                                  Variable-Length Protein Sequences  . . . 1648--1659
           Sunildatt Sharma and   
     Sanjeev Narayan Sharma and   
                   Rajiv Saxena   Identification of Short Exons Disunited
                                  by a Short Intron in Eukaryotic DNA
                                  Regions  . . . . . . . . . . . . . . . . 1660--1670
                   Min Wang and   
             Ting-Zhu Huang and   
                  Jian Fang and   
           Vince D. Calhoun and   
                   Yu-Ping Wang   Integration of Imaging (epi)Genomics
                                  Data for the Study of Schizophrenia
                                  Using Group Sparse Joint Nonnegative
                                  Matrix Factorization . . . . . . . . . . 1671--1681
                   Lan Zhao and   
                       Hong Yan   MCNF: a Novel Method for Cancer
                                  Subtyping by Integrating Multi-Omics and
                                  Clinical Data  . . . . . . . . . . . . . 1682--1690
    Matthieu Pichené and   
  Sucheendra K. Palaniappan and   
                 Eric Fabre and   
                  Blaise Genest   Modeling Variability in Populations of
                                  Cells Using Approximated Multivariate
                                  Distributions  . . . . . . . . . . . . . 1691--1702
                 Yuan Zhang and   
                Haihong Liu and   
                Zhouhong Li and   
              Zhonghua Miao and   
                       Jin Zhou   Oscillatory Dynamics of p53-Mdm2 Circuit
                                  in Response to DNA Damage Caused by
                                  Ionizing Radiation . . . . . . . . . . . 1703--1713
                   Sijia Wu and   
                Xiaoming Wu and   
                   Jie Tian and   
                Xiaobo Zhou and   
                     Liyu Huang   PredictFP2: a New Computational Model to
                                  Predict Fusion Peptide Domain in All
                                  Retroviruses . . . . . . . . . . . . . . 1714--1720
                   Laiyi Fu and   
                 Qinke Peng and   
                      Ling Chai   Predicting DNA Methylation States with
                                  Hybrid Information Based Deep-Learning
                                  Model  . . . . . . . . . . . . . . . . . 1721--1728
              Sushmita Paul and   
                      Madhumita   RFCM$^3$: Computational Method for
                                  Identification of miRNA--mRNA Regulatory
                                  Modules in Cervical Cancer . . . . . . . 1729--1740
                  Zhen Shen and   
               Su-Ping Deng and   
                De-Shuang Huang   RNA-Protein Binding Sites Prediction via
                                  Multi Scale Convolutional Gated
                                  Recurrent Unit Networks  . . . . . . . . 1741--1750
                  Saad Raza and   
               Ghulam Abbas and   
             Syed Sikander Azam   Screening Pipeline for Flavivirus Based
                                  Inhibitors for Zika Virus NS1  . . . . . 1751--1761
             Keisuke Kawano and   
              Satoshi Koide and   
                   Chie Imamura   Seq2seq Fingerprint with Byte-Pair
                                  Encoding for Predicting Changes in
                                  Protein Stability upon Single Point
                                  Mutation . . . . . . . . . . . . . . . . 1762--1772

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 17, Number 6, November, 2020

                     Da Yan and   
                    Xin Gao and   
             Samah J. Fodeh and   
                   Jake Y. Chen   Guest Editorial for Selected Papers from
                                  BIOKDD 2018 and DMBIH 2018 . . . . . . . 1832--1834
         Michael Sokolovsky and   
         Francisco Guerrero and   
     Sarun Paisarnsrisomsuk and   
              Carolina Ruiz and   
              Sergio A. Alvarez   Deep Learning for Automated Feature
                                  Discovery and Classification of Sleep
                                  Stages . . . . . . . . . . . . . . . . . 1835--1845
    Matthew B. A. McDermott and   
              Jennifer Wang and   
              Wen-Ning Zhao and   
         Steven D. Sheridan and   
            Peter Szolovits and   
               Isaac Kohane and   
        Stephen J. Haggarty and   
                  Roy H. Perlis   Deep Learning Benchmarks on L1000 Gene
                                  Expression Data  . . . . . . . . . . . . 1846--1857
               Jingyi Zheng and   
              Fushing Hsieh and   
                    Linqiang Ge   A Data-Driven Approach to Predict and
                                  Classify Epileptic Seizures from
                                  Brain-Wide Calcium Imaging Video Data    1858--1870
                Hongming Xu and   
                 Sunho Park and   
                 Tae Hyun Hwang   Computerized Classification of Prostate
                                  Cancer Gleason Scores from Whole Slide
                                  Images . . . . . . . . . . . . . . . . . 1871--1882
            Shreyasi Pathak and   
           Jorit van Rossen and   
             Onno Vijlbrief and   
            Jeroen Geerdink and   
           Christin Seifert and   
             Maurice van Keulen   Post-Structuring Radiology Reports of
                                  Breast Cancer Patients for Clinical
                                  Quality Assurance  . . . . . . . . . . . 1883--1894
      Enrique Noriega-Atala and   
               Paul D. Hein and   
         Shraddha S. Thumsi and   
                 Zechy Wong and   
                   Xia Wang and   
            Sean M. Hendryx and   
            Clayton T. Morrison   Extracting Inter-Sentence Relations for
                                  Associating Biological Context with
                                  Events in Biomedical Texts . . . . . . . 1895--1906
          Jonathon A. Gibbs and   
           Michael P. Pound and   
           Andrew P. French and   
            Darren M. Wells and   
            Erik H. Murchie and   
               Tony P. Pridmore   Active Vision and Surface Reconstruction
                                  for $3$D Plant Shoot Modelling . . . . . 1907--1917
              Xiaoyang Jing and   
                 Qiwen Dong and   
              Daocheng Hong and   
                      Ruqian Lu   Amino Acid Encoding Methods for Protein
                                  Sequences: a Comprehensive Review and
                                  Assessment . . . . . . . . . . . . . . . 1918--1931
                Soumya Paul and   
                     Cui Su and   
                   Jun Pang and   
                 Andrzej Mizera   An Efficient Approach Towards the
                                  Source-Target Control of Boolean
                                  Networks . . . . . . . . . . . . . . . . 1932--1945
                Letu Qingge and   
              Killian Smith and   
                Sean Jungst and   
                Baihui Wang and   
                  Qing Yang and   
                     Binhai Zhu   Approaching the One-Sided Exemplar
                                  Adjacency Number Problem . . . . . . . . 1946--1954
      Mohammad Bozlul Karim and   
                 Ming Huang and   
                 Naoaki Ono and   
           Shigehiko Kanaya and   
              Md. Altaf-Ul-Amin   BiClusO: a Novel Biclustering Approach
                                  and Its Application to Species-VOC
                                  Relational Data  . . . . . . . . . . . . 1955--1965
              Guang-Hui Liu and   
              Bei-Wei Zhang and   
                  Gang Qian and   
                   Bin Wang and   
                     Bo Mao and   
          Isabelle Bichindaritz   Bioimage-Based Prediction of Protein
                                  Subcellular Location in Human Tissue
                                  with Ensemble Features and Deep Networks 1966--1980
            Nicola Paoletti and   
                Kin Sum Liu and   
               Hongkai Chen and   
            Scott A. Smolka and   
                       Shan Lin   Data-Driven Robust Control for a
                                  Closed-Loop Artificial Pancreas  . . . . 1981--1993
                   Jian Liu and   
                  Qiuru Liu and   
                  Lei Zhang and   
                  Shuhui Su and   
                 Yongzhuang Liu   Enabling Massive XML-Based Biological
                                  Data Management in HBase . . . . . . . . 1994--2004
               Pratik Dutta and   
              Sriparna Saha and   
            Saraansh Chopra and   
                Varnika Miglani   Ensembling of Gene Clusters Utilizing
                                  Deep Learning and Protein-Protein
                                  Interaction Information  . . . . . . . . 2005--2016
                     Lun Hu and   
                 Pengwei Hu and   
                    Xin Luo and   
               Xiaohui Yuan and   
                   Zhu-Hong You   Incorporating the Coevolving Information
                                  of Substrates in Predicting HIV-1
                                  Protease Cleavage Sites  . . . . . . . . 2017--2028
                   Xinyi Yu and   
                 Wenge Rong and   
             Jingshuang Liu and   
                  Deyu Zhou and   
             Yuanxin Ouyang and   
                    Zhang Xiong   LSTM-Based End-to-End Framework for
                                  Biomedical Event Extraction  . . . . . . 2029--2039
               Ehsan Kazemi and   
          Matthias Grossglauser   MPGM: Scalable and Accurate Multiple
                                  Network Alignment  . . . . . . . . . . . 2040--2052
                  Wei Zhang and   
                     Jia Xu and   
                     Xiufen Zou   Predicting Essential Proteins by
                                  Integrating Network Topology,
                                  Subcellular Localization Information,
                                  Gene Expression Profile and GO
                                  Annotation Data  . . . . . . . . . . . . 2053--2061
                 Zengyou He and   
                   Can Zhao and   
                  Hao Liang and   
                      Bo Xu and   
                       Quan Zou   Protein Complexes Identification with
                                  Family-Wise Error Rate Control . . . . . 2062--2073
           Midusha Shrestha and   
             Truong X. Tran and   
           Bidhan Bhattarai and   
              Marc L. Pusey and   
               Ramazan S. Aygun   Schema Matching and Data Integration
                                  with Consistent Naming on Protein
                                  Crystallization Screens  . . . . . . . . 2074--2085
          Thomas C. Carroll and   
       Jude-Thaddeus Ojiaku and   
            Prudence W. H. Wong   Semiglobal Sequence Alignment with Gaps
                                  Using GPU  . . . . . . . . . . . . . . . 2086--2097
            Shun-Ichi Azuma and   
            Toshimitsu Kure and   
                Toshiharu Sugie   Structural Bistability Analysis of
                                  Flower-Shaped and Chain-Shaped Boolean
                                  Networks . . . . . . . . . . . . . . . . 2098--2106
                 John A. Rhodes   Topological Metrizations of Trees, and
                                  New Quartet Methods of Tree Inference    2107--2118
              Gui-Jun Zhang and   
               Xiao-Qi Wang and   
                  Lai-Fa Ma and   
              Liu-Jing Wang and   
                     Jun Hu and   
                  Xiao-Gen Zhou   Two-Stage Distance Feature-based
                                  Optimization Algorithm for \em De novo
                                  Protein Structure Prediction . . . . . . 2119--2130
            Adeola Ogunleye and   
                  Qing-Guo Wang   XGBoost Model for Chronic Kidney Disease
                                  Diagnosis  . . . . . . . . . . . . . . . 2131--2140
              Matteo Manica and   
              Raphael Polig and   
            Mitra Purandare and   
              Roland Mathis and   
       Christoph Hagleitner and   
María Rodríguez Martínez   FPGA Accelerated Analysis of Boolean
                                  Gene Regulatory Networks . . . . . . . . 2141--2147
                  Ming Xiao and   
               Xiangyu Yang and   
                     Jun Yu and   
                       Le Zhang   CGIDLA: Developing the Web Server for
                                  CpG Island Related Density and LAUPs
                                  (Lineage-Associated Underrepresented
                                  Permutations) Study  . . . . . . . . . . 2148--2154
              Manuela Petti and   
           Daniele Bizzarri and   
        Antonella Verrienti and   
               Rosa Falcone and   
                 Lorenzo Farina   Connectivity Significance for Disease
                                  Gene Prioritization in an Expanding
                                  Universe . . . . . . . . . . . . . . . . 2155--2161


IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 18, Number 1, January, 2021

  Carlos Martín-Vide and   
Miguel A. Vega-Rodríguez   \booktitleAlgorithms for Computational
                                  Biology: Sixth Edition . . . . . . . . . 1--1
                   Thien Le and   
                   Aaron Sy and   
             Erin K. Molloy and   
                Qiuyi Zhang and   
                 Satish Rao and   
                   Tandy Warnow   Using Constrained-INC for Large-Scale
                                  Gene Tree and Species Tree Estimation    2--15
            Sridevi Maharaj and   
                Taotao Qian and   
                Zarin Ohiba and   
                    Wayne Hayes   Common Neighbors Extension of the Sticky
                                  Model for PPI Networks Evaluated by
                                  Global and Local Graphlet Similarity . . 16--26
                  Peng Xiao and   
                 Xingyu Cai and   
        Sanguthevar Rajasekaran   EMS3: an Improved Algorithm for Finding
                                  Edit-Distance Based Motifs . . . . . . . 27--37
                    Liu Liu and   
                  Reza Zare and   
                   Shuihua Wang   Guest Editorial: Transfer Learning
                                  Methods Used in Medical Imaging and
                                  Health Informatics . . . . . . . . . . . 38--39
              Yizhang Jiang and   
                Xiaoqing Gu and   
                 Dongrui Wu and   
               Wenlong Hang and   
                   Jing Xue and   
                    Shi Qiu and   
                  Chin-Teng Lin   A Novel Negative-Transfer-Resistant
                                  Fuzzy Clustering Model With a Shared
                                  Cross-Domain Transfer Latent Space and
                                  its Application to Brain CT Image
                                  Segmentation . . . . . . . . . . . . . . 40--52
                Kaijian Xia and   
               TongGuang Ni and   
              Hongsheng Yin and   
                        Bo Chen   Cross-Domain Classification Model With
                                  Knowledge Utilization Maximization for
                                  Recognition of Epileptic EEG Signals . . 53--61
               Chenxi Huang and   
                  Yisha Lan and   
                  Gaowei Xu and   
               Xiaojun Zhai and   
                  Jipeng Wu and   
                    Fan Lin and   
               Nianyin Zeng and   
                Qingqi Hong and   
                E. Y. K. Ng and   
              Yonghong Peng and   
                   Fei Chen and   
                   Guokai Zhang   A Deep Segmentation Network of
                                  Multi-Scale Feature Fusion Based on
                                  Attention Mechanism for IVOCT Lumen
                                  Contour  . . . . . . . . . . . . . . . . 62--69
             Pengjiang Qian and   
               Jiamin Zheng and   
              Qiankun Zheng and   
                   Yuan Liu and   
                Tingyu Wang and   
               Rose Al Helo and   
            Atallah Baydoun and   
              Norbert Avril and   
            Rodney J. Ellis and   
                Harry Friel and   
       Melanie S. Traughber and   
               Ajit Devaraj and   
            Bryan Traughber and   
               Raymond F. Muzic   Transforming UTE-mDixon MR
                                  Abdomen--Pelvis Images Into CT by
                                  Jointly Leveraging Prior Knowledge and
                                  Partial Supervision  . . . . . . . . . . 70--82
               Rishav Singh and   
              Tanveer Ahmed and   
              Abhinav Kumar and   
           Amit Kumar Singh and   
          Anil Kumar Pandey and   
             Sanjay Kumar Singh   Imbalanced Breast Cancer Classification
                                  Using Transfer Learning  . . . . . . . . 83--93
                   Xiang Yu and   
                 Cheng Kang and   
           David S. Guttery and   
            Seifedine Kadry and   
                  Yang Chen and   
                  Yu-Dong Zhang   ResNet--SCDA--50 for Breast Abnormality
                                  Classification . . . . . . . . . . . . . 94--102
                Jintai Chen and   
               Haochao Ying and   
                Xuechen Liu and   
                Jingjing Gu and   
                Ruiwei Feng and   
              Tingting Chen and   
                Honghao Gao and   
                        Jian Wu   A Transfer Learning Based
                                  Super-Resolution Microscopy for Biopsy
                                  Slice Images: The Joint Methods
                                  Perspective  . . . . . . . . . . . . . . 103--113
                   Yong Jin and   
             Zhenjiang Qian and   
             Shengrong Gong and   
                   Weiyong Yang   Learning Transferable Driven and Drone
                                  Assisted Sustainable and Robust Regional
                                  Disease Surveillance for Smart
                                  Healthcare . . . . . . . . . . . . . . . 114--125
                Hansaim Lim and   
                        Lei Xie   A New Weighted Imputed
                                  Neighborhood-Regularized
                                  Tri-Factorization One-Class
                                  Collaborative Filtering Algorithm:
                                  Application to Target Gene Prediction of
                                  Transcription Factors  . . . . . . . . . 126--137
            Daniel R. Allen and   
       Sharma V. Thankachan and   
                      Bojian Xu   An Ultra-Fast and Parallelizable
                                  Algorithm for Finding $k$-Mismatch
                                  Shortest Unique Substrings . . . . . . . 138--148
             P. Tabaszewski and   
          P. Górecki and   
                  A. Markin and   
                T. Anderson and   
                  O. Eulenstein   Consensus of All Solutions for
                                  Intractable Phylogenetic Tree Inference  149--161
    Srilakshmi Pattabiraman and   
                   Tandy Warnow   Profile Hidden Markov Models Are Not
                                  Identifiable . . . . . . . . . . . . . . 162--172
                 Jiaqi Guan and   
                  Runzhe Li and   
                   Sheng Yu and   
                  Xuegong Zhang   A Method for Generating Synthetic
                                  Electronic Medical Record Text . . . . . 173--182
                  Ruiqi Qin and   
                   Lei Duan and   
                Huiru Zheng and   
              Jesse Li-Ling and   
                Kaiwen Song and   
                    Yidan Zhang   An Ontology-Independent Representation
                                  Learning for Similar Disease Detection
                                  Based on Multi-Layer Similarity Network  183--193
                   Wei Long and   
                  Tiange Li and   
                  Yang Yang and   
                  Hong-Bin Shen   FlyIT: \bionameDrosophila Embryogenesis
                                  Image Annotation based on Image Tiling
                                  and Convolutional Neural Networks  . . . 194--204
                 Suyang Dai and   
                 Yuxia Ding and   
                Zihan Zhang and   
                Wenxuan Zuo and   
               Xiaodi Huang and   
                   Shanfeng Zhu   GrantExtractor: Accurate Grant Support
                                  Information Extraction from Biomedical
                                  Fulltext Based on Bi-LSTM-CRF  . . . . . 205--215
                    Bo Yang and   
                Yupei Zhang and   
               Shanmin Pang and   
               Xuequn Shang and   
               Xueqing Zhao and   
                    Minghui Han   Integrating Multi-Omic Data With Deep
                                  Subspace Fusion Clustering for Cancer
                                  Subtype Prediction . . . . . . . . . . . 216--226
                     Lei Du and   
                  Kefei Liu and   
                Xiaohui Yao and   
        Shannon L. Risacher and   
                 Junwei Han and   
           Andrew J. Saykin and   
                    Lei Guo and   
                        Li Shen   Multi-Task Sparse Canonical Correlation
                                  Analysis with Application to Multi-Modal
                                  Brain Imaging Genetics . . . . . . . . . 227--239
              Jianliang Gao and   
                  Ling Tian and   
                 Tengfei Lv and   
               Jianxin Wang and   
                    Bo Song and   
                     Xiaohua Hu   Protein2Vec: Aligning Multiple PPI
                                  Networks with Representation Learning    240--249
              Cameron Chalk and   
             Niels Kornerup and   
               Wyatt Reeves and   
              David Soloveichik   Composable Rate-Independent Computation
                                  in Continuous Chemical Reaction Networks 250--260
             Sara-Jane Dunn and   
              Hillel Kugler and   
                 Boyan Yordanov   Formal Analysis of Network Motifs Links
                                  Structure to Function in Biological
                                  Programs . . . . . . . . . . . . . . . . 261--271
                Pavol Bokes and   
              Michal Hojcka and   
                 Abhyudai Singh   MicroRNA Based Feedforward Control of
                                  Intrinsic Gene Expression Noise  . . . . 272--282
               Keenan Breik and   
              Cameron Chalk and   
                 David Doty and   
                David Haley and   
              David Soloveichik   Programming Substrate-Independent
                                  Kinetic Barriers With Thermodynamic
                                  Binding Networks . . . . . . . . . . . . 283--295
                   Min Zeng and   
                     Min Li and   
                 Zhihui Fei and   
              Fang-Xiang Wu and   
                 Yaohang Li and   
                     Yi Pan and   
                   Jianxin Wang   A Deep Learning Framework for
                                  Identifying Essential Proteins by
                                  Integrating Multiple Types of Biological
                                  Information  . . . . . . . . . . . . . . 296--305
                 Quanhua Mu and   
                   Jiguang Wang   CNAPE: a Machine Learning Method for
                                  Copy Number Alteration Prediction from
                                  Gene Expression  . . . . . . . . . . . . 306--311

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 18, Number 2, March, 2021

   Titinunt Kitrungrotsakul and   
               Xian-Hau Han and   
             Yutaro Iwamoto and   
            Satoko Takemoto and   
               Hideo Yokota and   
             Sari Ipponjima and   
              Tomomi Nemoto and   
                  Wei Xiong and   
                   Yen-Wei Chen   A Cascade of 2.5D CNN and Bidirectional
                                  CLSTM Network for Mitotic Cell Detection
                                  in $4$D Microscopy Image . . . . . . . . 396--404
                  Wen Zhang and   
                Zhishuai Li and   
               Wenzheng Guo and   
                Weitai Yang and   
                     Feng Huang   A Fast Linear Neighborhood
                                  Similarity-Based Network Link Inference
                                  Method to Predict MicroRNA--Disease
                                  Associations . . . . . . . . . . . . . . 405--415
            Biing-Feng Wang and   
             Krister M. Swenson   A Faster Algorithm for Computing the
                                  Kernel of Maximum Agreement Subtrees . . 416--430
                  Yunpei Xu and   
               Hong-Dong Li and   
                     Yi Pan and   
                   Feng Luo and   
              Fang-Xiang Wu and   
                   Jianxin Wang   A Gene Rank Based Approach for Single
                                  Cell Similarity Assessment and
                                  Clustering . . . . . . . . . . . . . . . 431--442
               Sahar Araghi and   
                   Thanh Nguyen   A Hybrid Supervised Approach to Human
                                  Population Identification Using Genomics
                                  Data . . . . . . . . . . . . . . . . . . 443--454
             Hsin-Hung Chou and   
             Ching-Tien Hsu and   
              Li-Hsuan Chen and   
              Yue-Cheng Lin and   
                 Sun-Yuan Hsieh   A Novel Branch-and-Bound Algorithm for
                                  the Protein Folding Problem in the $3$D
                                  HP Model . . . . . . . . . . . . . . . . 455--462
                 Huimin Luo and   
               Jianxin Wang and   
                  Cheng Yan and   
                     Min Li and   
              Fang-Xiang Wu and   
                         Yi Pan   A Novel Drug Repositioning Approach
                                  Based on Collaborative Metric Learning   463--471
 Seyedeh Shaghayegh Sadeghi and   
       Mohammad Reza Keyvanpour   An Analytical Review of Computational
                                  Drug Repurposing . . . . . . . . . . . . 472--488
            Anupam Banerjee and   
                 Kuntal Pal and   
                   Pralay Mitra   An Evolutionary Profile Guided Greedy
                                  Parallel Replica-Exchange Monte Carlo
                                  Search Algorithm for Rapid Convergence
                                  in Protein Design  . . . . . . . . . . . 489--499
                 Wanrong Gu and   
                 Ziye Zhang and   
                Xianfen Xie and   
                      Yichen He   An Improved Muti-Task Learning Algorithm
                                  for Analyzing Cancer Survival Data . . . 500--511
                 Kevin Chow and   
           Aisharjya Sarkar and   
              Rasha Elhesha and   
            Pietro Cinaglia and   
                   Ahmet Ay and   
                  Tamer Kahveci   \pkgANCA: Alignment-Based Network
                                  Construction Algorithm . . . . . . . . . 512--524
     Miguel González and   
  Cristina Gutiérrez and   
        Rodrigo Martínez   Bayesian Inference in Y-Linked Two-Sex
                                  Branching Processes with Mutations: ABC
                                  Approach . . . . . . . . . . . . . . . . 525--538
                 Xiguo Yuan and   
                   Jiaao Yu and   
                 Jianing Xi and   
                Liying Yang and   
             Junliang Shang and   
                     Zhe Li and   
                     Junbo Duan   \pkgCNV\_IFTV: an Isolation Forest and
                                  Total Variation-Based Detection of CNVs
                                  from Short-Read Sequencing Data  . . . . 539--549
              Sourav Biswas and   
                Sumanta Ray and   
      Sanghamitra Bandyopadhyay   Colored Network Motif Analysis by
                                  Dynamic Programming Approach: an
                                  Application in Host Pathogen Interaction
                                  Network  . . . . . . . . . . . . . . . . 550--561
            Jacob C. Kimmel and   
            Andrew S. Brack and   
            Wallace F. Marshall   Deep Convolutional and Recurrent Neural
                                  Networks for Cell Motility
                                  Discrimination and Prediction  . . . . . 562--574
                     Min Li and   
                  Yake Wang and   
              Ruiqing Zheng and   
                Xinghua Shi and   
                 Yaohang Li and   
              Fang-Xiang Wu and   
                   Jianxin Wang   DeepDSC: a Deep Learning Method to
                                  Predict Drug Sensitivity of Cancer Cell
                                  Lines  . . . . . . . . . . . . . . . . . 575--582
             Jingrong Zhang and   
                 Zihao Wang and   
                Zhiyong Liu and   
                       Fa Zhang   Improve the Resolution and Parallel
                                  Performance of the Three-Dimensional
                                  Refine Algorithm in RELION Using CUDA
                                  and MPI  . . . . . . . . . . . . . . . . 583--595
             Muhammad Awais and   
              Waqar Hussain and   
         Yaser Daanial Khan and   
              Nouman Rasool and   
            Sher Afzal Khan and   
                  Kuo-Chen Chou   \pkgiPhosH-PseAAC: Identify
                                  Phosphohistidine Sites in Proteins by
                                  Blending Statistical Moments and
                                  Position Relative Features According to
                                  the Chou's 5-Step Rule and General
                                  Pseudo Amino Acid Composition  . . . . . 596--610
                  Cheng Yan and   
                Guihua Duan and   
              Fang-Xiang Wu and   
                     Yi Pan and   
                   Jianxin Wang   \pkgMCHMDA: Predicting Microbe-Disease
                                  Associations Based on Similarities and
                                  Low-Rank Matrix Completion . . . . . . . 611--620
                 Cheng Peng and   
                   Xinyu Wu and   
                   Wen Yuan and   
               Xinran Zhang and   
                   Yu Zhang and   
                        Ying Li   \pkgMGRFE: Multilayer Recursive Feature
                                  Elimination Based on an Embedded Genetic
                                  Algorithm for Cancer Classification  . . 621--632
          Alexandre Gondeau and   
              Zahia Aouabed and   
              Mohamed Hijri and   
        Pedro R. Peres-Neto and   
            Vladimir Makarenkov   Object Weighting: a New Clustering
                                  Approach to Deal with Outliers and
                                  Cluster Overlap in Computational Biology 633--643
     Alireza Karbalayghareh and   
              Xiaoning Qian and   
            Edward R. Dougherty   Optimal Bayesian Transfer Learning for
                                  Count Data . . . . . . . . . . . . . . . 644--655
Andrés F. López-Lopera and   
           Nicolas Durrande and   
     Mauricio A. Álvarez   Physically-Inspired Gaussian Process
                                  Models for Post-Transcriptional
                                  Regulation in \bionameDrosophila . . . . 656--666
                Qinhu Zhang and   
                  Zhen Shen and   
                De-Shuang Huang   Predicting in-vitro Transcription
                                  Factor Binding Sites Using DNA Sequence
                                  $+$ Shape  . . . . . . . . . . . . . . . 667--676
               Jingxuan Qiu and   
                 Tianyi Qiu and   
                Qingli Dong and   
                  Dongpo Xu and   
                 Xiang Wang and   
                   Qi Zhang and   
                   Jing Pan and   
                       Qing Liu   Predicting the Antigenic Relationship of
                                  Foot-and-Mouth Disease Virus for Vaccine
                                  Selection Through a Computational Model  677--685
                 Chen Zhang and   
                    Yanrui Ding   Probing the Relation Between Community
                                  Evolution in Dynamic Residue Interaction
                                  Networks and Xylanase Thermostability    686--696
              Gui-Jun Zhang and   
                Teng-Yu Xie and   
              Xiao-Gen Zhou and   
              Liu-Jing Wang and   
                         Jun Hu   Protein Structure Prediction Using
                                  Population-Based Algorithm Guided by
                                  Information Entropy  . . . . . . . . . . 697--707
              Saikat Biswas and   
              Pabitra Mitra and   
     Krothapalli Sreenivasa Rao   Relation Prediction of Co-Morbid
                                  Diseases Using Knowledge Graph
                                  Completion . . . . . . . . . . . . . . . 708--717
                Xiaona Song and   
                    Mi Wang and   
                 Shuai Song and   
                   Choon Ki Ahn   Sampled-Data State Estimation of
                                  Reaction Diffusion Genetic Regulatory
                                  Networks via Space-Dividing Approaches   718--730
                  Guimu Guo and   
               Hongzhi Chen and   
                     Da Yan and   
                James Cheng and   
               Jake Y. Chen and   
                   Zechen Chong   Scalable De Novo Genome Assembly Using a
                                  Pregel-Like Graph-Parallel System  . . . 731--744

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 18, Number 3, May / June, 2021

                     Da Yan and   
          Sharma Thankachan and   
                   Jake Y. Chen   Guest Editorial for Selected Papers From
                                  BIOKDD 2019  . . . . . . . . . . . . . . 809--810
            Vineet K. Raghu and   
                  Xiaoyu Ge and   
              Arun Balajiee and   
           Daniel J. Shirer and   
                   Isha Das and   
        Panayiotis V. Benos and   
           Panos K. Chrysanthis   A Pipeline for Integrated Theory and
                                  Data-Driven Modeling of Biomedical Data  811--822
              Tianwen Jiang and   
               Qingkai Zeng and   
                  Tong Zhao and   
                   Bing Qin and   
                   Ting Liu and   
           Nitesh V. Chawla and   
                     Meng Jiang   Biomedical Knowledge Graphs Construction
                                  From Conditional Statements  . . . . . . 823--835
       Jithin K. Sreedharan and   
         Krzysztof Turowski and   
           Wojciech Szpankowski   Revisiting Parameter Estimation in
                                  Biological Networks: Influence of
                                  Symmetries . . . . . . . . . . . . . . . 836--849
                     Ke Yan and   
                  Zhiwei Ji and   
                    Qun Jin and   
                  Qing-Guo Wang   Guest Editorial: Machine Learning for
                                  AI-Enhanced Healthcare and Medical
                                  Services: New Development and Promising
                                  Solution . . . . . . . . . . . . . . . . 850--851
                 Sheng Lian and   
                     Lei Li and   
                Guiren Lian and   
                  Xiao Xiao and   
                Zhiming Luo and   
                      Shaozi Li   A Global and Local Enhanced Residual
                                  U-Net for Accurate Retinal Vessel
                                  Segmentation . . . . . . . . . . . . . . 852--862
                 Huijuan Lu and   
                 Huiyun Gao and   
                 Minchao Ye and   
                    Xiuhui Wang   A Hybrid Ensemble Algorithm Combining
                                  AdaBoost and Genetic Algorithm for
                                  Cancer Classification with Gene
                                  Expression Data  . . . . . . . . . . . . 863--870
                Xiaodan Yan and   
               Baojiang Cui and   
                    Yang Xu and   
                 Peilin Shi and   
                      Ziqi Wang   A Method of Information Protection for
                                  Collaborative Deep Learning under GAN
                                  Model Attack . . . . . . . . . . . . . . 871--881
             Qingchen Zhang and   
             Changchuan Bai and   
           Laurence T. Yang and   
                Zhikui Chen and   
                    Peng Li and   
                        Hang Yu   A Unified Smart Chinese Medicine
                                  Framework for Healthcare and Medical
                                  Services . . . . . . . . . . . . . . . . 882--890
                 Dehua Chen and   
               Meihua Huang and   
                      Weimin Li   Knowledge-Powered Deep Breast Tumor
                                  Classification With Multiple Medical
                                  Reports  . . . . . . . . . . . . . . . . 891--901
                Yiyuan Chen and   
                Yufeng Wang and   
                  Liang Cao and   
                        Qun Jin   CCFS: a Confidence-Based Cost-Effective
                                  Feature Selection Scheme for Healthcare
                                  Data Classification  . . . . . . . . . . 902--911
              Xiaokang Zhou and   
                     Yue Li and   
                      Wei Liang   CNN-RNN Based Intelligent Recommendation
                                  for Online Medical Pre-Diagnosis Support 912--921
                     Lu Yan and   
              Weihong Huang and   
                Liming Wang and   
                  Song Feng and   
              Yonghong Peng and   
                       Jie Peng   Data-Enabled Digestive Medicine: a New
                                  Big Data Analytics Platform  . . . . . . 922--931
     Mauricio Guevara Souza and   
           Edgar E. Vallejo and   
                  Karol Estrada   Detecting Clustered Independent Rare
                                  Variant Associations Using Genetic
                                  Algorithms . . . . . . . . . . . . . . . 932--939
               Yongjin Zhou and   
              Weijian Huang and   
                   Pei Dong and   
                   Yong Xia and   
                  Shanshan Wang   D-UNet: a Dimension-Fusion U Shape
                                  Network for Chronic Stroke Lesion
                                  Segmentation . . . . . . . . . . . . . . 940--950
                  Yaqi Wang and   
               Lingling Sun and   
                        Qun Jin   Enhanced Diagnosis of Pneumothorax with
                                  an Improved Real-Time Augmentation for
                                  Imbalanced Chest X-rays Data Based on
                                  DCNN . . . . . . . . . . . . . . . . . . 951--962
                Xiuhui Wang and   
               Shiling Feng and   
                     Wei Qi Yan   Human Gait Recognition Based on
                                  Self-Adaptive Hidden Markov Model  . . . 963--972
          Jayanta Kumar Pal and   
         Shubhra Sankar Ray and   
                  Sankar K. Pal   Identifying Drug Resistant miRNAs Using
                                  Entropy Based Ranking  . . . . . . . . . 973--984
                  Bing Wang and   
              Changqing Mei and   
              Yuanyuan Wang and   
                Yuming Zhou and   
              Mu-Tian Cheng and   
             Chun-Hou Zheng and   
                   Lei Wang and   
                  Jun Zhang and   
                  Peng Chen and   
                      Yan Xiong   Imbalance Data Processing Strategy for
                                  Protein Interaction Sites Prediction . . 985--994
                Xiran Jiang and   
                  Jiaxin Li and   
               Yangyang Kan and   
                     Tao Yu and   
               Shijie Chang and   
              Xianzheng Sha and   
              Hairong Zheng and   
                 Yahong Luo and   
                  Shanshan Wang   MRI Based Radiomics Approach With Deep
                                  Learning for Prediction of Vessel
                                  Invasion in Early-Stage Cervical Cancer  995--1002
                   Cheng Li and   
                  Jingxu Xu and   
                 Qiegen Liu and   
               Yongjin Zhou and   
                  Lisha Mou and   
                   Zuhui Pu and   
                   Yong Xia and   
              Hairong Zheng and   
                  Shanshan Wang   Multi-View Mammographic Density
                                  Classification by Dilated and
                                  Attention-Guided Residual Learning . . . 1003--1013
                 Ali Cakmak and   
                 M. Hasan Celik   Personalized Metabolic Analysis of
                                  Diseases . . . . . . . . . . . . . . . . 1014--1025
                Wenyan Wang and   
                Yuming Zhou and   
              Mu-Tian Cheng and   
                   Yan Wang and   
             Chun-Hou Zheng and   
                  Yan Xiong and   
                  Peng Chen and   
                  Zhiwei Ji and   
                      Bing Wang   Potential Pathogenic Genes
                                  Prioritization Based on Protein Domain
                                  Interaction Network Analysis . . . . . . 1026--1034
             Souad Bouasker and   
             Wissem Inoubli and   
            Sadok Ben Yahia and   
                    Gayo Diallo   Pregnancy Associated Breast Cancer Gene
                                  Expressions: New Insights on Their
                                  Regulation Based on Rare Correlated
                                  Patterns . . . . . . . . . . . . . . . . 1035--1048
                 Jiechen Li and   
               Haochen Zhao and   
               Zhanwei Xuan and   
                 Jingwen Yu and   
                 Xiang Feng and   
                    Bo Liao and   
                       Lei Wang   A Novel Approach for Potential Human
                                  LncRNA-Disease Association Prediction
                                  Based on Local Random Walk . . . . . . . 1049--1059
                    Min Liu and   
                  Yalan Liu and   
                 Weili Qian and   
                    Yaonan Wang   DeepSeed Local Graph Matching for
                                  Densely Packed Cells Tracking  . . . . . 1060--1069
                 Zhen Zhang and   
                 Junwei Luo and   
                 Juan Shang and   
                     Min Li and   
              Fang-Xiang Wu and   
                     Yi Pan and   
                   Jianxin Wang   Deletion Detection Method Using the
                                  Distribution of Insert Size and a
                                  Precise Alignment Strategy . . . . . . . 1070--1081
                Tingting Yu and   
               Jianxing Liu and   
            Qingshuang Zeng and   
                      Ligang Wu   Dissipativity-Based Filtering for
                                  Switched Genetic Regulatory Networks
                                  with Stochastic Disturbances and
                                  Time-Varying Delays  . . . . . . . . . . 1082--1092
                    Ying An and   
              Nengjun Huang and   
               Xianlai Chen and   
               Fangxiang Wu and   
                   Jianxin Wang   High-Risk Prediction of Cardiovascular
                                  Diseases via Attention-Based Deep Neural
                                  Networks . . . . . . . . . . . . . . . . 1093--1105
              Qingfeng Chen and   
                 Dehuan Lai and   
                    Wei Lan and   
                   Ximin Wu and   
               Baoshan Chen and   
                    Jin Liu and   
        Yi-Ping Phoebe Chen and   
                   Jianxin Wang   ILDMSF: Inferring Associations Between
                                  Long Non-Coding RNA and Disease Based on
                                  Multi-Similarity Fusion  . . . . . . . . 1106--1112

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 18, Number 4, July / August, 2021

              Dong-Qing Wei and   
       Aman Chandra Kaushik and   
        Gurudeeban Selvaraj and   
                         Yi Pan   Editorial: Computational Genomics and
                                  Molecular Medicine for Emerging COVID-19 1227--1229
                Chunmei Cui and   
              Chuanbo Huang and   
                 Wanlu Zhou and   
                Xiangwen Ji and   
             Fenghong Zhang and   
                 Liang Wang and   
                  Yuan Zhou and   
                    Qinghua Cui   \geneAGTR2, One Possible Novel Key Gene
                                  for the Entry of SARS-CoV-2 Into Human
                                  Cells  . . . . . . . . . . . . . . . . . 1230--1233
            Yadunath Pathak and   
        Piyush Kumar Shukla and   
                     K. V. Arya   Deep Bidirectional Classification Model
                                  for COVID-19 Disease Infected Patients   1234--1241
                Jinxiong Lv and   
                  Shikui Tu and   
                         Lei Xu   Detection of Phenotype-Related Mutations
                                  of COVID-19 via the Whole Genomic Data   1242--1249
                  Ming Xiao and   
                Guangdi Liu and   
              Jianghang Xie and   
                 Zichun Dai and   
                  Zihao Wei and   
                  Ziyao Ren and   
                     Jun Yu and   
                       Le Zhang   2019nCoVAS: Developing the Web Service
                                  for Epidemic Transmission Prediction,
                                  Genome Analysis, and Psychological
                                  Stress Assessment for 2019-nCoV  . . . . 1250--1261
       Chandrabose Selvaraj and   
Dhurvas Chandrasekaran Dinesh and   
               Umesh Panwar and   
                Evzen Boura and   
            Sanjeev Kumar Singh   High-Throughput Screening and Quantum
                                  Mechanics for Identifying Potent
                                  Inhibitors Against Mac1 Domain of
                                  SARS-CoV-2 Nsp3  . . . . . . . . . . . . 1262--1270
          Broto Chakrabarty and   
             Dibyajyoti Das and   
      Gopalakrishnan Bulusu and   
                     Arijit Roy   Network-Based Analysis of Fatal
                                  Comorbidities of COVID-19 and Potential
                                  Therapeutics . . . . . . . . . . . . . . 1271--1280
          Elmeri M. Jokinen and   
       Krishnasamy Gopinath and   
           Sami T. Kurkinen and   
       Olli T. Pentikäinen   Detection of Binding Sites on SARS-CoV-2
                                  Spike Protein Receptor-Binding Domain by
                                  Molecular Dynamics Simulations in Mixed
                                  Solvents . . . . . . . . . . . . . . . . 1281--1289
                Deshan Zhou and   
             Shaoliang Peng and   
              Dong-Qing Wei and   
                   Wu Zhong and   
                  Yutao Dou and   
                    Xiaolan Xie   LUNAR: Drug Screening for Novel
                                  Coronavirus Based on Representation
                                  Learning Graph Convolutional Network . . 1290--1298
       Aman Chandra Kaushik and   
              Aamir Mehmood and   
        Gurudeeban Selvaraj and   
               Xiaofeng Dai and   
                     Yi Pan and   
                  Dong-Qing Wei   CoronaPep: an Anti-Coronavirus Peptide
                                  Generation Tool  . . . . . . . . . . . . 1299--1304
                 Zhimiao Yu and   
                  Jiarui Lu and   
                   Yuan Jin and   
                      Yang Yang   KenDTI: an Ensemble Model for Predicting
                                  Drug-Target Interaction by Integrating
                                  Multi-Source Information . . . . . . . . 1305--1314
                ShanShan Hu and   
                  DeNan Xia and   
                  Benyue Su and   
                  Peng Chen and   
                  Bing Wang and   
                      Jinyan Li   A Convolutional Neural Network System to
                                  Discriminate Drug-Target Interactions    1315--1324
                   Enze Liu and   
                     Jin Li and   
       Garrett H. Kinnebrew and   
              Pengyue Zhang and   
                  Yan Zhang and   
                Lijun Cheng and   
                        Lang Li   A Fast and Furious Bayesian Network and
                                  Its Application of Identifying Colon
                                  Cancer to Liver Metastasis Gene
                                  Regulatory Networks  . . . . . . . . . . 1325--1335
     Hector Carrillo-Cabada and   
              Jeremy Benson and   
           Asghar M. Razavi and   
           Brianna Mulligan and   
          Michel A. Cuendet and   
            Harel Weinstein and   
             Michela Taufer and   
                 Trilce Estrada   A Graphic Encoding Method for
                                  Quantitative Classification of Protein
                                  Structure and Representation of
                                  Conformational Changes . . . . . . . . . 1336--1349
               Aiying Zhang and   
                  Jian Fang and   
                 Wenxing Hu and   
           Vince D. Calhoun and   
                   Yu-Ping Wang   A Latent Gaussian Copula Model for Mixed
                                  Data Analysis in Brain Imaging Genetics  1350--1360
         Ulavappa B. Angadi and   
   Krishna Kumar Chaturvedi and   
          Sudhir Srivastava and   
                       Anil Rai   A Novel Way of Comparing Protein $3$D
                                  Structure Using Graph Partitioning
                                  Approach . . . . . . . . . . . . . . . . 1361--1368
               Liguang Wang and   
                 Yujia Wang and   
                      Yi Fu and   
                  Yunge Gao and   
                  Jiawei Du and   
                  Chen Yang and   
                   Jianxiao Liu   AFSBN: a Method of Artificial Fish Swarm
                                  Optimizing Bayesian Network for
                                  Epistasis Detection  . . . . . . . . . . 1369--1383
                Ziying Yang and   
                 Guoxian Yu and   
                  Maozu Guo and   
                 Jiantao Yu and   
           Xiangliang Zhang and   
                       Jun Wang   CDPath: Cooperative Driver Pathways
                                  Discovery Using Integer Linear
                                  Programming and Markov Clustering  . . . 1384--1395
                Bing Nan Li and   
                 Xinle Wang and   
                  Rong Wang and   
                  Teng Zhou and   
                 Rongke Gao and   
          Edward J. Ciaccio and   
                 Peter H. Green   Celiac Disease Detection From
                                  Videocapsule Endoscopy Images Using
                                  Strip Principal Component Analysis . . . 1396--1404
                     Yan Ge and   
          Philipp Rosendahl and   
       Claudio Durán and   
        Nicole Töpfner and   
                Sara Ciucci and   
                Jochen Guck and   
     Carlo Vittorio Cannistraci   Cell Mechanics Based Computational
                                  Classification of Red Blood Cells Via
                                  Machine Intelligence Applied to
                                  Morpho-Rheological Markers . . . . . . . 1405--1415
                Wenju Zhang and   
               Zhewei Liang and   
                   Xin Chen and   
                    Lei Xin and   
               Baozhen Shan and   
                Zhigang Luo and   
                        Ming Li   ChimST: an Efficient Spectral Library
                                  Search Tool for Peptide Identification
                                  from Chimeric Spectra in Data-Dependent
                                  Acquisition  . . . . . . . . . . . . . . 1416--1425
        Sidharth Maheshwari and   
    Venkateshwarlu Y. Gudur and   
              Rishad Shafik and   
                 Ian Wilson and   
              Alex Yakovlev and   
                  Amit Acharyya   CORAL: Verification-Aware OpenCL Based
                                  Read Mapper for Heterogeneous Systems    1426--1438
               Yingwen Zhao and   
                   Jun Wang and   
                  Maozu Guo and   
           Xiangliang Zhang and   
                     Guoxian Yu   Cross-Species Protein Function
                                  Prediction with Asynchronous-Random Walk 1439--1450
                  Jun Zhang and   
               Qingcai Chen and   
                        Bin Liu   DeepDRBP-2L: a New Genome Annotation
                                  Predictor for Identifying DNA-Binding
                                  Proteins and RNA-Binding Proteins Using
                                  Convolutional Neural Network and Long
                                  Short-Term Memory  . . . . . . . . . . . 1451--1463
             Shaoliang Peng and   
                Yaning Yang and   
                    Wei Liu and   
                     Fei Li and   
                   Xiangke Liao   Discriminant Projection Shared
                                  Dictionary Learning for Classification
                                  of Tumors Using Gene Expression Data . . 1464--1473
               Furkan Ozden and   
            Metin Can Siper and   
              Necmi Acarsoy and   
            Tugrulcan Elmas and   
                Bryan Marty and   
                 Xinjian Qi and   
              A. Ercument Cicek   DORMAN: Database of Reconstructed
                                  MetAbolic Networks . . . . . . . . . . . 1474--1480
                     Yue Hu and   
               Jin-Xing Liu and   
              Ying-Lian Gao and   
                 Junliang Shang   DSTPCA: Double-Sparse Constrained Tensor
                                  Principal Component Analysis Method for
                                  Feature Selection  . . . . . . . . . . . 1481--1491
                Xingyu Liao and   
                     Min Li and   
                 Junwei Luo and   
                    You Zou and   
              Fang-Xiang Wu and   
                     Yi-Pan and   
                   Feng Luo and   
                   Jianxin Wang   EPGA-SC: a Framework for \em de novo
                                  Assembly of Single-Cell Sequencing Reads 1492--1503
             Afsaneh Javadi and   
          Faezeh Keighobadi and   
             Vahab Nekoukar and   
               Marzieh Ebrahimi   Finite-Set Model Predictive Control of
                                  Melanoma Cancer Treatment Using
                                  Signaling Pathway Inhibitor of Cancer
                                  Stem Cell  . . . . . . . . . . . . . . . 1504--1511
                  Chao Wang and   
                   Lei Gong and   
                Shiming Lei and   
                Haijie Fang and   
                      Xi Li and   
                  Aili Wang and   
                    Xuehai Zhou   GenSeq+: a Scalable High-Performance
                                  Accelerator for Genome Sequencing  . . . 1512--1523

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 18, Number 5, September / October, 2021

                Kaijian Xia and   
              Yizhang Jiang and   
               Yudong Zhang and   
                         Wen Si   Guest Editorial: Advanced
                                  Machine-Learning Methods for
                                  Brain-Machine Interfacing or
                                  Brain-Computer Interfacing . . . . . . . 1643--1644
                Xiaotong Gu and   
                 Zehong Cao and   
            Alireza Jolfaei and   
                    Peng Xu and   
                 Dongrui Wu and   
             Tzyy-Ping Jung and   
                  Chin-Teng Lin   EEG-Based Brain-Computer Interfaces
                                  (BCIs): a Survey of Recent Studies on
                                  Signal Sensing Technologies and
                                  Computational Intelligence Approaches
                                  and Their Applications . . . . . . . . . 1645--1666
             Yuanpeng Zhang and   
                Ziyuan Zhou and   
                 Wenjie Pan and   
                 Heming Bai and   
                    Wei Liu and   
                    Li Wang and   
                     Chuang Lin   Epilepsy Signal Recognition Using Online
                                  Transfer TSK Fuzzy Classifier Underlying
                                  Classification Error and Joint
                                  Distribution Consensus Regularization    1667--1678
                Xiaoqing Gu and   
                 Cong Zhang and   
                   TongGuang Ni   A Hierarchical Discriminative Sparse
                                  Representation Classifier for EEG Signal
                                  Detection  . . . . . . . . . . . . . . . 1679--1687
                  Zhihan Lv and   
                 Liang Qiao and   
               Qingjun Wang and   
            Francesco Piccialli   Advanced Machine-Learning Methods for
                                  Brain-Computer Interfacing . . . . . . . 1688--1698
                     Bo Lin and   
             Shuiguang Deng and   
                Honghao Gao and   
                    Jianwei Yin   A Multi-Scale Activity Transition
                                  Network for Data Translation in EEG
                                  Signals Decoding . . . . . . . . . . . . 1699--1709
                Shuaiqi Liu and   
                    Xu Wang and   
                  Ling Zhao and   
                   Jie Zhao and   
                     Qi Xin and   
                  Shui-Hua Wang   Subject-Independent Emotion Recognition
                                  of EEG Signals Based on Dynamic
                                  Empirical Convolutional Neural Network   1710--1721
               Chenxi Huang and   
                Yutian Xiao and   
                      Gaowei Xu   Predicting Human Intention-Behavior
                                  Through EEG Signal Analysis Using
                                  Multi-Scale CNN  . . . . . . . . . . . . 1722--1729
            De-Shuang Huang and   
     Vitoantonio Bevilacqua and   
             M. Michael Gromiha   Guest Editorial for Special Section on
                                  the 15th International Conference on
                                  Intelligent Computing (ICIC) . . . . . . 1730--1732
                  Kai Zheng and   
               Zhu-Hong You and   
                   Lei Wang and   
                  Yi-Ran Li and   
                Ji-Ren Zhou and   
                   Hai-Tao Zeng   MISSIM: an Incremental Learning-Based
                                  Model With Applications to the
                                  Prediction of miRNA-Disease Association  1733--1742
                Qinhu Zhang and   
                Dailun Wang and   
              Kyungsook Han and   
                De-Shuang Huang   Predicting TF-DNA Binding Motifs from
                                  ChIP-seq Datasets Using the Bag-Based
                                  Classifier Combined With a Multi-Fold
                                  Learning Scheme  . . . . . . . . . . . . 1743--1751
                 Hongjie Wu and   
               Huajing Ling and   
                    Lei Gao and   
                  Qiming Fu and   
                Weizhong Lu and   
                 Yijie Ding and   
                  Min Jiang and   
                       Haiou Li   Empirical Potential Energy Function
                                  Toward ab Initio Folding G
                                  Protein-Coupled Receptors  . . . . . . . 1752--1762
                    Yue Liu and   
               Shu-Lin Wang and   
             Jun-Feng Zhang and   
                  Wei Zhang and   
                    Su Zhou and   
                         Wen Li   DMFMDA: Prediction of Microbe-Disease
                                  Associations Based on Deep Matrix
                                  Factorization Using Bayesian
                                  Personalized Ranking . . . . . . . . . . 1763--1772
                  Xinguo Lu and   
                 Xinyu Wang and   
                    Li Ding and   
                  Jinxin Li and   
                    Yan Gao and   
                       Keren He   frDriver: a Functional Region Driver
                                  Identification for Protein Sequence  . . 1773--1783
                  Jiang Xie and   
                 Chang Zhao and   
                 Jiamin Sun and   
                  Jiaxin Li and   
               Fuzhang Yang and   
                  Jiao Wang and   
                       Qing Nie   Prediction of Essential Genes in
                                  Comparison States Using Machine Learning 1784--1792
                Qinhu Zhang and   
                   Wenbo Yu and   
              Kyungsook Han and   
             Asoke K. Nandi and   
                De-Shuang Huang   Multi-Scale Capsule Network for
                                  Predicting DNA-Protein Binding Sites . . 1793--1800
                  Menglu Li and   
                 Yanan Wang and   
                    Fuyi Li and   
                   Yun Zhao and   
                 Mengya Liu and   
                Sijia Zhang and   
                 Yannan Bin and   
               A. Ian Smith and   
           Geoffrey I. Webb and   
                    Jian Li and   
             Jiangning Song and   
                    Junfeng Xia   A Deep Learning-Based Method for
                                  Identification of Bacteriophage-Host
                                  Interaction  . . . . . . . . . . . . . . 1801--1810
                 Xiguo Yuan and   
                 Junping Li and   
                    Jun Bai and   
                     Jianing Xi   A Local Outlier Factor-Based Detection
                                  of Copy Number Variations From NGS Data  1811--1820
              Hai-Hui Huang and   
                     Yong Liang   A Novel Cox Proportional Hazards Model
                                  for High-Dimensional Genomic Data in
                                  Cancer Prognosis . . . . . . . . . . . . 1821--1830
               Jinhao Zhang and   
                Zehua Zhang and   
                Lianrong Pu and   
                 Jijun Tang and   
                        Fei Guo   AIEpred: an Ensemble Predictive Model of
                                  Classifier Chain to Identify
                                  Anti-Inflammatory Peptides . . . . . . . 1831--1840
                  Ying Qian and   
                   Yu Zhang and   
                 Jiongmin Zhang   Alignment-Free Sequence Comparison With
                                  Multiple $k$ Values  . . . . . . . . . . 1841--1849
                 Benlian Xu and   
                   Jian Shi and   
                  Mingli Lu and   
              Jinliang Cong and   
                  Ling Wang and   
                    Brett Nener   An Automated Cell Tracking Approach With
                                  Multi-Bernoulli Filtering and Ant Colony
                                  Labor Division . . . . . . . . . . . . . 1850--1863
               Gautam Kumar and   
              Rajnish Kumar and   
            Manoj Kumar Pal and   
          Nilotpal Pramanik and   
           Tapobrata Lahiri and   
               Ankita Gupta and   
                   Saket Pandey   APT: an Automated Probe Tracker From
                                  Gene Expression Data . . . . . . . . . . 1864--1874
                  Yue Zhang and   
             Chunfang Zheng and   
              Sindeed Islam and   
               Yong-Min Kim and   
                  David Sankoff   Branching Out to Speciation in a Model
                                  of Fractionation: The Malvaceae  . . . . 1875--1884
         Atefeh Ghasemnejad and   
             Samira Bazmara and   
             Mahsa Shadmani and   
        Kamran Pooshang Bagheri   Designing a New Multi-Epitope Pertussis
                                  Vaccine with Highly Population Coverage
                                  Based on a Novel Sequence and Structural
                                  Filtration Algorithm . . . . . . . . . . 1885--1892
                 Xiguo Yuan and   
                Xiangyan Xu and   
               Haiyong Zhao and   
                     Junbo Duan   ERINS: Novel Sequence Insertion
                                  Detection by Constructing an Extended
                                  Reference  . . . . . . . . . . . . . . . 1893--1901
              Chetna Kumari and   
          Muhammad Abulaish and   
                 Naidu Subbarao   Exploring Molecular Descriptors and
                                  Fingerprints to Predict mTOR Kinase
                                  Inhibitors using Machine Learning
                                  Techniques . . . . . . . . . . . . . . . 1902--1913
              Jiaojiao Chen and   
                Jianbo Jiao and   
               Shengfeng He and   
               Guoqiang Han and   
                       Jing Qin   Few-Shot Breast Cancer Metastases
                                  Classification via Unsupervised Cell
                                  Ranking  . . . . . . . . . . . . . . . . 1914--1923
               Belal Medhat and   
                  Ahmed Shawish   FLR: a Revolutionary Alignment-Free
                                  Similarity Analysis Methodology for
                                  DNA-Sequences  . . . . . . . . . . . . . 1924--1936
                Cangzhi Jia and   
                 Meng Zhang and   
                Cunshuo Fan and   
                    Fuyi Li and   
                 Jiangning Song   Formator: Predicting Lysine Formylation
                                  Sites Based on the Most Distant
                                  Undersampling and Safe-Level Synthetic
                                  Minority Oversampling  . . . . . . . . . 1937--1945

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 18, Number 6, November / December, 2021

                 Srinivas Aluru   Editorial: From the New Editor-in-Chief  2058--2058
  Carlos Martín-Vide and   
Miguel A. Vega-Rodríguez   \booktitleAlgorithms for Computational
                                  Biology: Seventh Edition . . . . . . . . 2059--2060
          Tathagata Debnath and   
                  Mingzhou Song   Fast Optimal Circular Clustering and
                                  Applications on Round Genomes  . . . . . 2061--2071
             Shaoheng Liang and   
              Qingnan Liang and   
                   Rui Chen and   
                       Ken Chen   Stratified Test Accurately Identifies
                                  Differentially Expressed Genes Under
                                  Batch Effects in Single-Cell Data  . . . 2072--2079
   Andre Rodrigues Oliveira and   
      Géraldine Jean and   
           Guillaume Fertin and   
        Klairton Lima Brito and   
               Ulisses Dias and   
                    Zanoni Dias   Sorting Permutations by Intergenic
                                  Operations . . . . . . . . . . . . . . . 2080--2093
           Gabriel Siqueira and   
        Klairton Lima Brito and   
               Ulisses Dias and   
                    Zanoni Dias   Heuristics for Genome Rearrangement
                                  Distance With Replicated Genes . . . . . 2094--2108
         Nickolas Steinauer and   
                Kevin Zhang and   
                   Chun Guo and   
                  Jinsong Zhang   Computational Modeling of Gene-Specific
                                  Transcriptional Repression, Activation
                                  and Chromatin Interactions in
                                  Leukemogenesis by LASSO-Regularized
                                  Logistic Regression  . . . . . . . . . . 2109--2122
               Louxin Zhang and   
             Shaoliang Peng and   
        Yi-Ping Phoebe Chen and   
              David Sankoff and   
                Guoliang Li and   
                  Hong-Yu Zhang   Guest Editorial for the 17th Asia
                                  Pacific Bioinformatics Conference  . . . 2123--2124
      Pawe\l Górecki and   
          Oliver Eulenstein and   
                   Jerzy Tiuryn   The Unconstrained Diameters of the
                                  Duplication-Loss Cost and the Loss Cost  2125--2135
            Melissa Grueter and   
               Kalani Duran and   
           Ramya Ramalingam and   
            Ran Libeskind-Hadas   Reconciliation Reconsidered: In Search
                                  of a Most Representative Reconciliation
                                  in the Duplication-Transfer-Loss Model   2136--2143
                 Haoxing Du and   
               Yi Sheng Ong and   
             Marina Knittel and   
             Ross Mawhorter and   
                    Nuo Liu and   
             Gianluca Gross and   
                 Reiko Tojo and   
        Ran Libeskind-Hadas and   
                    Yi-Chieh Wu   Multiple Optimal Reconciliations Under
                                  the Duplication-Loss-Coalescence Model   2144--2156
                Hongzhe Guo and   
                   Yilei Fu and   
                    Yan Gao and   
                   Junyi Li and   
                Yadong Wang and   
                         Bo Liu   deGSM: Memory Scalable Construction Of
                                  Large Scale de Bruijn Graph  . . . . . . 2157--2166
                     Cui Su and   
                   Jun Pang and   
                    Soumya Paul   Towards Optimal Decomposition of Boolean
                                  Networks . . . . . . . . . . . . . . . . 2167--2176
               Tom Hartmann and   
                Max Bannach and   
              Martin Middendorf   Sorting Signed Permutations by Inverse
                                  Tandem Duplication Random Losses . . . . 2177--2188
       Nguyen Quoc Khanh Le and   
                 Binh P. Nguyen   Prediction of FMN Binding Sites in
                                  Electron Transport Chains Based on $2$-D
                                  CNN and PSSM Profiles  . . . . . . . . . 2189--2197
 Ozan Firat Özgül and   
             Batuhan Bardak and   
                     Mehmet Tan   A Convolutional Deep Clustering
                                  Framework for Gene Expression Time
                                  Series . . . . . . . . . . . . . . . . . 2198--2207
                Fuhao Zhang and   
                  Hong Song and   
                   Min Zeng and   
              Fang-Xiang Wu and   
                 Yaohang Li and   
                     Yi Pan and   
                         Min Li   A Deep Learning Framework for Gene
                                  Ontology Annotations With Sequence- and
                                  Network-Based Information  . . . . . . . 2208--2217
                  Zilu Wang and   
               Qinghui Hong and   
                  Xiaoping Wang   A Memristive Circuit Implementation of
                                  Eyes State Detection in Fatigue Driving
                                  Based on Biological Long Short-Term
                                  Memory Rule  . . . . . . . . . . . . . . 2218--2229
  Pablo Nascimento da Silva and   
         Alexandre Plastino and   
               Fabio Fabris and   
                Alex A. Freitas   A Novel Feature Selection Method for
                                  Uncertain Features: an Application to
                                  the Prediction of Pro-\slash
                                  Anti-Longevity Genes . . . . . . . . . . 2230--2238
                    Dong Li and   
                Zhisong Pan and   
                    Guyu Hu and   
            Graham Anderson and   
                        Shan He   Active Module Identification From
                                  Multilayer Weighted Gene Co-Expression
                                  Networks: a Continuous Optimization
                                  Approach . . . . . . . . . . . . . . . . 2239--2248
                 Qiong Fang and   
                   Dewei Su and   
                 Wilfred Ng and   
                   Jianlin Feng   An Effective Biclustering-Based
                                  Framework for Identifying Cell
                                  Subpopulations From scRNA-seq Data . . . 2249--2260
                 Junyi Chen and   
                 Junhui Hou and   
                   Ka-Chun Wong   Categorical Matrix Completion With
                                  Active Learning for High-Throughput
                                  Screening  . . . . . . . . . . . . . . . 2261--2270
       Oyetunji E. Ogundijo and   
                  Kaiyi Zhu and   
              Xiaodong Wang and   
           Dimitris Anastassiou   Characterizing Intra-Tumor Heterogeneity
                                  From Somatic Mutations Without
                                  Copy-Neutral Assumption  . . . . . . . . 2271--2280
               Shaoxun Yuan and   
                  Haitao Li and   
               Jiansheng Wu and   
                       Xiao Sun   Classification of Mild Cognitive
                                  Impairment With Multimodal Data Using
                                  Both Labeled and Unlabeled Samples . . . 2281--2290
            Anne-Marie Lyne and   
          Le\"\ila Perié   Comparing Phylogenetic Approaches to
                                  Reconstructing Cell Lineage From
                                  Microsatellites With Missing Data  . . . 2291--2301
           Guillermo Blanco and   
       Borja Sánchez and   
                Lorena Ruiz and   
   Florentino Fdez-Riverola and   
         Abelardo Margolles and   
  Anália Lourenço   Computational Approach to the Systematic
                                  Prediction of Glycolytic Abilities:
                                  Looking Into Human Microbiota  . . . . . 2302--2313
               Eyla Willing and   
                 Jens Stoye and   
     Marília D. V. Braga   Computing the Inversion-Indel Distance   2314--2326
                Junzhong Ji and   
                        Yao Yao   Convolutional Neural Network With
                                  Graphical Lasso to Extract Sparse
                                  Topological Features for Brain Disease
                                  Classification . . . . . . . . . . . . . 2327--2338
        Annalisa Occhipinti and   
             Youssef Hamadi and   
              Hillel Kugler and   
 Christoph M. Wintersteiger and   
             Boyan Yordanov and   
                Claudio Angione   Discovering Essential Multiple Gene
                                  Effects Through Large Scale
                                  Optimization: an Application to Human
                                  Cancer Metabolism  . . . . . . . . . . . 2339--2352
                   Min Zeng and   
               Chengqian Lu and   
                 Zhihui Fei and   
              Fang-Xiang Wu and   
                 Yaohang Li and   
               Jianxin Wang and   
                         Min Li   DMFLDA: a Deep Learning Framework for
                                  Predicting lncRNA--Disease Associations  2353--2363


IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 19, Number 1, January, 2022

                  Sunny Sun and   
            Yi-Ping Phoebe Chen   Editorial  . . . . . . . . . . . . . . . 1--2
                     Hui Bi and   
                 Shumei Cao and   
                Hanying Yan and   
              Zhongyi Jiang and   
                  Jun Zhang and   
                       Ling Zou   Resting State Functional Connectivity
                                  Analysis During General Anesthesia: a
                                  High-Density EEG Study . . . . . . . . . 3--13
           Pierrick Craveur and   
           Tarun J. Narwani and   
   Narayanaswamy Srinivasan and   
      Jean-Christophe Gelly and   
            Joseph Rebehmed and   
        Alexandre G. de Brevern   Shaking the $ \beta $-Bulges . . . . . . 14--18
            Madhusudan Paul and   
                   Ashish Anand   A New Family of Similarity Measures for
                                  Scoring Confidence of Protein
                                  Interactions Using Gene Ontology . . . . 19--30
               Runhua Huang and   
            Chengchuang Lin and   
                  Aihua Yin and   
               Hanbiao Chen and   
                     Li Guo and   
                Gansen Zhao and   
                Xiaomao Fan and   
               Shuangyin Li and   
                     Jinji Yang   A Clinical Dataset and Various Baselines
                                  for Chromosome Instance Segmentation . . 31--39
                  Ying Qian and   
                 Xuelian Li and   
                 Qian Zhang and   
                 Jiongmin Zhang   \pkgSPP-CPI: Predicting
                                  Compound--Protein Interactions Based On
                                  Neural Networks  . . . . . . . . . . . . 40--47
                   Jin Zhao and   
                 Haodi Feng and   
                 Daming Zhu and   
                         Yu Lin   \pkgMultiTrans: an Algorithm for Path
                                  Extraction Through Mixed Integer Linear
                                  Programming for Transcriptome Assembly   48--56
   Anuradha Wickramarachchi and   
                         Yu Lin   \pkgGraphPlas: Refined Classification of
                                  Plasmid Sequences Using Assembly Graphs  57--67
                   Shuai Lu and   
                 Yuguang Li and   
                   Fei Wang and   
                Xiaofei Nan and   
                  Shoutao Zhang   Leveraging Sequential and Spatial
                                  Neighbors Information by Using CNNs
                                  Linked With GCNs for Paratope Prediction 68--74
                 Tzu-Hsien Yang   An Aggregation Method to Identify the
                                  RNA Meta-Stable Secondary Structure and
                                  its Functionally Interpretable Structure
                                  Ensemble . . . . . . . . . . . . . . . . 75--86
   Trinh-Trung-Duong Nguyen and   
               The-Anh Tran and   
       Nguyen-Quoc-Khanh Le and   
             Dinh-Minh Pham and   
                      Yu-Yen Ou   An Extensive Examination of Discovering
                                  5-Methylcytosine Sites in Genome-Wide
                                  DNA Promoters Using Machine Learning
                                  Based Approaches . . . . . . . . . . . . 87--94
         Barbara Di Camillo and   
               Giuseppe Nicosia   Guest Editorial: Deep Learning For
                                  Genomics . . . . . . . . . . . . . . . . 95--96
              Jim Clauwaert and   
                Willem Waegeman   Novel Transformer Networks for Improved
                                  Sequence Labeling in genomics  . . . . . 97--106
                 Zhong Chen and   
             Wensheng Zhang and   
               Hongwen Deng and   
                      Kun Zhang   Effective Cancer Subtype and Stage
                                  Prediction via Dropfeature-DNNs  . . . . 107--120
        Francisco Cristovao and   
         Silvia Cascianelli and   
             Arif Canakoglu and   
                Mark Carman and   
                 Luca Nanni and   
              Pietro Pinoli and   
                Marco Masseroli   Investigating Deep Learning Based Breast
                                  Cancer Subtyping Using Pan-Cancer and
                                  Multi-Omic Data  . . . . . . . . . . . . 121--134
              Gautier Viaud and   
      Prasanna Mayilvahanan and   
          Paul-Henry Courn\`ede   Representation Learning for the
                                  Clustering of Multi-Omics Data . . . . . 135--145
                Tuan Nguyen and   
         Giang T. T. Nguyen and   
                Thin Nguyen and   
                     Duc-Hau Le   Graph Convolutional Networks for Drug
                                  Response Prediction  . . . . . . . . . . 146--154
         Satyajit Mahapatra and   
            Vivek Raj Gupta and   
       Sitanshu Sekhar Sahu and   
                 Ganapati Panda   Deep Neural Network and Extreme Gradient
                                  Boosting Based Hybrid Classifier for
                                  Improved Prediction of Protein-Protein
                                  Interaction  . . . . . . . . . . . . . . 155--165
                Zhipeng Cai and   
                     Min Li and   
                    Pavel Skums   Guest Editors' Introduction to the
                                  Special Section on Bioinformatics
                                  Research and Applications  . . . . . . . 166--167
                  Cheng Yan and   
                Guihua Duan and   
                Yayan Zhang and   
              Fang-Xiang Wu and   
                     Yi Pan and   
                   Jianxin Wang   Predicting Drug-Drug Interactions Based
                                  on Integrated Similarity and
                                  Semi-Supervised Learning . . . . . . . . 168--179
               Fengpan Zhao and   
                Pavel Skums and   
            Alex Zelikovsky and   
            Eric L. Sevigny and   
      Monica Haavisto Swahn and   
         Sheryl M. Strasser and   
                  Yan Huang and   
                       Yubao Wu   Computational Approaches to Detect
                                  Illicit Drug Ads and Find Vendor
                                  Communities Within Social Media
                                  Platforms  . . . . . . . . . . . . . . . 180--191
            Sudipta Acharya and   
               Laizhong Cui and   
                         Yi Pan   A Refined 3-in-1 Fused Protein
                                  Similarity Measure: Application in
                                  Threshold-Free Hub Detection . . . . . . 192--206
                Zhipeng Cai and   
            Giri Narasimhan and   
                    Pavel Skums   Guest Editors' Introduction to the
                                  Special Section on Bioinformatics
                                  Research and Applications  . . . . . . . 207--208
                   Shan Gao and   
                 Renmin Han and   
              Xiangrui Zeng and   
                Zhiyong Liu and   
                     Min Xu and   
                       Fa Zhang   Macromolecules Structural Classification
                                  With a $3$D Dilated Dense Network in
                                  Cryo-Electron Tomography . . . . . . . . 209--219
             Davide Storato and   
                   Matteo Comin   \pkgK2Mem: Discovering Discriminative
                                  $K$-mers From Sequencing Data for
                                  Metagenomic Reads Classification . . . . 220--229
                Saurav Dhar and   
            Chengchen Zhang and   
             Ion I. Mandoiu and   
                Mukul S. Bansal   \pkgTNet: Transmission Network Inference
                                  Using Within-Host Strain Diversity and
                                  its Application to Geographical Tracking
                                  of COVID-19 Spread . . . . . . . . . . . 230--242
                   Jun Wang and   
              Huiling Zhang and   
                    Wei Ren and   
                  Maozu Guo and   
                     Guoxian Yu   \pkgEpiMC: Detecting Epistatic
                                  Interactions Using Multiple Clusterings  243--254
          Sunil Kumar P. V. and   
            Adheeba Thahsin and   
                   Manju M. and   
                   Gopakumar G.   A Heterogeneous Information Network
                                  Model for Long Non-Coding RNA Function
                                  Prediction . . . . . . . . . . . . . . . 255--266
                Hansheng Li and   
                JianPing Li and   
                 Yuxin Kang and   
               Chunbao Wang and   
                Feihong Liu and   
                  Wenli Hui and   
                  Qirong Bo and   
                    Lei Cui and   
                   Jun Feng and   
                       Lin Yang   A Novel Encoding and Decoding
                                  Calibration Guiding Pathway for
                                  Pathological Image Analysis  . . . . . . 267--274
                 Sadaf Gull and   
                  Fayyaz Minhas   \pkgAMP$_0$: Species-Specific Prediction
                                  of Anti-microbial Peptides Using Zero
                                  and Few Shot Learning  . . . . . . . . . 275--283

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 19, Number 2, March, 2022

         Pietro Hiram Guzzi and   
                 Marinka Zitnik   Editorial Deep Learning and Graph
                                  Embeddings for Network Biology . . . . . 653--654
                     Jin Li and   
                Jingru Wang and   
                     Hao Lv and   
             Zhuoxuan Zhang and   
                    Zaixia Wang   IMCHGAN: Inductive Matrix Completion
                                  With Heterogeneous Graph Attention
                                  Networks for Drug-Target Interactions
                                  Prediction . . . . . . . . . . . . . . . 655--665
               Xiaoyong Pan and   
                   Lei Chen and   
                    Min Liu and   
                 Zhibin Niu and   
                  Tao Huang and   
                    Yu-Dong Cai   Identifying Protein Subcellular
                                  Locations With Embeddings-Based node2loc 666--675
                  Kishan KC and   
                     Rui Li and   
                   Feng Cui and   
                  Anne R. Haake   Predicting Biomedical Interactions With
                                  Higher-Order Graph Convolutional
                                  Networks . . . . . . . . . . . . . . . . 676--687
                Xiujuan Lei and   
               Jiaojiao Tie and   
                         Yi Pan   Inferring Metabolite-Disease Association
                                  Using Graph Convolutional Networks . . . 688--698
              Jianliang Gao and   
                Tengfei Lyu and   
                  Fan Xiong and   
               Jianxin Wang and   
                  Weimao Ke and   
                        Zhao Li   Predicting the Survival of Cancer
                                  Patients With Multimodal Graph Neural
                                  Network  . . . . . . . . . . . . . . . . 699--709
         Giang T. T. Nguyen and   
                  Hoa D. Vu and   
                     Duc-Hau Le   Integrating Molecular Graph Data of
                                  Drugs and Multiple -Omic Data of Cell
                                  Lines for Drug Response Prediction . . . 710--717
            Tri Minh Nguyen and   
                Thin Nguyen and   
               Thao Minh Le and   
                    Truyen Tran   GEFA: Early Fusion Approach in
                                  Drug-Target Affinity Prediction  . . . . 718--728
             Ichcha Manipur and   
                Mario Manzo and   
             Ilaria Granata and   
          Maurizio Giordano and   
            Lucia Maddalena and   
            Mario R. Guarracino   Netpro2vec: a Graph Embedding Framework
                                  for Biomedical Applications  . . . . . . 729--740
               Yuanfang Ren and   
           Aisharjya Sarkar and   
          Pierangelo Veltri and   
                   Ahmet Ay and   
                 Alin Dobra and   
                  Tamer Kahveci   Pattern Discovery in Multilayer Networks 741--752
                  Zhen Shen and   
                Qinhu Zhang and   
              Kyungsook Han and   
                De-Shuang Huang   A Deep Learning Model for RNA-Protein
                                  Binding Preference Prediction Based on
                                  Hierarchical LSTM and Attention Network  753--762
                   Zhen Gao and   
               Yu-Tian Wang and   
                Qing-Wen Wu and   
                     Lei Li and   
              Jian-Cheng Ni and   
                 Chun-Hou Zheng   A New Method Based on Matrix Completion
                                  and Non-Negative Matrix Factorization
                                  for Predicting Disease-Associated miRNAs 763--772
            Koushik Mallick and   
              Saurav Mallik and   
  Sanghamitra Bandyopadhyay and   
              Sikim Chakraborty   A Novel Graph Topology-Based
                                  GO-Similarity Measure for Signature
                                  Detection From Multi-Omics Data and its
                                  Application to Other Problems  . . . . . 773--785
                  Xin Huang and   
              Zhenqian Liao and   
                   Bing Liu and   
                Fengmei Tao and   
                  Benzhe Su and   
                    Xiaohui Lin   A Novel Method for Constructing
                                  Classification Models by Combining
                                  Different Biomarker Patterns . . . . . . 786--794
               Shi-Hao Feng and   
               Chun-Qiu Xia and   
             Pei-Dong Zhang and   
                  Hong-Bin Shen   \em Ab-Initio Membrane Protein
                                  Amphipathic Helix Structure Prediction
                                  Using Deep Neural Networks . . . . . . . 795--805
            Trinh Van Giang and   
             Tatsuya Akutsu and   
              Kunihiko Hiraishi   An FVS-Based Approach to Attractor
                                  Detection in Asynchronous Random Boolean
                                  Networks . . . . . . . . . . . . . . . . 806--818
               Yiding Zhang and   
                Lyujie Chen and   
                        Shao Li   CIPHER-SC: Disease-Gene Association
                                  Inference Using Graph Convolution on a
                                  Context-Aware Network With Single-Cell
                                  Data . . . . . . . . . . . . . . . . . . 819--829
           Aisharjya Sarkar and   
             Prabhat Mishra and   
                  Tamer Kahveci   Data Perturbation and Recovery of Time
                                  Series Gene Expression Data  . . . . . . 830--842
               Sachin Bhatt and   
              Prithvi Singh and   
             Archana Sharma and   
                 Arpita Rai and   
              Ravins Dohare and   
            Shweta Sankhwar and   
               Akash Sharma and   
               Mansoor Ali Syed   Deciphering Key Genes and miRNAs
                                  Associated With Hepatocellular Carcinoma
                                  via Network-Based Approach . . . . . . . 843--853
                 Yu-Ting Su and   
                     Yao Lu and   
                   Mei Chen and   
                      An-An Liu   Deep Reinforcement Learning-Based
                                  Progressive Sequence Saliency Discovery
                                  Network for Mitosis Detection In
                                  Time-Lapse Phase-Contrast Microscopy
                                  Images . . . . . . . . . . . . . . . . . 854--865
                    Ben Cao and   
                     Xue Ii and   
             Xiaokang Zhang and   
                   Bin Wang and   
                Qiang Zhang and   
                   Xiaopeng Wei   Designing Uncorrelated Address Constrain
                                  for DNA Storage by DMVO Algorithm  . . . 866--877
                 Boxin Guan and   
                 Yuhai Zhao and   
                   Ying Yin and   
                        Yuan Li   Detecting Disease-Associated SNP--SNP
                                  Interactions Using Progressive Screening
                                  Memetic Algorithm  . . . . . . . . . . . 878--887
                     Ho Bae and   
                Seonwoo Min and   
              Hyun-Soo Choi and   
                   Sungroh Yoon   DNA Privacy: Analyzing Malicious DNA
                                  Sequences Using Deep Neural Networks . . 888--898
                 Seonho Kim and   
                    Juntae Yoon   Dual Triggered Correspondence Topic
                                  (DTCT) model for MeSH annotation . . . . 899--911
Christian Ponte-Fernández and   
Jorge González-Domínguez and   
Antonio Carvajal-Rodríguez and   
  María J. Martín   Evaluation of Existing Methods for
                                  High-Order Epistasis Detection . . . . . 912--926
            Tapan Chowdhury and   
        Susanta Chakraborty and   
                   Argha Nandan   GPU Accelerated Drug Application on
                                  Signaling Pathways Containing Multiple
                                  Faults Using Boolean Networks  . . . . . 927--939
          Edward E. Seabolt and   
                Gowri Nayar and   
        Harsha Krishnareddy and   
             Akshay Agarwal and   
            Kristen L. Beck and   
         Ignacio Terrizzano and   
              Eser Kandogan and   
              Mark Kunitomi and   
                  Mary Roth and   
          Vandana Mukherjee and   
               James H. Kaufman   Functional Genomics Platform, a
                                  Cloud-Based Platform for Studying
                                  Microbial Life at Scale  . . . . . . . . 940--952
                   Fei Wang and   
                Yulian Ding and   
                Xiujuan Lei and   
                    Bo Liao and   
                  Fang-Xiang Wu   Identifying Gene Signatures for Cancer
                                  Drug Repositioning Based on Sample
                                  Clustering . . . . . . . . . . . . . . . 953--965
             Meshari Alazmi and   
                  Olaa Motwalli   Immuno-Informatics Based Peptides: an
                                  Approach for Vaccine Development Against
                                  Outer Membrane Proteins of
                                  \bionamePseudomonas Genus  . . . . . . . 966--973
             Khalique Newaz and   
            Tijana Milenkovi\'c   Inference of a Dynamic Aging-related
                                  Biological Subnetwork via Network
                                  Propagation  . . . . . . . . . . . . . . 974--988

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 19, Number 3, May, 2022

         Stephen Kwok-Wing Tsui   Editorial  . . . . . . . . . . . . . . . 1255--1256
             Jiongmin Zhang and   
                    Man Zhu and   
                      Ying Qian   protein2vec: Predicting Protein--Protein
                                  Interactions Based on LSTM . . . . . . . 1257--1266
              Byungkyu Park and   
                   Wook Lee and   
                  Kyungsook Han   A New Approach to Deriving Prognostic
                                  Gene Pairs From Cancer Patient-Specific
                                  Gene Correlation Networks  . . . . . . . 1267--1276
                   Yanbo Li and   
                         Yu Lin   DCHap: a Divide-and-Conquer Haplotype
                                  Phasing Algorithm for Third-Generation
                                  Sequences  . . . . . . . . . . . . . . . 1277--1284
            Chengchuang Lin and   
                Gansen Zhao and   
               Zhirong Yang and   
                  Aihua Yin and   
               Xinming Wang and   
                     Li Guo and   
               Hanbiao Chen and   
                 Zhaohui Ma and   
                   Lei Zhao and   
                  Haoyu Luo and   
              Tianxing Wang and   
                Bichao Ding and   
              Xiongwen Pang and   
                     Qiren Chen   CIR-Net: Automatic Classification of
                                  Human Chromosome Based on
                                  Inception-ResNet Architecture  . . . . . 1285--1293
             Shengtian Sang and   
                Xiaoxia Liu and   
                Xiaoyu Chen and   
                        Di Zhao   A Scalable Embedding Based Neural
                                  Network Method for Discovering Knowledge
                                  From Biomedical Literature . . . . . . . 1294--1301
                 Sun Ah Kim and   
                Nayeon Kang and   
                   Taesung Park   Hierarchical Structured Component
                                  Analysis for Microbiome Data Using
                                  Taxonomy Assignments . . . . . . . . . . 1302--1312
             Ken Hung-On Yu and   
                Xiunan Fang and   
                 Haobin Yao and   
                    Bond Ng and   
             Tak Kwan Leung and   
             Ling-Ling Wang and   
                 Chi Ho Lin and   
         Agnes Sze Wah Chan and   
            Wai Keung Leung and   
              Suet Yi Leung and   
             Joshua Wing Kei Ho   Evaluation of Experimental Protocols for
                                  Shotgun Whole-Genome Metagenomic
                                  Discovery of Antibiotic Resistance Genes 1313--1321
                 Yingjun Ma and   
                Tingting He and   
                 Yuting Tan and   
                 Xingpeng Jiang   Seq-BEL: Sequence-Based Ensemble
                                  Learning for Predicting Virus-Human
                                  Protein--Protein Interaction . . . . . . 1322--1333
              Xiuzhen Huang and   
                   Yu Zhang and   
                       Xuan Guo   Editorial  . . . . . . . . . . . . . . . 1334--1335
             Sina Abdollahi and   
              Peng-Chan Lin and   
              Jung-Hsien Chiang   DiaDeL: an Accurate Deep Learning-Based
                                  Model With Mutational Signatures for
                                  Predicting Metastasis Stage and Cancer
                                  Types  . . . . . . . . . . . . . . . . . 1336--1343
                Nahim Adnan and   
                Maryam Zand and   
            Tim H. M. Huang and   
                   Jianhua Ruan   Construction and Evaluation of Robust
                                  Interpretation Models for Breast Cancer
                                  Metastasis Prediction  . . . . . . . . . 1344--1353
               Tapas Bhadra and   
              Saurav Mallik and   
                 Amir Sohel and   
                 Zhongming Zhao   Unsupervised Feature Selection Using an
                                  Integrated Strategy of Hierarchical
                                  Clustering With Singular Value
                                  Decomposition: an Integrative Biomarker
                                  Discovery Method With Application to
                                  Acute Myeloid Leukemia . . . . . . . . . 1354--1364
                Lien A. Bui and   
             Dacosta Yeboah and   
         Louis Steinmeister and   
                 Sima Azizi and   
             Daniel B. Hier and   
           Donald C. Wunsch and   
          Gayla R. Olbricht and   
             Tayo Obafemi-Ajayi   Heterogeneity in Blood Biomarker
                                  Trajectories After Mild TBI Revealed by
                                  Unsupervised Learning  . . . . . . . . . 1365--1378
        Elisabetta Manduchi and   
                Trang T. Le and   
                 Weixuan Fu and   
                 Jason H. Moore   Genetic Analysis of Coronary Artery
                                  Disease Using Tree-Based Automated
                                  Machine Learning Informed By
                                  Biology-Based Feature Selection  . . . . 1379--1386
               Jason Causey and   
      Jonathan Stubblefield and   
                Jake Qualls and   
            Jennifer Fowler and   
                Lingrui Cai and   
                Karl Walker and   
              Yuanfang Guan and   
                  Xiuzhen Huang   An Ensemble of U-Net Models for Kidney
                                  Tumor Segmentation With CT Images  . . . 1387--1392
                 Lechuan Li and   
             Chonghao Zhang and   
                  Shiyu Liu and   
                Hannah Guan and   
                       Yu Zhang   Age Prediction by DNA Methylation in
                                  Neural Networks  . . . . . . . . . . . . 1393--1402
                  Madhumita and   
                  Sushmita Paul   A Feature Weighting-Assisted Approach
                                  for Cancer Subtypes Identification From
                                  Paired Expression Profiles . . . . . . . 1403--1414
                 Lewei Zhou and   
                Yucong Tang and   
                    Guiying Yan   A New Estimation Method for the
                                  Biological Interaction Predicting
                                  Problems . . . . . . . . . . . . . . . . 1415--1423
                Chengye Zou and   
               Xiaopeng Wei and   
                Qiang Zhang and   
                  Changjun Zhou   A Novel Adaptive Linear Neuron Based on
                                  DNA Strand Displacement Reaction Network 1424--1434
                  Hao Jiang and   
                   Fei Zhan and   
               Congtao Wang and   
               Jianfeng Qiu and   
                  Yansen Su and   
              Chunhou Zheng and   
               Xingyi Zhang and   
                Xiangxiang Zeng   A Robust Algorithm Based on Link Label
                                  Propagation for Identifying Functional
                                  Modules From Protein--Protein
                                  Interaction Networks . . . . . . . . . . 1435--1448
            Sanjay Bankapur and   
                  Nagamma Patil   An Effective Multi-Label Protein
                                  Sub-Chloroplast Localization Prediction
                                  by Skipped-Grams of Evolutionary
                                  Profiles Using Deep Neural Network . . . 1449--1458
             Liangliang Liu and   
               Shaojie Tang and   
              Fang-Xiang Wu and   
               Yu-Ping Wang and   
                   Jianxin Wang   An Ensemble Hybrid Feature Selection
                                  Method for Neuropsychiatric Disorder
                                  Classification . . . . . . . . . . . . . 1459--1471
           Maryam Pouryahya and   
                Jung Hun Oh and   
           Pedram Javanmard and   
           James C. Mathews and   
            Zehor Belkhatir and   
            Joseph O. Deasy and   
            Allen R. Tannenbaum   aWCluster: a Novel Integrative
                                  Network-Based Clustering of Multiomics
                                  for Subtype Analysis of Cancer Data  . . 1472--1483
                   Hu Zhang and   
              Jingsong Chen and   
                   Tianhai Tian   Bayesian Inference of Stochastic Dynamic
                                  Models Using Early-Rejection Methods
                                  Based on Sequential Stochastic
                                  Simulations  . . . . . . . . . . . . . . 1484--1494
  Daiane Aparecida Zuanetti and   
           Luis Aparecido Milan   Bayesian Modeling for Epistasis Analysis
                                  Using Data-Driven Reversible Jump  . . . 1495--1506
   Alex M. Ascensión and   
  Marcos J. Araúzo-Bravo   BigMPI4py: Python Module for
                                  Parallelization of Big Data Objects
                                  Discloses Germ Layer Specific DNA
                                  Demethylation Motifs . . . . . . . . . . 1507--1522
               Conghua Wang and   
                Haihong Liu and   
              Zhonghua Miao and   
                       Jin Zhou   Circadian Rhythm Regulated by Tumor
                                  Suppressor p53 and Time Delay in
                                  Unstressed Cells . . . . . . . . . . . . 1523--1530
            Abhinandan Khan and   
                Goutam Saha and   
                Rajat Kumar Pal   Controlling the Effects of External
                                  Perturbations on a Gene Regulatory
                                  Network Using
                                  Proportional-Integral-Derivative
                                  Controller . . . . . . . . . . . . . . . 1531--1544
            Omid Abbaszadeh and   
            Ali Azarpeyvand and   
       Alireza Khanteymoori and   
                   Abbas Bahari   Data-Driven and Knowledge-Based
                                  Algorithms for Gene Network
                                  Reconstruction on High-Dimensional Data  1545--1557

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 19, Number 4, July, 2022

                        Jian Ma   Guest Editorial for Selected Papers From
                                  ACM-BCB 2019 . . . . . . . . . . . . . . 1919
                    Yue Guo and   
                 Oleh Krupa and   
                Jason Stein and   
                 Guorong Wu and   
            Ashok Krishnamurthy   SAU-Net: a Unified Network for Cell
                                  Counting in $2$D and $3$D Microscopy
                                  Images . . . . . . . . . . . . . . . . . 1920--1932
            John Lazarsfeld and   
  Jonathan Rodríguez and   
                 Mert Erden and   
                 Yuelin Liu and   
                Lenore J. Cowen   Majority Vote Cascading: a
                                  Semi-Supervised Framework for Improving
                                  Protein Function Prediction  . . . . . . 1933--1945
               Mira Barshai and   
               Alice Aubert and   
                Yaron Orenstein   G4detector: Convolutional Neural Network
                                  to Predict DNA G-Quadruplexes  . . . . . 1946--1955
              Pietro Pinoli and   
                Gaia Ceddia and   
               Stefano Ceri and   
                Marco Masseroli   Predicting Drug Synergism by Means of
                                  Non-Negative Matrix Tri-Factorization    1956--1967
                   Yang Qiu and   
                 Yang Zhang and   
                 Yifan Deng and   
                Shichao Liu and   
                      Wen Zhang   A Comprehensive Review of Computational
                                  Methods For Drug-Drug Interaction
                                  Detection  . . . . . . . . . . . . . . . 1968--1985
            Yuanying Zhuang and   
              Xiangrong Liu and   
                  Yue Zhong and   
                     Longxin Wu   A Deep Ensemble Predictor for
                                  Identifying Anti-Hypertensive Peptides
                                  Using Pretrained Protein Embedding . . . 1986--1992
                  Xingyi Li and   
                   Ju Xiang and   
              Fang-Xiang Wu and   
                         Min Li   A Dual Ranking Algorithm Based on the
                                  Multiplex Network for Heterogeneous
                                  Complex Disease Analysis . . . . . . . . 1993--2002
                  Xibin Jia and   
                  Zheng Sun and   
                    Qing Mi and   
              Zhenghan Yang and   
                     Dawei Yang   A Multimodality-Contribution-Aware
                                  TripNet for Histologic Grading of
                                  Hepatocellular Carcinoma . . . . . . . . 2003--2016
               Shiming Wang and   
                     Jie Li and   
                Yadong Wang and   
                     Liran Juan   A Neighborhood-Based Global Network
                                  Model to Predict Drug-Target
                                  Interactions . . . . . . . . . . . . . . 2017--2025
              Xiaojian Ding and   
                   Fan Yang and   
                Yaoyi Zhong and   
                        Jie Cao   A Novel Recursive Gene Selection Method
                                  Based on Least Square Kernel Extreme
                                  Learning Machine . . . . . . . . . . . . 2026--2038
             Anik Chaudhuri and   
        Anwoy Kumar Mohanty and   
            Manoranjan Satpathy   A Parallelizable Model for Analyzing
                                  Cancer Tissue Heterogeneity  . . . . . . 2039--2048
                  Cunmei Ji and   
                Yutian Wang and   
                   Zhen Gao and   
                     Lei Li and   
               Jiancheng Ni and   
                  Chunhou Zheng   A Semi-Supervised Learning Method for
                                  MiRNA-Disease Association Prediction
                                  Based on Variational Autoencoder . . . . 2049--2059
        Raktim Kumar Mondol and   
            Nhan Duy Truong and   
              Mohammad Reza and   
            Samuel Ippolito and   
          Esmaeil Ebrahimie and   
                   Omid Kavehei   AFExNet: an Adversarial Autoencoder for
                                  Differentiating Breast Cancer Sub-Types
                                  and Extracting Biologically Relevant
                                  Genes  . . . . . . . . . . . . . . . . . 2060--2070
                Jingjing Ma and   
               Haitao Jiang and   
                 Daming Zhu and   
                    Runmin Yang   Algorithms and Hardness for Scaffold
                                  Filling to Maximize Increased
                                  Duo-Preservations  . . . . . . . . . . . 2071--2079
             Atheer Matroud and   
        Christopher Tuffley and   
                  Michael Hendy   An Asymmetric Alignment Algorithm for
                                  Estimating Ancestor-Descendant Edit
                                  Distance for Tandem Repeats  . . . . . . 2080--2091
               Qichang Zhao and   
               Mengyun Yang and   
            Zhongjian Cheng and   
                 Yaohang Li and   
                   Jianxin Wang   Biomedical Data and Deep Learning
                                  Computational Models for Predicting
                                  Compound-Protein Relations . . . . . . . 2092--2110
               Debraj Ghosh and   
                    Rajat K. De   Block Search Stochastic Simulation
                                  Algorithm (\em BlSSSA): a Fast
                                  Stochastic Simulation Algorithm for
                                  Modeling Large Biochemical Networks  . . 2111--2123
           Ritabrata Sanyal and   
                Devroop Kar and   
                     Ram Sarkar   Carcinoma Type Classification From
                                  High-Resolution Breast Microscopy Images
                                  Using a Hybrid Ensemble of Deep
                                  Convolutional Features and Gradient
                                  Boosting Trees Classifiers . . . . . . . 2124--2136
              Lopamudra Dey and   
           Anirban Mukhopadhyay   Compact Genetic Algorithm-Based Feature
                                  Selection for Sequence-Based Prediction
                                  of Dengue--Human Protein Interactions    2137--2148
               Changli Feng and   
                     Jin Wu and   
                 Haiyan Wei and   
                     Lei Xu and   
                       Quan Zou   CRCF: a Method of Identifying Secretory
                                  Proteins of Malaria Parasites  . . . . . 2149--2157
            Cheng-Hong Yang and   
               Kuo-Chuan Wu and   
              Li-Yeh Chuang and   
                Hsueh-Wei Chang   DeepBarcoding: Deep Learning for Species
                                  Classification Using DNA Barcoding . . . 2158--2165
                 Guoxian Yu and   
                Yeqian Yang and   
               Yangyang Yan and   
                  Maozu Guo and   
           Xiangliang Zhang and   
                       Jun Wang   DeepIDA: Predicting Isoform-Disease
                                  Associations by Data Fusion and Deep
                                  Neural Networks  . . . . . . . . . . . . 2166--2176
                   Jun Wang and   
                 Long Zhang and   
                    An Zeng and   
                  Dawen Xia and   
                 Jiantao Yu and   
                     Guoxian Yu   DeepIII: Predicting Isoform-Isoform
                                  Interactions by Deep Neural Networks and
                                  Data Fusion  . . . . . . . . . . . . . . 2177--2187
               Zhonghao Liu and   
                   Jing Jin and   
                  Yuxin Cui and   
                Zheng Xiong and   
             Alireza Nasiri and   
                  Yong Zhao and   
                     Jianjun Hu   DeepSeqPanII: an Interpretable Recurrent
                                  Neural Network Model With Attention
                                  Mechanism for Peptide-HLA Class II
                                  Binding Prediction . . . . . . . . . . . 2188--2196
Betül Güvenç Paltun and   
               Samuel Kaski and   
              Hiroshi Mamitsuka   DIVERSE: Bayesian Data IntegratiVE
                                  Learning for Precise Drug ResponSE
                                  Prediction . . . . . . . . . . . . . . . 2197--2207
            Zhongjian Cheng and   
                  Cheng Yan and   
              Fang-Xiang Wu and   
                   Jianxin Wang   Drug-Target Interaction Prediction Using
                                  Multi-Head Self-Attention and Graph
                                  Attention Network  . . . . . . . . . . . 2208--2218
                Dongyuan Li and   
               Shuyao Zhang and   
                      Xiaoke Ma   Dynamic Module Detection in Temporal
                                  Attributed Networks of Cancers . . . . . 2219--2230
                 Chuang Liu and   
                    Yao Dai and   
                  Keping Yu and   
                    Zi-Ke Zhang   Enhancing Cancer Driver Gene Prediction
                                  by Protein--Protein Interaction Network  2231--2240
                   Yan Wang and   
                  Lei Zhang and   
                    Xin Shu and   
               Yangqin Feng and   
                   Zhang Yi and   
                        Qing Lv   Feature-Sensitive Deep Convolutional
                                  Neural Network for Multi-Instance Breast
                                  Cancer Detection . . . . . . . . . . . . 2241--2251

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 19, Number 5, 2022

                     Da Yan and   
                   Hong Qin and   
              Hsiang-Yun Wu and   
                   Jake Y. Chen   Guest Editorial for Selected Papers From
                                  BIOKDD 2020  . . . . . . . . . . . . . . 2545--2546
        Rayol Mendonca-Neto and   
                     Zhi Li and   
           David Fenyö and   
           Claudio T. Silva and   
 Fabíola G. Nakamura and   
            Eduardo F. Nakamura   A Gene Selection Method Based on
                                  Outliers for Breast Cancer Subtype
                                  Classification . . . . . . . . . . . . . 2547--2559
               Yuanyuan Jin and   
                   Wendi Ji and   
                  Wei Zhang and   
                Xiangnan He and   
                 Xinyu Wang and   
                  Xiaoling Wang   A KG-Enhanced Multi-Graph Neural Network
                                  for Attentive Herb Recommendation  . . . 2560--2571
         Andreia S. Martins and   
             Marta Gromicho and   
               Susana Pinto and   
         Mamede de Carvalho and   
                Sara C. Madeira   Learning Prognostic Models Using Disease
                                  Progression Patterns: Predicting the
                                  Need for Non-Invasive Ventilation in
                                  Amyotrophic Lateral Sclerosis  . . . . . 2572--2583
                Qingyu Chen and   
               Jingcheng Du and   
               Alexis Allot and   
                     Zhiyong Lu   LitMC-BERT: Transformer-Based
                                  Multi-Label Classification of Biomedical
                                  Literature With An Application on
                                  COVID-19 Literature Curation . . . . . . 2584--2595
          Jaswanth K. Yella and   
                  Anil G. Jegga   MGATRx: Discovering Drug Repositioning
                                  Candidates Using Multi-View Graph
                                  Attention  . . . . . . . . . . . . . . . 2596--2604
                 Jieli Zhou and   
                 Baoyu Jing and   
                  Zeya Wang and   
                 Hongyi Xin and   
                  Hanghang Tong   SODA: Detecting COVID-19 in Chest X-Rays
                                  With Semi-Supervised Open Set Domain
                                  Adaptation . . . . . . . . . . . . . . . 2605--2612
               Xiaojuan Guo and   
                 Kewei Chen and   
               Yinghua Chen and   
             Chengjie Xiong and   
                      Yi Su and   
                     Li Yao and   
                 Eric M. Reiman   A Computational Monte Carlo Simulation
                                  Strategy to Determine the Temporal
                                  Ordering of Abnormal Age Onset Among
                                  Biomarkers of Alzheimer's Disease 2613--2622
              Zhankun Xiong and   
                 Feng Huang and   
                 Ziyan Wang and   
                Shichao Liu and   
                      Wen Zhang   A Multimodal Framework for Improving \em
                                  in Silico Drug Repositioning With the
                                  Prior Knowledge From Knowledge Graphs    2623--2631
                  Qiao Ning and   
               Xiaowei Zhao and   
                    Zhiqiang Ma   A Novel Method for Identification of
                                  Glutarylation Sites Combining
                                  Borderline-SMOTE With Tomek Links
                                  Technique in Imbalanced Data . . . . . . 2632--2641
              Matthew LeMay and   
        Ran Libeskind-Hadas and   
                    Yi-Chieh Wu   A Polynomial-Time Algorithm for
                                  Minimizing the Deep Coalescence Cost for
                                  Level-1 Species Networks . . . . . . . . 2642--2653
                  Xuan Yang and   
                  Chen Yang and   
                 Jimeng Lei and   
                   Jianxiao Liu   An Approach of Epistasis Detection Using
                                  Integer Linear Programming Optimizing
                                  Bayesian Network . . . . . . . . . . . . 2654--2671
                    Chao Li and   
                    Jun Sun and   
                  Li-Wei Li and   
                 Xiaojun Wu and   
                  Vasile Palade   An Effective Swarm Intelligence
                                  Optimization Algorithm for Flexible
                                  Ligand Docking . . . . . . . . . . . . . 2672--2684
              Ashish Ranjan and   
David Fernández-Baca and   
          Sudhakar Tripathi and   
                  Akshay Deepak   An Ensemble Tf-Idf Based Approach to
                                  Protein Function Prediction via Sequence
                                  Segmentation . . . . . . . . . . . . . . 2685--2696
Venkateshwarlu Yellaswamy Gudur and   
        Sidharth Maheshwari and   
              Amit Acharyya and   
                  Rishad Shafik   An FPGA Based Energy-Efficient Read
                                  Mapper With Parallel Filtering and
                                  In-Situ Verification . . . . . . . . . . 2697--2711
                  Xinyi Qin and   
                   Lu Zhang and   
                    Min Liu and   
                   Ziwei Xu and   
                 Guangzhong Liu   ASFold-DNN: Protein Fold Recognition
                                  Based on Evolutionary Features With
                                  Variable Parameters Using Full Connected
                                  Neural Network . . . . . . . . . . . . . 2712--2722
             Jianhong Cheng and   
                   Wei Zhao and   
                    Jin Liu and   
                Xingzhi Xie and   
                Shangjie Wu and   
             Liangliang Liu and   
                 Hailin Yue and   
                 Junjian Li and   
               Jianxin Wang and   
                        Jun Liu   Automated Diagnosis of COVID-19 Using
                                  Deep Supervised Autoencoder With
                                  Multi-View Features From CT Images . . . 2723--2736
               Zhihao Huang and   
                   Yan Wang and   
                      Xiaoke Ma   Clustering of Cancer Attributed Networks
                                  by Dynamically and Jointly Factorizing
                                  Multi-Layer Graphs . . . . . . . . . . . 2737--2748
              Muhammad Arif and   
             Muhammad Kabir and   
                Saeed Ahmed and   
                  Abid Khan and   
                    Fang Ge and   
               Adel Khelifi and   
                    Dong-Jun Yu   DeepCPPred: a Deep Learning Framework
                                  for the Discrimination of
                                  Cell-Penetrating Peptides and Their
                                  Uptake Efficiencies  . . . . . . . . . . 2749--2759
                  Yuqian Pu and   
                  Jiawei Li and   
                 Jijun Tang and   
                        Fei Guo   DeepFusionDTA: Drug-Target Binding
                                  Affinity Prediction With Information
                                  Fusion and Hybrid Deep-Learning Ensemble
                                  Model  . . . . . . . . . . . . . . . . . 2760--2769
               Pratik Dutta and   
       Aditya Prakash Patra and   
                  Sriparna Saha   DeePROG: Deep Attention-Based Model for
                                  Diseased Gene Prognosis by Fusing
                                  Multi-Omics Data . . . . . . . . . . . . 2770--2781
              Weizhong Zhao and   
              Jinyong Zhang and   
                Jincai Yang and   
             Xingpeng Jiang and   
                    Tingting He   Document-Level Chemical-Induced Disease
                                  Relation Extraction via Hierarchical
                                  Representation Learning  . . . . . . . . 2782--2793
             Hamda B. Ajmal and   
              Michael G. Madden   Dynamic Bayesian Network Learning to
                                  Infer Sparse Models From Time Series
                                  Gene Expression Data . . . . . . . . . . 2794--2805
                   Jian Liu and   
               Jialiang Sun and   
                 Yongzhuang Liu   Effective Identification of Bacterial
                                  Genomes From Short and Long Read
                                  Sequencing Data  . . . . . . . . . . . . 2806--2816
            Debopriya Ghosh and   
                 Javier Cabrera   Enriched Random Forest for High
                                  Dimensional Genomic Data . . . . . . . . 2817--2828
                   Pei Wang and   
                    Daojie Wang   Gene Differential Co-Expression Networks
                                  Based on RNA-Seq: Construction and Its
                                  Applications . . . . . . . . . . . . . . 2829--2841
                 Musab Naik and   
                 Luis Rueda and   
             Akram Vasighizaker   Identification of Enriched Regions in
                                  ChIP-Seq Data via a Linear-Time
                                  Multi-Level Thresholding Algorithm . . . 2842--2850
              Young-Joon Ko and   
                Sangsoo Kim and   
               Cheol-Ho Pan and   
                   Keunwan Park   Identification of Functional Microbial
                                  Modules Through Network-Based Analysis
                                  of Meta-Microbial Features Using Matrix
                                  Factorization  . . . . . . . . . . . . . 2851--2862
               Junrong Song and   
                   Wei Peng and   
                      Feng Wang   Identifying Cancer Patient Subgroups by
                                  Finding Co-Modules From the Driver
                                  Mutation Profiles and Downstream Gene
                                  Expression Profiles  . . . . . . . . . . 2863--2872
                Siyuan Zhao and   
                   Jun Meng and   
                 Qiang Kang and   
                     Yushi Luan   Identifying LncRNA-Encoded Short
                                  Peptides Using Optimized Hybrid Features
                                  and Ensemble Learning  . . . . . . . . . 2873--2881

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 19, Number 6, 2022

                     Da Yan and   
             Zhaohui S. Qin and   
     Debswapna Bhattacharya and   
                   Jake Y. Chen   Guest Editorial for Selected Papers From
                                  BIOKDD 2021  . . . . . . . . . . . . . . 3068--3069
                   Cheng Ye and   
               Rowan Swiers and   
             Stephen Bonner and   
                    Ian Barrett   A Knowledge Graph-Enhanced Tensor
                                  Factorisation Model for Discovering Drug
                                  Targets  . . . . . . . . . . . . . . . . 3070--3080
                  Ngan Dong and   
        Stefanie Mücke and   
                   Megha Khosla   MuCoMiD: a Multitask Graph Convolutional
                                  Learning Framework for MiRNA-Disease
                                  Association Prediction . . . . . . . . . 3081--3092
                Raquel Aoki and   
             Frederick Tung and   
            Gabriel L. Oliveira   Heterogeneous Multi-Task Learning With
                                  Expert Diversity . . . . . . . . . . . . 3093--3102
                     Emre Sefer   BioCode: a Data-Driven Procedure to
                                  Learn the Growth of Biological Networks  3103--3113
         Kingshuk Mukherjee and   
         Daniel Dole-Muinos and   
         Massimiliano Rossi and   
              Ayomide Ajayi and   
            Mattia Prosperi and   
              Christina Boucher   Finding Overlapping Rmaps via Clustering 3114--3123
            De-Shuang Huang and   
              Kyungsook Han and   
                 Tatsuya Akutsu   Guest Editorial for Special Section on
                                  the 16th International Conference on
                                  Intelligent Computing (ICIC) . . . . . . 3124--3125
            Tengsheng Jiang and   
                 Yuhui Chen and   
               Shixuan Guan and   
               Zhongtian Hu and   
                Weizhong Lu and   
                  Qiming Fu and   
                 Yijie Ding and   
                   Haiou Li and   
                     Hongjie Wu   G Protein-Coupled Receptor Interaction
                                  Prediction Based on Deep Transfer
                                  Learning . . . . . . . . . . . . . . . . 3126--3134
             Hsin-Hung Chou and   
             Ching-Tien Hsu and   
               Chin-Wei Hsu and   
               Kai-Hsun Yao and   
             Hao-Ching Wang and   
                 Sun-Yuan Hsieh   Novel Algorithm for Improved Protein
                                  Classification Using Graph Similarity    3135--3143
                Qinhu Zhang and   
              Yindong Zhang and   
                 Siguo Wang and   
             Zhan-Heng Chen and   
           Valeriya Gribova and   
Vladimir Fedorovich Filaretov and   
                De-Shuang Huang   Predicting In-Vitro DNA--Protein Binding
                                  With a Spatially Aligned Fusion of
                                  Sequence and Shape . . . . . . . . . . . 3144--3153
                   Min Fang and   
                  Yufeng He and   
                  Zhihua Du and   
            Vladimir N. Uversky   DeepCLD: an Efficient Sequence-Based
                                  Predictor of Intrinsically Disordered
                                  Proteins . . . . . . . . . . . . . . . . 3154--3159
                  Xinguo Lu and   
                  Jinxin Li and   
               Zhenghao Zhu and   
                   Yue Yuan and   
              Guanyuan Chen and   
                       Keren He   Predicting miRNA--Disease Associations
                                  via Combining Probability Matrix Feature
                                  Decomposition With Neighbor Learning . . 3160--3170
                Qing-Wen Wu and   
                Rui-Fen Cao and   
               Jun-Feng Xia and   
              Jian-Cheng Ni and   
             Chun-Hou Zheng and   
                     Yan-Sen Su   Extra Trees Method for Predicting
                                  LncRNA--Disease Association Based On
                                  Multi-Layer Graph Embedding Aggregation  3171--3178
                      Bo Li and   
                 Yihui Tian and   
                  Yang Tian and   
               Shihua Zhang and   
                 Xiaolong Zhang   Predicting Cancer Lymph-Node Metastasis
                                  From LncRNA Expression Profiles Using
                                  Local Linear Reconstruction Guided
                                  Distance Metric Learning . . . . . . . . 3179--3189
                     Wen Li and   
                Shulin Wang and   
                  Junlin Xu and   
                       Ju Xiang   Inferring Latent MicroRNA--Disease
                                  Associations on a Gene-Mediated
                                  Tripartite Heterogeneous Multiplexing
                                  Network  . . . . . . . . . . . . . . . . 3190--3201
                 Yulian Xie and   
                    Min Liu and   
                Shirui Zhou and   
                    Yaonan Wang   A Deep Local Patch Matching Network for
                                  Cell Tracking in Microscopy Image
                                  Sequences Without Registration . . . . . 3202--3212
             Huang Zhanpeng and   
                     Wu Jiekang   A Multiview Clustering Method With
                                  Low-Rank and Sparsity Constraints for
                                  Cancer Subtyping . . . . . . . . . . . . 3213--3223
                   Nassima Aleb   A Mutual Attention Model for Drug Target
                                  Binding Affinity Prediction  . . . . . . 3224--3232
               Jianshen Zhu and   
          Naveed Ahmed Azam and   
                  Fan Zhang and   
      Aleksandar Shurbevski and   
           Kazuya Haraguchi and   
                 Liang Zhao and   
          Hiroshi Nagamochi and   
                 Tatsuya Akutsu   A Novel Method for Inferring Chemical
                                  Compounds With Prescribed Topological
                                  Substructures Based on Integer
                                  Programming  . . . . . . . . . . . . . . 3233--3245
                Yueran Yang and   
                   Yu Zhang and   
                   Shuai Li and   
                Xubin Zheng and   
               Man-Hon Wong and   
            Kwong-Sak Leung and   
                    Lixin Cheng   A Robust and Generalizable
                                  Immune-Related Signature for Sepsis
                                  Diagnostics  . . . . . . . . . . . . . . 3246--3254
                  Xinzhe Ni and   
                 Bohao Geng and   
                Haoyu Zheng and   
                 Jiawei Shi and   
                    Gang Hu and   
                   Jianzhao Gao   Accurate Estimation of Single-Cell
                                  Differentiation Potency Based on Network
                                  Topology and Gene Ontology Information   3255--3262
                  Yiming Li and   
                   Min Zeng and   
                   Yifan Wu and   
                 Yaohang Li and   
                         Min Li   Accurate Prediction of Human Essential
                                  Proteins Using Ensemble Deep Learning    3263--3271
                 Jingshu Bi and   
              Yuanjie Zheng and   
             Chongjing Wang and   
                    Yanhui Ding   An Attention Based Bidirectional LSTM
                                  Method to Predict the Binding of TCR and
                                  Epitope  . . . . . . . . . . . . . . . . 3272--3280
               Sepideh Mazrouee   ARHap: Association Rule Haplotype
                                  Phasing  . . . . . . . . . . . . . . . . 3281--3294
                   Jiani Ma and   
                  Lin Zhang and   
                 Shaojie Li and   
                        Hui Liu   BRPCA: Bounded Robust Principal
                                  Component Analysis to Incorporate
                                  Similarity Network for
                                  N7-Methylguanosine(mo$^7$G) Site-Disease
                                  Association Prediction . . . . . . . . . 3295--3306
           Ghazaleh Parvini and   
          Katherine Braught and   
    David Fernández-Baca   Checking Phylogenetics Decisiveness in
                                  Theory and in Practice . . . . . . . . . 3307--3316
           Enzo Battistella and   
         Maria Vakalopoulou and   
                  Roger Sun and   
       Théo Estienne and   
          Marvin Lerousseau and   
            Sergey Nikolaev and   
Émilie Alvarez Andres and   
     Alexandre Carré and   
   Stéphane Niyoteka and   
           Charlotte Robert and   
             Nikos Paragios and   
            Éric Deutsch   COMBING: Clustering in Oncology for
                                  Mathematical and Biological
                                  Identification of Novel Gene Signatures  3317--3331
             Aanchal Mongia and   
          Emilie Chouzenoux and   
               Angshul Majumdar   Computational Prediction of Drug-Disease
                                  Association Based on Graph-Regularized
                                  One Bit Matrix Completion  . . . . . . . 3332--3339
                Omar Shetta and   
           Mahesan Niranjan and   
         Srinandan Dasmahapatra   Convex Multi-View Clustering Via Robust
                                  Low Rank Approximation With Application
                                  to Multi-Omic Data . . . . . . . . . . . 3340--3352
      Mattias Åkesson and   
             Prashant Singh and   
              Fredrik Wrede and   
              Andreas Hellander   Convolutional Neural Networks as Summary
                                  Statistics for Approximate Bayesian
                                  Computation  . . . . . . . . . . . . . . 3353--3365


IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 20, Number 1, 2023

               Qiaoming Liu and   
                Xudong Zhao and   
                    Guohua Wang   A Clustering Ensemble Method for Cell
                                  Type Detection by Multiobjective
                                  Particle Optimization  . . . . . . . . . 1--14
                    Kun Liu and   
               Hong-Dong Li and   
                 Yaohang Li and   
                   Jun Wang and   
                   Jianxin Wang   A Comparison of Topologically
                                  Associating Domain Callers Based on Hi-C
                                  Data . . . . . . . . . . . . . . . . . . 15--29
                  Jan Klosa and   
                 Noah Simon and   
          Volkmar Liebscher and   
          Dörte Wittenburg   A Fitted Sparse-Group Lasso for
                                  Genome-Based Evaluations . . . . . . . . 30--38
            Chengzhuan Yang and   
               Lincong Fang and   
                    Qian Yu and   
                        Hui Wei   A Learning Robust and Discriminative
                                  Shape Descriptor for Plant Species
                                  Identification . . . . . . . . . . . . . 39--51
                  Feng Zhou and   
              Meng-Meng Yin and   
              Jing-Xiu Zhao and   
             Junliang Shang and   
                   Jin-Xing Liu   A Method Based On Dual-Network
                                  Information Fusion to Predict
                                  MiRNA--Disease Associations  . . . . . . 52--60
                   Qiang Yu and   
                 Xiao Zhang and   
                    Yana Hu and   
              Shengpin Chen and   
                    Liying Yang   A Method for Predicting DNA Motif Length
                                  Based On Deep Learning . . . . . . . . . 61--73
              Weixian Huang and   
                 Kaiwen Tan and   
                 Ziye Zhang and   
                 Jinlong Hu and   
                   Shoubin Dong   A Review of Fusion Methods for Omics and
                                  Imaging Data . . . . . . . . . . . . . . 74--93
              Ashish Ranjan and   
             Archana Tiwari and   
                  Akshay Deepak   A Sub-Sequence Based Approach to Protein
                                  Function Prediction via Multi-Attention
                                  Based Multi-Aspect Network . . . . . . . 94--105
                    Jun Bai and   
               Chuantao Yin and   
              Jianfei Zhang and   
               Yanmeng Wang and   
                    Yi Dong and   
                 Wenge Rong and   
                    Zhang Xiong   Adversarial Knowledge Distillation Based
                                  Biomedical Factoid Question Answering    106--118
     Katrin Sophie Bohnsack and   
               Marika Kaden and   
                 Julia Abel and   
                Thomas Villmann   Alignment-Free Sequence Comparison: a
                                  Systematic Survey From a Machine
                                  Learning Perspective . . . . . . . . . . 119--135
        Steffy Maria Joseph and   
                P. S. Sathidevi   An Automated cDNA Microarray Image
                                  Analysis for the Determination of Gene
                                  Expression Ratios  . . . . . . . . . . . 136--150
              Sahar Iravani and   
               Tim O. F. Conrad   An Interpretable Deep Learning Approach
                                  for Biomarker Detection in LC-MS
                                  Proteomics Data  . . . . . . . . . . . . 151--161
                Kanchan Jha and   
                  Sriparna Saha   Analyzing Effect of Multi-Modality in
                                  Predicting Protein-Protein Interactions  162--173
         Shankarachary Ragi and   
          Md Hafizur Rahman and   
          Jamison Duckworth and   
       Kalimuthu Jawaharraj and   
            Parvathi Chundi and   
     Venkataramana Gadhamshetty   Artificial Intelligence-Driven Image
                                  Analysis of Bacterial Cells and Biofilms 174--184
                  Hao Zhang and   
                Chuanxu Yan and   
                  Yewei Xia and   
                Jihong Guan and   
                  Shuigeng Zhou   Causal Gene Identification Using
                                  Non-Linear Regression-Based Independence
                                  Tests  . . . . . . . . . . . . . . . . . 185--195
                Naser Anjum and   
          Raian Latif Nabil and   
         Rakibul Islam Rafi and   
     Md. Shamsuzzoha Bayzid and   
               M. Saifur Rahman   CD-MAWS: an Alignment-Free Phylogeny
                                  Estimation Method Using Cosine Distance
                                  on Minimal Absent Word Sets  . . . . . . 196--205
                   Tuan D. Pham   Classification of \bionameCaenorhabditis
                                  elegans Locomotion Behaviors With
                                  Eigenfeature-Enhanced Long Short-Term
                                  Memory Networks  . . . . . . . . . . . . 206--216
             Ichcha Manipur and   
          Maurizio Giordano and   
          Marina Piccirillo and   
   Seetharaman Parashuraman and   
                Lucia Maddalena   Community Detection in Protein--Protein
                                  Interaction Networks and Applications    217--237
             Rizwan Qureshi and   
                    Bin Zou and   
                Tanvir Alam and   
                     Jia Wu and   
           Victor H. F. Lee and   
                       Hong Yan   Computational Methods for the Analysis
                                  and Prediction of EGFR-Mutated Lung
                                  Cancer Drug Resistance: Recent Advances
                                  in Drug Design, Challenges and Future
                                  Prospects  . . . . . . . . . . . . . . . 238--255
                Jingbo Yang and   
                Denan Zhang and   
                 Yiyang Cai and   
                   Kexin Yu and   
                Mingming Li and   
                    Lei Liu and   
                    Xiujie Chen   Computational Prediction of Drug
                                  Phenotypic Effects Based on
                                  Substructure-Phenotype Associations  . . 256--265
                   Wook Lee and   
                Seokwoo Lee and   
                  Kyungsook Han   Constructing a Cancer Patient-Specific
                                  Network Based on Second-Order Partial
                                  Correlations of Gene Expression and DNA
                                  Methylation  . . . . . . . . . . . . . . 266--276
                Zhi-Hao Liu and   
                 Cun-Mei Ji and   
              Jian-Cheng Ni and   
               Yu-Tian Wang and   
               Li-Juan Qiao and   
                 Chun-Hou Zheng   Convolution Neural Networks Using Deep
                                  Matrix Factorization for Predicting
                                  Circrna-Disease Association  . . . . . . 277--284
                   Yang Hua and   
              Xiaoning Song and   
               Zhenhua Feng and   
                Xiao-Jun Wu and   
              Josef Kittler and   
                    Dong-Jun Yu   CPInformer for Efficient and Robust
                                  Compound-Protein Interaction Prediction  285--296
                 Kailong Li and   
                 Lijun Quan and   
                 Yelu Jiang and   
                     Yan Li and   
                Yiting Zhou and   
                Tingfang Wu and   
                      Qiang Lyu   ctP$^2$ISP: Protein--Protein Interaction
                                  Sites Prediction Using Convolution and
                                  Transformer With Data Augmentation . . . 297--306
                 Xiuquan Du and   
                      Jiajia Hu   Deep Multi-Label Joint Learning for RNA
                                  and DNA-Binding Proteins Prediction  . . 307--320
              Xiao-Hui Yang and   
                  Zi-Jun Xi and   
                Jie-Ping Li and   
               Xin-Lei Feng and   
              Xiao-Hong Zhu and   
                  Si-Yi Guo and   
                 Chun-Peng Song   Deep Transfer Learning-Based
                                  Multi-Object Detection for Plant Stomata
                                  Phenotypic Traits Intelligent
                                  Recognition  . . . . . . . . . . . . . . 321--329
              Onur Can Uner and   
         Halil Ibrahim Kuru and   
          R. Gokberk Cinbis and   
               Oznur Tastan and   
              A. Ercument Cicek   DeepSide: a Deep Learning Approach for
                                  Drug Side Effect Prediction  . . . . . . 330--339
                 Zimo Huang and   
                   Jun Wang and   
               Zhongmin Yan and   
                    Lin Wan and   
                      Maozu Guo   Differential Gene Expression Prediction
                                  by Ensemble Deep Networks on Histone
                                  Modification Data  . . . . . . . . . . . 340--351
               Jinghang Lin and   
               Xiaoran Tong and   
                  Chenxi Li and   
                        Qing Lu   Expectile Neural Networks for Genetic
                                  Data Analysis of Complex Diseases  . . . 352--359
             Lucia Williams and   
       Alexandru I. Tomescu and   
                  Brendan Mumey   Flow Decomposition With Subpath
                                  Constraints  . . . . . . . . . . . . . . 360--370

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 20, Number 2, March, 2023

Isabel González-Crespo and   
Antonio Gómez-Caamaño and   
Óscar López Pouso and   
            John D. Fenwick and   
             Juan Pardo-Montero   A Biomathematical Model of Tumor
                                  Response to Radioimmunotherapy With $
                                  \alpha $PDL1 and $ \alpha $CTLA4 . . . . 808--821
                   Xiong Li and   
                Yangkai Lin and   
              Chengwang Xie and   
                   Zejun Li and   
                   Min Chen and   
                  Peng Wang and   
                      Juan Zhou   A Clustering Method Unifying Cell-Type
                                  Recognition and Subtype Identification
                                  for Tumor Heterogeneity Analysis . . . . 822--832
                     Min Li and   
                  Wenbo Shi and   
                Fuhao Zhang and   
                   Min Zeng and   
                     Yaohang Li   A Deep Learning Framework for Predicting
                                  Protein Functions With Co-Occurrence of
                                  GO Terms . . . . . . . . . . . . . . . . 833--842
              Xiaoqing Peng and   
               Wenjin Zhang and   
                 Wanxin Cui and   
               Binrong Ding and   
               Qingtong Lyu and   
                   Jianxin Wang   ADmeth: a Manually Curated Database for
                                  the Differential Methylation in
                                  Alzheimer's Disease  . . . . . . . . . . 843--851
               Qichang Zhao and   
                Guihua Duan and   
               Mengyun Yang and   
            Zhongjian Cheng and   
                 Yaohang Li and   
                   Jianxin Wang   AttentionDTA: Drug-Target Binding
                                  Affinity Prediction by Sequence-Based
                                  Deep Learning With Attention Mechanism   852--863
                Jiasheng Si and   
                    Liu Sun and   
                  Deyu Zhou and   
                    Jie Ren and   
                         Lin Li   Biomedical Argument Mining Based on
                                  Sequential Multi-Task Learning . . . . . 864--874
            Mahdieh Ghasemi and   
            Maseud Rahgozar and   
                  Kaveh Kavousi   Complex Disease Genes Identification
                                  Using a Heterogeneous Network Embedding
                                  Approach . . . . . . . . . . . . . . . . 875--882
               Dong Jun Jee and   
                 Yixin Kong and   
                    Hyonho Chun   Deep Nonnegative Matrix Factorization
                                  Using a Variational Autoencoder With
                                  Application to Single-Cell RNA
                                  Sequencing Data  . . . . . . . . . . . . 883--893
                Volkan Altuntas   Diffusion Alignment Coefficient (DAC): a
                                  Novel Similarity Metric for
                                  Protein-Protein Interaction Network  . . 894--903
           Mobeen Ur Rehman and   
               Hilal Tayara and   
                   Kil To Chong   DL-m6A: Identification of
                                  N6-Methyladenosine Sites in Mammals
                                  Using Deep Learning Based on Different
                                  Encoding Schemes . . . . . . . . . . . . 904--911
                Zhong-Ze Yu and   
            Chun-Xiang Peng and   
                    Jun Liu and   
                 Biao Zhang and   
              Xiao-Gen Zhou and   
                  Gui-Jun Zhang   DomBpred: Protein Domain Boundary
                                  Prediction Based on Domain-Residue
                                  Clustering Using Inter-Residue Distance  912--922
                  Xin Huang and   
                  Benzhe Su and   
                 Chenbo Zhu and   
                   Xinyu He and   
                    Xiaohui Lin   Dynamic Network Construction for
                                  Identifying Early Warning Signals Based
                                  On a Data-Driven Approach: Early
                                  Diagnosis Biomarker Discovery for
                                  Gastric Cancer . . . . . . . . . . . . . 923--931
                   Xuan Lin and   
                   Zhe Quan and   
               Zhi-Jie Wang and   
                    Yan Guo and   
            Xiangxiang Zeng and   
                   Philip S. Yu   Effectively Identifying Compound-Protein
                                  Interaction Using Graph Neural
                                  Representation . . . . . . . . . . . . . 932--943
               Yongxian Fan and   
                Guicong Sun and   
                   Xiaoyong Pan   ELMo4m6A: a Contextual Language
                                  Embedding-Based Predictor for Detecting
                                  RNA N6-Methyladenosine Sites . . . . . . 944--954
             Shamima Rashid and   
            Suresh Sundaram and   
                Chee Keong Kwoh   Empirical Study of Protein Feature
                                  Representation on Deep Belief Networks
                                  Trained With Small Data for Secondary
                                  Structure Prediction . . . . . . . . . . 955--966
                  Chao Wang and   
                   Quan Zou and   
                    Ying Ju and   
                        Hua Shi   Enhancer-FRL: Improved and Robust
                                  Identification of Enhancers and Their
                                  Activities Using Feature Representation
                                  Learning . . . . . . . . . . . . . . . . 967--975
                Shichao Liu and   
                 Yang Zhang and   
                  Yuxin Cui and   
                   Yang Qiu and   
                 Yifan Deng and   
             Zhongfei Zhang and   
                      Wen Zhang   Enhancing Drug-Drug Interaction
                                  Prediction Using Deep Attention Neural
                                  Networks . . . . . . . . . . . . . . . . 976--985
                  Yang Shen and   
                 Jinlin Zhu and   
              Zhaohong Deng and   
                  Wenwei Lu and   
                  Hongchao Wang   EnsDeepDP: an Ensemble Deep Learning
                                  Approach for Disease Prediction Through
                                  Metagenomics . . . . . . . . . . . . . . 986--998
          Leandro Di Persia and   
                Tiago Lopez and   
               Agustin Arce and   
            Diego H. Milone and   
             Georgina Stegmayer   exp2GO: Improving Prediction of
                                  Functions in the Gene Ontology With
                                  Expression Data  . . . . . . . . . . . . 999--1008
        Filippo Castiglione and   
          Christine Nardini and   
                Elia Onofri and   
             Marco Pedicini and   
                    Paolo Tieri   Explainable Drug Repurposing Approach
                                  From Biased Random Walks . . . . . . . . 1009--1019
            Tri Minh Nguyen and   
            Thomas P. Quinn and   
                Thin Nguyen and   
                    Truyen Tran   Explaining Black Box Drug Target
                                  Prediction Through Model Agnostic
                                  Counterfactual Samples . . . . . . . . . 1020--1029
               Chunyan Tang and   
                Cheng Zhong and   
                  Mian Wang and   
                  Fengfeng Zhou   FMGNN: a Method to Predict
                                  Compound-Protein Interaction With
                                  Pharmacophore Features and
                                  Physicochemical Properties of Amino
                                  Acids  . . . . . . . . . . . . . . . . . 1030--1040
                  Jiwen Liu and   
              Zhufang Kuang and   
                       Lei Deng   GCNPCA: miRNA-Disease Associations
                                  Prediction Algorithm Based on Graph
                                  Convolutional Neural Networks  . . . . . 1041--1052
                  Zhen Tian and   
              Haichuan Fang and   
                Zhixia Teng and   
                    Yangdong Ye   GOGCN: Graph Convolutional Network on
                                  Gene Ontology for Functional Similarity
                                  Analysis of Genes  . . . . . . . . . . . 1053--1064
                  Thang Chu and   
          Thuy Trang Nguyen and   
              Bui Duong Hai and   
           Quang Huy Nguyen and   
                    Tuan Nguyen   Graph Transformer for Drug Response
                                  Prediction . . . . . . . . . . . . . . . 1065--1072
       Bryan Herrera-Romero and   
Diego Almeida-Galárraga and   
          Graciela M. Salum and   
  Fernando Villalba-Meneses and   
Marco Esteban Gudiño-Gomezjurado   GUSignal: an Informatics Tool to Analyze
                                  Glucuronidase Gene Expression in
                                  \bionameArabidopsis thaliana Roots . . . 1073--1080
                 Junwei Sun and   
                 Haoping Ji and   
              Yingcong Wang and   
                   Yanfeng Wang   Hybrid Projective Synchronization via PI
                                  Controller Based on DNA Strand
                                  Displacement . . . . . . . . . . . . . . 1081--1091
                Vicky Zheng and   
       Ahmet Erdem Sariyuce and   
                  Jaroslaw Zola   Identifying Taxonomic Units in
                                  Metagenomic DNA Streams on Mobile
                                  Devices  . . . . . . . . . . . . . . . . 1092--1103
          Yasin Görmez and   
                    Zafer Aydin   IGPRED-MultiTask: a Deep Learning Model
                                  to Predict Protein Secondary Structure,
                                  Torsion Angles and Solvent Accessibility 1104--1113
                Yongping Du and   
                 Jingya Yan and   
                  Yuxuan Lu and   
               Yiliang Zhao and   
                    Xingnan Jin   Improving Biomedical Question Answering
                                  by Data Augmentation and Model Weighting 1114--1124

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 20, Number 3, May, 2023

  Carlos Martín-Vide and   
Miguel A. Vega-Rodríguez   Algorithms for Computational Biology:
                                  Eighth Edition . . . . . . . . . . . . . 1626--1627
Alexsandro Oliveira Alexandrino and   
        Klairton Lima Brito and   
   Andre Rodrigues Oliveira and   
               Ulisses Dias and   
                    Zanoni Dias   Reversal and Indel Distance With
                                  Intergenic Region Information  . . . . . 1628--1640
        Klairton Lima Brito and   
Alexsandro Oliveira Alexandrino and   
   Andre Rodrigues Oliveira and   
               Ulisses Dias and   
                    Zanoni Dias   Genome Rearrangement Distance With a
                                  Flexible Intergenic Regions Aspect . . . 1641--1653
               Kaari Landry and   
             Aivee Teodocio and   
              Manuel Lafond and   
        Olivier Tremblay-Savard   Defining Phylogenetic Network Distances
                                  Using Cherry Operations  . . . . . . . . 1654--1666
                 Chenqi Mou and   
                      Wenwen Ju   Sparse Triangular Decomposition for
                                  Computing Equilibria of Biological
                                  Dynamic Systems Based on Chordal Graphs  1667--1678
             David Schaller and   
         Manuela Geiß and   
              Marc Hellmuth and   
               Peter F. Stadler   Best Match Graphs With Binary Trees  . . 1679--1690
                    Yin Yao and   
                Martin C. Frith   Improved DNA-Versus-Protein Homology
                                  Search for Protein Fossils . . . . . . . 1691--1699
              Paul Zaharias and   
           Vladimir Smirnov and   
                   Tandy Warnow   Large-Scale Multiple Sequence Alignment
                                  and the Maximum Weight Trace Alignment
                                  Merging Problem  . . . . . . . . . . . . 1700--1712
                  Kaitao Wu and   
               Lexiang Wang and   
                     Bo Liu and   
                   Yang Liu and   
                Yadong Wang and   
                       Junyi Li   PSPGO: Cross-Species Heterogeneous
                                  Network Propagation for Protein Function
                                  Prediction . . . . . . . . . . . . . . . 1713--1724
    Alejandro F. Villaverde and   
      Elba Raimúndez and   
              Jan Hasenauer and   
                 Julio R. Banga   Assessment of Prediction Uncertainty
                                  Quantification Methods in Systems
                                  Biology  . . . . . . . . . . . . . . . . 1725--1736
               Jinmiao Song and   
              Shengwei Tian and   
                    Long Yu and   
                Qimeng Yang and   
                Yuanxu Wang and   
                  Qiguo Dai and   
                  Xiaodong Duan   ISLMI: Predicting lncRNA--miRNA
                                  Interactions Based on Information
                                  Injection and Second-Order Graph
                                  Convolution Network  . . . . . . . . . . 1737--1745
                   Yan Kang and   
               Haining Wang and   
                     Bin Pu and   
                    Liu Tao and   
               Jianguo Chen and   
                   Philip S. Yu   A Hybrid Two-Stage
                                  Teaching-Learning-Based Optimization
                                  Algorithm for Feature Selection in
                                  Bioinformatics . . . . . . . . . . . . . 1746--1760
                 Pranab Das and   
             Yogita Thakran and   
         S. R. Ngamwal Anal and   
                  Vipin Pal and   
                     Anju Yadav   BRMCF: Binary Relevance and MLSMOTE
                                  Based Computational Framework to Predict
                                  Drug Functions From Chemical and
                                  Biological Properties of Drugs . . . . . 1761--1773
                  Wen-Yu Xi and   
                  Feng Zhou and   
              Ying-Lian Gao and   
               Jin-Xing Liu and   
                 Chun-Hou Zheng   LDCMFC: Predicting Long Non-Coding RNA
                                  and Disease Association Using
                                  Collaborative Matrix Factorization Based
                                  on Correntropy . . . . . . . . . . . . . 1774--1782
       Ramkishore Bhattacharyya   Bidirectional Association Discovery
                                  Leads to Precise Identification of Lung
                                  Cancer Biomarkers and Genome Taxa Class  1783--1794
    Vianney Kengne Tchendji and   
Franklin Ingrid Kamga Youmbi and   
Clémentin Tayou Djamegni and   
           Jerry Lacmou Zeutouo   A Parallel Tiled and Sparsified
                                  Four-Russians Algorithm for Nussinov's
                                  RNA Folding  . . . . . . . . . . . . . . 1795--1806
                     Jie Xu and   
               Guanxue Yang and   
                 Guohai Liu and   
                        Hui Liu   Inferring Gene Regulatory Networks via
                                  Ensemble Path Consistency Algorithm
                                  Based on Conditional Mutual Information  1807--1816
          Pradeep Kumar Das and   
            Biswajeet Sahoo and   
                  Sukadev Meher   An Efficient Detection and
                                  Classification of Acute Leukemia Using
                                  Transfer Learning and Orthogonal Softmax
                                  Layer-Based Model  . . . . . . . . . . . 1817--1828
Marcelo Rodrigues de Holanda Maia and   
         Alexandre Plastino and   
               Alex Freitas and   
João Pedro de Magalhães   Interpretable Ensembles of Classifiers
                                  for Uncertain Data With Bioinformatics
                                  Applications . . . . . . . . . . . . . . 1829--1841
                Shutao Chen and   
                  Lin Zhang and   
              Xiangzhi Chen and   
                        Hui Liu   FGFICA: Independent Component Analysis
                                  of Fusion Genomic Features for Mining
                                  Epi-Transcriptome Profiling Data . . . . 1842--1853
                     Hui Yu and   
                KangKang Li and   
                     JianYu Shi   DGANDDI: Double Generative Adversarial
                                  Networks for Drug-Drug Interaction
                                  Prediction . . . . . . . . . . . . . . . 1854--1863
                    Jun Bai and   
               Chuantao Yin and   
                  Zimeng Wu and   
              Jianfei Zhang and   
               Yanmeng Wang and   
                 Guanyi Jia and   
                 Wenge Rong and   
                    Zhang Xiong   Improving Biomedical ReQA With
                                  Consistent NLI-Transfer and
                                  Post-Whitening . . . . . . . . . . . . . 1864--1875
               Xiangbin Lin and   
             Weizhuang Kong and   
                 Jianxiu Li and   
               Xuexiao Shao and   
            Changting Jiang and   
                  Ruilan Yu and   
                 Xiaowei Li and   
                         Bin Hu   Aberrant Static and Dynamic Functional
                                  Brain Network in Depression Based on EEG
                                  Source Localization  . . . . . . . . . . 1876--1889
    Prasun Chandra Tripathi and   
                     Soumen Bag   An Attention-Guided CNN Framework for
                                  Segmentation and Grading of Glioma Using
                                  $3$D MRI Scans . . . . . . . . . . . . . 1890--1904
                 Shuhui Liu and   
                Yupei Zhang and   
                   Xuequn Shang   GLassonet: Identifying Discriminative
                                  Gene Sets Among Molecular Subtypes of
                                  Breast Cancer  . . . . . . . . . . . . . 1905--1916
                Hegang Chen and   
                   Yuyin Lu and   
               Yuedong Yang and   
                    Yanghui Rao   A Drug Combination Prediction Framework
                                  Based on Graph Convolutional Network and
                                  Heterogeneous Information  . . . . . . . 1917--1925
              Shengli Zhang and   
                  Yuanyuan Jing   PreVFs-RG: a Deep Hybrid Model for
                                  Identifying Virulence Factors Based on
                                  Residual Block and Gated Recurrent Unit  1926--1934
               Minghua Zhao and   
                   Min Yuan and   
                Yaning Yang and   
                   Steven X. Xu   CPGL: Prediction of Compound-Protein
                                  Interaction by Integrating Graph
                                  Attention Network With Long Short-Term
                                  Memory Neural Network  . . . . . . . . . 1935--1942
               Qichang Zhao and   
                Guihua Duan and   
               Haochen Zhao and   
                  Kai Zheng and   
                 Yaohang Li and   
                   Jianxin Wang   GIFDTI: Prediction of Drug-Target
                                  Interactions Based on Global Molecular
                                  and Intermolecular Interaction
                                  Representation Learning  . . . . . . . . 1943--1952
                    Qi Dang and   
                 Yong Liang and   
                Dong Ouyang and   
                   Rui Miao and   
                Caijin Ling and   
               Xiaoying Liu and   
                    Shengli Xie   Improved Computational
                                  Drug-Repositioning by Self-Paced
                                  Non-Negative Matrix Tri-Factorization    1953--1962

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 20, Number 4, July, 2023

                Honghao Gao and   
               Zijian Zhang and   
Ramón J. Durán Barroso   Guest Editorial Special Issue on
                                  Multi-Modal Biomedical Computing-Deep
                                  Transfer Learning  . . . . . . . . . . . 2363--2366
                   Wei Wang and   
                  Xinhua Yu and   
                    Bo Fang and   
                   Yue Zhao and   
              Yongyong Chen and   
                    Wei Wei and   
                    Junxin Chen   Cross-Modality LGE-CMR Segmentation
                                  Using Image-to-Image Translation Based
                                  Data Augmentation  . . . . . . . . . . . 2367--2375
                 Zhichen Ni and   
              Honglong Chen and   
                     Zhe Li and   
              Xiaomeng Wang and   
                     Na Yan and   
                Weifeng Liu and   
                       Feng Xia   MSCET: a Multi-Scenario Offloading
                                  Schedule for Biomedical Data Processing
                                  and Analysis in Cloud-Edge-Terminal
                                  Collaborative Vehicular Networks . . . . 2376--2386
             Yuanpeng Zhang and   
                Kaijian Xia and   
              Yizhang Jiang and   
             Pengjiang Qian and   
                 Weiwei Cai and   
                Chengyu Qiu and   
               Khin Wee Lai and   
                     Dongrui Wu   Multi-Modality Fusion & Inductive
                                  Knowledge Transfer Underlying Non-Sparse
                                  Multi-Kernel Learning and Distribution
                                  Adaption . . . . . . . . . . . . . . . . 2387--2397
                   Nan Chen and   
                    Man Guo and   
                Yongchao Li and   
                  Xiping Hu and   
                 Zhijun Yao and   
                         Bin Hu   Estimation of Discriminative Multimodal
                                  Brain Network Connectivity Using
                                  Message-Passing-Based Nonlinear Network
                                  Fusion . . . . . . . . . . . . . . . . . 2398--2406
                Jinxia Wang and   
                 Liang Qiao and   
                  Haibin Lv and   
                      Zhihan Lv   Deep Transfer Learning-Based Multi-Modal
                                  Digital Twins for Enhancement and
                                  Diagnostic Analysis of Brain MRI Image   2407--2419
          Fayaz Ali Dharejo and   
            Muhammad Zawish and   
                Farah Deeba and   
              Yuanchun Zhou and   
                  Kapal Dev and   
         Sunder Ali Khowaja and   
  Nawab Muhammad Faseeh Qureshi   Multimodal-Boost: Multimodal Medical
                                  Image Super-Resolution Using
                                  Multi-Attention Network With Wavelet
                                  Transform  . . . . . . . . . . . . . . . 2420--2433
                Yuexin Bian and   
                Jintai Chen and   
               Xiaojun Chen and   
              Xiaoxian Yang and   
              Danny Z. Chen and   
                        Jian Wu   Identifying Electrocardiogram
                                  Abnormalities Using a
                                  Handcrafted-Rule-Enhanced Neural Network 2434--2444
                Imran Ahmed and   
            Abdellah Chehri and   
              Gwanggil Jeon and   
            Francesco Piccialli   Automated Pulmonary Nodule
                                  Classification and Detection Using Deep
                                  Learning Architectures . . . . . . . . . 2445--2456
                 Qi-Qi Chen and   
               Zhao-Hui Sun and   
             Chuan-Feng Wei and   
               Edmond Q. Wu and   
                      Dong Ming   Semi-Supervised $3$D Medical Image
                                  Segmentation Based on Dual-Task
                                  Consistent Joint Learning and Task-Level
                                  Regularization . . . . . . . . . . . . . 2457--2467
            Mainak Adhikari and   
             Abhishek Hazra and   
                Sudarshan Nandy   Deep Transfer Learning for Communicable
                                  Disease Detection and Recommendation in
                                  Edge Networks  . . . . . . . . . . . . . 2468--2479
                Xiaolong Xu and   
                  Haoyan Xu and   
                Liying Wang and   
             Yuanyuan Zhang and   
                        Fu Xaio   Hygeia: a Multilabel Deep Learning-Based
                                  Classification Method for Imbalanced
                                  Electrocardiogram Data . . . . . . . . . 2480--2493
                   Yuxin Ma and   
                  Shuo Wang and   
                   Yang Hua and   
                   Ruhui Ma and   
                   Tao Song and   
                Zhengui Xue and   
                   Heng Cao and   
                   Haibing Guan   Perceptual Data Augmentation for
                                  Biomedical Coronary Vessel Segmentation  2494--2505
                Jianyuan Li and   
                  Xiong Luo and   
                  Huimin Ma and   
                   Wenbing Zhao   A Hybrid Deep Transfer Learning Model
                                  With Kernel Metric for COVID-19
                                  Pneumonia Classification Using Chest CT
                                  Images . . . . . . . . . . . . . . . . . 2506--2517
          Ilias Siniosoglou and   
         Vasileios Argyriou and   
   Panagiotis Sarigiannidis and   
              Thomas Lagkas and   
     Antonios Sarigiannidis and   
         Sotirios K. Goudos and   
                    Shaohua Wan   Post-Processing Fairness Evaluation of
                                  Federated Models: an Unsupervised
                                  Approach in Healthcare . . . . . . . . . 2518--2529
                Wentian Cai and   
                 Linsen Xie and   
               Weixian Yang and   
                 Yijiang Li and   
                   Ying Gao and   
                  Tingting Wang   DFTNet: Dual-Path Feature Transfer
                                  Network for Weakly Supervised Medical
                                  Image Segmentation . . . . . . . . . . . 2530--2540
               Qingbin Wang and   
                 Kaiyi Chen and   
                Wanrong Dou and   
                       Yutao Ma   Cross-Attention Based Multi-Resolution
                                  Feature Fusion Model for Self-Supervised
                                  Cervical OCT Image Classification  . . . 2541--2554
                     Ke Yan and   
                  Xinlu Guo and   
                  Zhiwei Ji and   
                  Xiaokang Zhou   Deep Transfer Learning for Cross-Species
                                  Plant Disease Diagnosis Adapting Mixed
                                  Subdomains . . . . . . . . . . . . . . . 2555--2564
                    Yi Ding and   
                    Xue Qin and   
             Mingfeng Zhang and   
                    Ji Geng and   
               Dajiang Chen and   
                  Fuhu Deng and   
                    Chunhe Song   RLSegNet: an Medical Image Segmentation
                                  Network Based on Reinforcement Learning  2565--2576
             Tingting Liang and   
               Congying Xia and   
               Ziqiang Zhao and   
               Yixuan Jiang and   
                   Yuyu Yin and   
                   Philip S. Yu   Transferring From Textual Entailment to
                                  Biomedical Named Entity Recognition  . . 2577--2586
               Abdul Qayyum and   
               Imran Razzak and   
                 M. Tanveer and   
               Moona Mazher and   
               Bandar Alhaqbani   High-Density Electroencephalography and
                                  Speech Signal Based Deep Framework for
                                  Clinical Depression Diagnosis  . . . . . 2587--2597
                  Sheng Ren and   
                  Kehua Guo and   
              Xiaokang Zhou and   
                     Bin Hu and   
                Feihong Zhu and   
                      Entao Luo   Medical Image Super-Resolution Based on
                                  Semantic Perception Transfer Learning    2598--2609

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 20, Number 5, 2023

              Mei-Neng Wang and   
                Xue-Jun Xie and   
               Zhu-Hong You and   
                  Leon Wong and   
                 Li-Ping Li and   
                 Zhan-Heng Chen   Combining $K$ Nearest Neighbor With
                                  Nonnegative Matrix Factorization for
                                  Predicting CircRNA-Disease Associations  2610--2618
               Shixuan Guan and   
                   Quan Zou and   
                 Hongjie Wu and   
                     Yijie Ding   Protein-DNA Binding Residues Prediction
                                  Using a Deep Learning Model With
                                  Hierarchical Feature Extraction  . . . . 2619--2628
               Zheng-Wei Li and   
              Qian-Kun Wang and   
              Chang-An Yuan and   
              Peng-Yong Han and   
               Zhu-Hong You and   
                       Lei Wang   Predicting MiRNA-Disease Associations by
                                  Graph Representation Learning Based on
                                  Jumping Knowledge Networks . . . . . . . 2629--2638
              Chengxi Huang and   
                   Wei Wang and   
                  Xin Zhang and   
              Shui-Hua Wang and   
                  Yu-Dong Zhang   Tuberculosis Diagnosis Using Deep
                                  Transferred EfficientNet . . . . . . . . 2639--2646
                    Qing Ye and   
             Xiaolong Zhang and   
                     Xiaoli Lin   Drug-Target Interaction Prediction via
                                  Graph Auto-Encoder and Multi-Subspace
                                  Deep Neural Networks . . . . . . . . . . 2647--2658
              Shanshan Wang and   
                  Ruoyou Wu and   
                   Cheng Li and   
                   Juan Zou and   
                Ziyao Zhang and   
                 Qiegen Liu and   
                     Yan Xi and   
                  Hairong Zheng   PARCEL: Physics-Based Unsupervised
                                  Contrastive Representation Learning for
                                  Multi-Coil MR Imaging  . . . . . . . . . 2659--2670
                Seokwoo Lee and   
                   Wook Lee and   
                 Shulei Ren and   
              Byungkyu Park and   
                  Kyungsook Han   Constructing Integrative ceRNA Networks
                                  and Finding Prognostic Biomarkers in
                                  Renal Cell Carcinoma . . . . . . . . . . 2671--2680
                  Xinguo Lu and   
              Guanyuan Chen and   
                  Jinxin Li and   
                Xiangjin Hu and   
                     Fengxu Sun   MAGCN: a Multiple Attention Graph
                                  Convolution Networks for Predicting
                                  Synthetic Lethality  . . . . . . . . . . 2681--2689
                Qinhu Zhang and   
                 Youhong Xu and   
                 Siguo Wang and   
                    Yong Wu and   
                Yuannong Ye and   
              Chang-An Yuan and   
           Valeriya Gribova and   
Vladimir Fedorovich Filaretov and   
                De-Shuang Huang   Using Fully Convolutional Network to
                                  Locate Transcription Factor Binding
                                  Sites Based on DNA Sequence and
                                  Conservation Information . . . . . . . . 2690--2699
        Abbas Saad Alatrany and   
                 Wasiq Khan and   
            Abir J. Hussain and   
           Jamila Mustafina and   
               Dhiya Al-Jumeily   Transfer Learning for Classification of
                                  Alzheimer's Disease Based on Genome Wide
                                  Data . . . . . . . . . . . . . . . . . . 2700--2711
               Haochen Zhao and   
                Guihua Duan and   
                    Peng Ni and   
                  Cheng Yan and   
                 Yaohang Li and   
                   Jianxin Wang   RNPredATC: a Deep Residual
                                  Learning-Based Model With Applications
                                  to the Prediction of Drug-ATC Code
                                  Association  . . . . . . . . . . . . . . 2712--2723
                    Wuli Xu and   
                   Lei Duan and   
                Huiru Zheng and   
              Jesse Li-Ling and   
              Weipeng Jiang and   
                Yidan Zhang and   
              Tingting Wang and   
                      Ruiqi Qin   An Integrative Disease Information
                                  Network Approach to Similar Disease
                                  Detection  . . . . . . . . . . . . . . . 2724--2735
              Kevin Sutanto and   
                Marcel Turcotte   Assessing Global-Local Secondary
                                  Structure Fingerprints to Classify RNA
                                  Sequences With Deep Learning . . . . . . 2736--2747
                   Wei Peng and   
                   Ming Liu and   
                    Wei Dai and   
                Tielin Chen and   
                      Yu Fu and   
                         Yi Pan   Multi-View Feature Aggregation for
                                  Predicting Microbe-Disease Association   2748--2758
            Ahmed Bin Zaman and   
           Toki Tahmid Inan and   
            Kenneth De Jong and   
                   Amarda Shehu   Adaptive Stochastic Optimization to
                                  Improve Protein Conformation Sampling    2759--2771
            Xiaoshuai Zhang and   
                 Lixin Wang and   
                Hucheng Liu and   
             Xiaofeng Zhang and   
                     Bo Liu and   
                Yadong Wang and   
                       Junyi Li   Prot2GO: Predicting GO Annotations From
                                  Protein Sequences and Interactions . . . 2772--2780
                Jiatao Chen and   
                Liang Zhang and   
                   Ke Cheng and   
                     Bo Jin and   
                Xinjiang Lu and   
                       Chao Che   Predicting Drug-Target Interaction Via
                                  Self-Supervised Learning . . . . . . . . 2781--2789
                   Jing Sun and   
                     Li Pan and   
                     Bin Li and   
                Haoyue Wang and   
                    Bo Yang and   
                      Wenbin Li   A Construction Method of Dynamic Protein
                                  Interaction Networks by Using Relevant
                                  Features of Gene Expression Data . . . . 2790--2801
                He-Ming Chu and   
            Xiang-Zhen Kong and   
               Jin-Xing Liu and   
             Chun-Hou Zheng and   
                      Han Zhang   A New Binary Biclustering Algorithm
                                  Based on Weight Adjacency Difference
                                  Matrix for Analyzing Gene Expression
                                  Data . . . . . . . . . . . . . . . . . . 2802--2809
                  Nan Sheng and   
                  Lan Huang and   
                   Ling Gao and   
                Yangkun Cao and   
                 Xuping Xie and   
                       Yan Wang   A Survey of Computational Methods and
                                  Databases for lncRNA-MiRNA Interaction
                                  Prediction . . . . . . . . . . . . . . . 2810--2826
                      Ji Lv and   
                 Guixia Liu and   
                    Yuan Ju and   
               Houhou Huang and   
                       Ying Sun   AADB: a Manually Collected Database for
                                  Combinations of Antibiotics With
                                  Adjuvants  . . . . . . . . . . . . . . . 2827--2836
             Yeganeh Madadi and   
     Aboozar Monavarfeshani and   
                   Hao Chen and   
           W. Daniel Stamer and   
         Robert W. Williams and   
                 Siamak Yousefi   Artificial Intelligence Models for Cell
                                  Type and Subtype Identification Based on
                                  Single-Cell RNA Sequencing Data in
                                  Vision Science . . . . . . . . . . . . . 2837--2852
                   Zhen Gao and   
                   Jin Tang and   
                Junfeng Xia and   
             Chun-Hou Zheng and   
                    Pi-Jing Wei   CNNGRN: a Convolutional Neural
                                  Network-Based Method for Gene Regulatory
                                  Network Inference From Bulk Time-Series
                                  Expression Data  . . . . . . . . . . . . 2853--2861
                     Yu Cao and   
                   Wenya Pi and   
                Chun-Yu Lin and   
        Ulrike Münzner and   
            Masahiro Ohtomo and   
                 Tatsuya Akutsu   Common Attractors in Multiple Boolean
                                  Networks . . . . . . . . . . . . . . . . 2862--2873
                Ze-Gang Wei and   
                    Xu Chen and   
             Xiao-Dan Zhang and   
                  Hao Zhang and   
               Xing-Guo Fan and   
               Hong-Yan Gao and   
                    Fei Liu and   
                        Yu Qian   Comparison of Methods for Biological
                                  Sequence Clustering  . . . . . . . . . . 2874--2888
       Nikolai Romashchenko and   
            Benjamin Linard and   
                Eric Rivals and   
                    Fabio Pardi   Computing Phylo-$k$-Mers . . . . . . . . 2889--2897
               Niannian Liu and   
                Zequn Zhang and   
                   Yanan Wu and   
              Yinglong Wang and   
                     Ying Liang   CRBSP:Prediction of CircRNA--RBP Binding
                                  Sites Based on Multimodal Intermediate
                                  Fusion . . . . . . . . . . . . . . . . . 2898--2906
                  Fan Zhang and   
                Yawei Zhang and   
                 Xiaoke Zhu and   
               Xiaopan Chen and   
                   Fuhao Lu and   
                  Xinhong Zhang   DeepSG2PPI: a Protein-Protein
                                  Interaction Prediction Method Based on
                                  Deep Learning  . . . . . . . . . . . . . 2907--2919
      Visweswaran Ravikumar and   
                    Tong Xu and   
           Wajd N. Al-Holou and   
              Salar Fattahi and   
                     Arvind Rao   Efficient Inference of Spatially-Varying
                                  Gaussian Markov Random Fields With
                                  Applications in Gene Regulatory Networks 2920--2932
                    Bo Zhao and   
                    Jun Bai and   
                    Chen Li and   
              Jianfei Zhang and   
                 Wenge Rong and   
             Yuanxin Ouyang and   
                    Zhang Xiong   Enhancing Biomedical ReQA With
                                  Adversarial Hard In-Batch Negative
                                  Samples  . . . . . . . . . . . . . . . . 2933--2944

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 20, Number 6, 2023

                Zhipeng Cai and   
                     Min Li and   
                Pavel Skums and   
                     Yanjie Wei   Guest Editors' Introduction to the
                                  Special Section on Bioinformatics
                                  Research and Applications  . . . . . . . 3329--3331
                 Hunmin Lee and   
                Mingon Kang and   
               Donghyun Kim and   
                 Daehee Seo and   
                     Yingshu Li   Epidemic Vulnerability Index for
                                  Effective Vaccine Distribution Against
                                  Pandemic . . . . . . . . . . . . . . . . 3332--3342
                  Qing Zhao and   
               Jianqiang Li and   
                 Linna Zhao and   
                    Zhichao Zhu   Knowledge Guided Feature Aggregation for
                                  the Prediction of Chronic Obstructive
                                  Pulmonary Disease With Chinese EMRs  . . 3343--3352
                Yueyue Wang and   
                Xiujuan Lei and   
                         Yi Pan   Microbe-Disease Association Prediction
                                  Using RGCN Through Microbe-Drug-Disease
                                  Network  . . . . . . . . . . . . . . . . 3353--3362
                   Wei Peng and   
                Zicheng Che and   
                    Wei Dai and   
                Shoulin Wei and   
                        Wei Lan   Predicting miRNA-Disease Associations
                                  From miRNA-Gene-Disease Heterogeneous
                                  Network With Multi-Relational Graph
                                  Convolutional Network Model  . . . . . . 3363--3375
                 Sarwan Ali and   
               Bikram Sahoo and   
         Muhammad Asad Khan and   
       Alexander Zelikovsky and   
           Imdad Ullah Khan and   
               Murray Patterson   Efficient Approximate Kernel Based Spike
                                  Sequence Classification  . . . . . . . . 3376--3388
                 Yuxia Guan and   
                    Ying An and   
                 Jingrui Xu and   
                   Ning Liu and   
                   Jianxin Wang   HA-ResNet: Residual Neural Network With
                                  Hidden Attention for ECG Arrhythmia
                                  Detection Using Two-Dimensional Signal   3389--3398
                   Qiang Li and   
                  Hong Song and   
                Zenghui Wei and   
                Fengbo Yang and   
                Jingfan Fan and   
                   Danni Ai and   
                 Yucong Lin and   
                Xiaoling Yu and   
                      Jian Yang   Densely Connected U-Net With Criss-Cross
                                  Attention for Automatic Liver Tumor
                                  Segmentation in CT Images  . . . . . . . 3399--3410
                 Zhilong Lv and   
                Yuexiao Lin and   
                    Rui Yan and   
                  Ying Wang and   
                       Fa Zhang   TransSurv: Transformer-Based Survival
                                  Analysis Model Integrating
                                  Histopathological Images and Genomic
                                  Data for Colorectal Cancer . . . . . . . 3411--3420
                 Cheng Chen and   
                  Yuguo Zha and   
                 Daming Zhu and   
                  Kang Ning and   
                    Xuefeng Cui   ContactLib-ATT: a Structure-Based Search
                                  Engine for Homologous Proteins . . . . . 3421--3429
                Jiamin Chen and   
              Jianliang Gao and   
                Tengfei Lyu and   
Babatounde Moctard Oloulade and   
                     Xiaohua Hu   AutoMSR: Auto Molecular Structure
                                  Representation Learning for Multi-label
                                  Metabolic Pathway Prediction . . . . . . 3430--3439
               Hong-Dong Li and   
                  Chao Deng and   
              Xiao-Qi Zhang and   
                  Cui-Xiang Lin   A Gene Set-Integrated Approach for
                                  Predicting Disease-Associated Genes  . . 3440--3450
                  Haitao Fu and   
               Cecheng Zhao and   
                Xiaohui Niu and   
                      Wen Zhang   DRLM: a Robust Drug Representation
                                  Learning Method and its Applications . . 3451--3460
                Yurong Qian and   
             Jingjing Zheng and   
                 Ying Jiang and   
                 Shaoqiu Li and   
                       Lei Deng   Prediction of circRNA-MiRNA Association
                                  Using Singular Value Decomposition and
                                  Graph Neural Networks  . . . . . . . . . 3461--3468
                Enhao Cheng and   
                   Jun Zhao and   
                  Hong Wang and   
              Shuguang Song and   
              Shuxian Xiong and   
                    Yanshen Sun   Dual Network Contrastive Learning for
                                  Predicting Microbe-Disease Associations  3469--3481
                Tiansu Gong and   
                  Fusong Ju and   
                 Shiwei Sun and   
                      Dongbo Bu   SASA-Net: a Spatial-Aware Self-Attention
                                  Mechanism for Building Protein $3$D
                                  Structure Directly From Inter- Residue
                                  Distances  . . . . . . . . . . . . . . . 3482--3488
                  Huan Wang and   
                Ruigang Liu and   
               Baijing Wang and   
                 Yifan Hong and   
                  Ziwen Cui and   
                      Qiufen Ni   Multitype Perception Method for
                                  Drug-Target Interaction Prediction . . . 3489--3498
               Qingqing Cao and   
              Jianping Zhao and   
                Haiyun Wang and   
                    Qi Guan and   
                  Chunhou Zheng   An Integrated Method Based on
                                  Wasserstein Distance and Graph for
                                  Cancer Subtype Discovery . . . . . . . . 3499--3510
             Abhijit Mondal and   
                Mukul S. Bansal   Generalizing the Domain-Gene-Species
                                  Reconciliation Framework to Microbial
                                  Genes and Domains  . . . . . . . . . . . 3511--3522
                  Han Zhang and   
                 Zexuan Zhu and   
                     Hui Li and   
                        Shan He   Network Biomarker Detection From Gene
                                  Co-Expression Network Using Gaussian
                                  Mixture Model Clustering . . . . . . . . 3523--3534
                 Wenming Wu and   
             Wensheng Zhang and   
                 Weimin Hou and   
                      Xiaoke Ma   Multi-View Clustering With Graph
                                  Learning for scRNA-Seq Data  . . . . . . 3535--3546
                  Dayun Liu and   
                Xianghui Li and   
           Liangliang Zhang and   
                 Xiaowen Hu and   
              Jiaxuan Zhang and   
                Zhirong Liu and   
                       Lei Deng   HGNNLDA: Predicting lncRNA-Drug
                                  Sensitivity Associations via a Dual
                                  Channel Hypergraph Neural Network  . . . 3547--3555
                  Jing Yang and   
                Zhengshu Lu and   
                    Xu Chen and   
                  Deling Xu and   
                  Dewu Ding and   
                    Yanrui Ding   GCNA-Cluster: a Gene Co-Expression
                                  Network Alignment to Cluster Cancer
                                  Patients Algorithm for Identifying
                                  Subtypes of Pancreatic Ductal
                                  Adenocarcinoma . . . . . . . . . . . . . 3556--3566
                  Baoli Jia and   
              Qingfang Meng and   
                Yuehui Chen and   
                    Hongri Yang   Prediction of Membrane Protein
                                  Amphiphilic Helix Based on Horizontal
                                  Visibility Graph and Graph Convolution
                                  Network  . . . . . . . . . . . . . . . . 3567--3574
            Yakub K. Saheed and   
          Bukola F. Balogun and   
     Braimah Joseph Odunayo and   
            Mustapha Abdulsalam   Microarray Gene Expression Data
                                  Classification via Wilcoxon Sign Rank
                                  Sum and Novel Grey Wolf Optimized
                                  Ensemble Learning Models . . . . . . . . 3575--3587
                Yinyin Gong and   
                     Rui Li and   
                     Bin Fu and   
                    Yan Liu and   
                Jilong Wang and   
                   Renfa Li and   
                  Danny Z. Chen   A CNN-LSTM Ensemble Model for Predicting
                                  Protein-Protein Interaction Binding
                                  Sites  . . . . . . . . . . . . . . . . . 3588--3599
                   Xin Wang and   
                     Jie Li and   
                    Guohua Wang   MicroRNA Promoter Identification in
                                  Human With a Three-level Prediction
                                  Method . . . . . . . . . . . . . . . . . 3600--3608
                  Yahui Cao and   
                  Tao Zhang and   
                   Xin Zhao and   
                    Xue Jia and   
                     Bingzhi Li   MooSeeker: a Metabolic Pathway Design
                                  Tool Based on Multi-Objective
                                  Optimization Algorithm . . . . . . . . . 3609--3622
               Taoning Chen and   
                Tingfang Wu and   
                   Deng Pan and   
                Jinxing Xie and   
                    Jin Zhi and   
               Xuejiao Wang and   
                 Lijun Quan and   
                      Qiang Lyu   TransRNAm: Identifying Twelve Types of
                                  RNA Modifications by an Interpretable
                                  Multi-Label Deep Learning Model Based on
                                  Transformer  . . . . . . . . . . . . . . 3623--3634
              Weizhong Zhao and   
                 Wenjie Yao and   
             Xingpeng Jiang and   
                Tingting He and   
                  Chuan Shi and   
                     Xiaohua Hu   An Explainable Framework for Predicting
                                  Drug-Side Effect Associations via
                                  Meta-Path-Based Feature Learning in
                                  Heterogeneous Information Network  . . . 3635--3647


IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 21, Number 1, 2024

             Yamane El Zein and   
              Mathieu Lemay and   
          Kévin Huguenin   PrivaTree: Collaborative
                                  Privacy-Preserving Training of Decision
                                  Trees on Biomedical Data . . . . . . . . 1--13
                    Chao Tu and   
                 Denghui Du and   
               Tieyong Zeng and   
                       Yu Zhang   Deep Multi-Dictionary Learning for
                                  Survival Prediction With Multi-Zoom
                                  Histopathological Whole Slide Images . . 14--25
              Jordan Morris and   
               Ashur Rafiev and   
            Graeme M. Bragg and   
            Mark L. Vousden and   
            David B. Thomas and   
              Alex Yakovlev and   
                Andrew D. Brown   An Event-Driven Approach to Genotype
                                  Imputation on a Custom RISC-V Cluster    26--35
       Souradipto Choudhuri and   
                       Keya Sau   CodonU: a Python Package for Codon Usage
                                  Analysis . . . . . . . . . . . . . . . . 36--44
               Shengpeng Yu and   
                  Hong Wang and   
                    Jing Li and   
                   Jun Zhao and   
                Cheng Liang and   
                    Yanshen Sun   A Multi-Relational Graph Encoder Network
                                  for Fine-Grained Prediction of
                                  MiRNA-Disease Associations . . . . . . . 45--56
                    Rui Guo and   
                    Xu Tian and   
                  Hanhe Lin and   
            Stephen McKenna and   
               Hong-Dong Li and   
                    Fei Guo and   
                        Jin Liu   Graph-Based Fusion of Imaging, Genetic
                                  and Clinical Data for Degenerative
                                  Disease Diagnosis  . . . . . . . . . . . 57--68
Jonas Kristiansen Nòland and   
            Steinar Thorvaldsen   The Exact Stochastic Process of the
                                  Haploid Multi-Allelic Wright--Fisher
                                  Mutation Model . . . . . . . . . . . . . 69--83
              Wenliang Tang and   
              Zhaohong Deng and   
                Hanwen Zhou and   
                  Wei Zhang and   
                  Fuping Hu and   
               Kup-Sze Choi and   
                   Shitong Wang   MVDINET: a Novel Multi-Level Enzyme
                                  Function Predictor With Multi-View Deep
                                  Interactive Learning . . . . . . . . . . 84--94
                Shujie Dong and   
              Yuansheng Liu and   
              Yongshun Gong and   
              Xiangjun Dong and   
                Xiangxiang Zeng   scCAN: Clustering With Adaptive
                                  Neighbor-Based Imputation Method for
                                  Single-Cell RNA-Seq Data . . . . . . . . 95--105
             Nicol\`o Rossi and   
             Nicola Gigante and   
         Nicola Vitacolonna and   
                   Carla Piazza   Inferring Markov Chains to Describe
                                  Convergent Tumor Evolution With CIMICE   106--119
                  Dandan Li and   
                  Zhen Xiao and   
                    Han Sun and   
             Xingpeng Jiang and   
              Weizhong Zhao and   
                   Xianjun Shen   Prediction of Drug--Disease Associations
                                  Based on Multi-Kernel Deep Learning
                                  Method in Heterogeneous Graph Embedding  120--128
               Changyong Yu and   
                 Yuhai Zhao and   
                   Chu Zhao and   
                 Jianyu Jin and   
                 Keming Mao and   
                    Guoren Wang   MiniDBG: a Novel and Minimal de Bruijn
                                  Graph for Read Mapping . . . . . . . . . 129--142
                   Wei Wang and   
                 Mengxue Yu and   
                    Bin Sun and   
                  Juntao Li and   
                   Dong Liu and   
              Hongjun Zhang and   
              Xianfang Wang and   
                       Yun Zhou   SMGCN: Multiple Similarity and Multiple
                                  Kernel Fusion Based Graph Convolutional
                                  Neural Network for Drug-Target
                                  Interactions Prediction  . . . . . . . . 143--154
            Rituparna Sinha and   
            Rajat Kumar Pal and   
                    Rajat K. De   ENLIGHTENMENT: a Scalable Annotated
                                  Database of Genomics and NGS-Based
                                  Nucleotide Level Profiles  . . . . . . . 155--168
            Eric J. Barnett and   
            Daniel G. Onete and   
               Asif Salekin and   
             Stephen V. Faraone   Genomic Machine Learning
                                  Meta-regression: Insights on
                                  Associations of Study Features With
                                  Reported Model Performance . . . . . . . 169--177
                 Yuerui Liu and   
             Yongquan Jiang and   
                  Fan Zhang and   
                       Yan Yang   A Novel Multi-Scale Graph Neural Network
                                  for Metabolic Pathway Prediction . . . . 178--187
               Junchang Xin and   
               Mingcan Wang and   
                  Luxuan Qu and   
                    Qi Chen and   
               Weiyiqi Wang and   
                  Zhiqiong Wang   BIC-LP: a Hybrid Higher-Order Dynamic
                                  Bayesian Network Score Function for Gene
                                  Regulatory Network Reconstruction  . . . 188--199
             Pengcheng Zeng and   
                   Zhixiang Lin   scICML: Information-Theoretic
                                  Co-Clustering-Based Multi-View Learning
                                  for the Integrative Analysis of
                                  Single-Cell Multi-Omics Data . . . . . . 200--207
             Bindi M. Nagda and   
            Van Minh Nguyen and   
                  Ryan T. White   promSEMBLE: Hard Pattern Mining and
                                  Ensemble Learning for Detecting DNA
                                  Promoter Sequences . . . . . . . . . . . 208--214

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 21, Number 2, March, 2024

              Fernando Cruz and   
         João Capela and   
 Eugénio C. Ferreira and   
               Miguel Rocha and   
                     Oscar Dias   BioISO: an Objective-Oriented
                                  Application for Assisting the Curation
                                  of Genome-Scale Metabolic Models . . . . 215--226
                  Hao Zhang and   
                  Jiao Jiao and   
              Tianheng Zhao and   
              Enshuang Zhao and   
                  Lanhui Li and   
                  Guihua Li and   
                Borui Zhang and   
                  Qing-Ming Qin   GERWR: Identifying the Key
                                  Pathogenicity-Associated sRNAs of
                                  \bionameMagnaporthe oryzae Infection in
                                  Rice Based on Graph Embedding and Random
                                  Walk With Restart  . . . . . . . . . . . 227--239
                Daniel Manu and   
               Jingjing Yao and   
                   Wuji Liu and   
                      Xiang Sun   GraphGANFed: a Federated Generative
                                  Framework for Graph-Structured Molecules
                                  Towards Efficient Drug Discovery . . . . 240--253
                 Zhao-Qi Hu and   
              Yuan-Mao Hung and   
                Li-Han Chen and   
            Liang-Chuan Lai and   
             Min-Hsiung Pan and   
             Eric Y. Chuang and   
                 Mong-Hsun Tsai   NURECON: a Novel Online System for
                                  Determining Nutrition Requirements Based
                                  on Microbial Composition . . . . . . . . 254--264
                 Sichen Jin and   
                Yijia Zhang and   
                  Huimin Yu and   
                      Mingyu Lu   SADR: Self-Supervised Graph Learning
                                  With Adaptive Denoising for Drug
                                  Repositioning  . . . . . . . . . . . . . 265--277
    Alina F. Leuchtenberger and   
             Arndt von Haeseler   Learning From an Artificial Neural
                                  Network in Phylogenetics . . . . . . . . 278--288
               Wenjing Wang and   
               Pengyong Han and   
                Zhengwei Li and   
                     Ru Nie and   
               Kangwei Wang and   
                   Lei Wang and   
                   Hongmei Liao   LMGATCDA: Graph Neural Network With
                                  Labeling Trick for Predicting
                                  circRNA-Disease Associations . . . . . . 289--300
                Tiantian Li and   
               Haitao Jiang and   
                 Binhai Zhu and   
               Lusheng Wang and   
                     Daming Zhu   Flanked Block-Interchange Distance on
                                  Strings  . . . . . . . . . . . . . . . . 301--311

IEEE\slash ACM Transactions on Computational Biology and Bioinformatics
Volume 21, Number 3, May, 2024

João Paulo Pereira Zanetti and   
       Lucas Peres Oliveira and   
       João Meidanis and   
           Leonid Chindelevitch   Counting Sorting Scenarios and
                                  Intermediate Genomes for the Rank
                                  Distance . . . . . . . . . . . . . . . . 316--327
                  Nan Sheng and   
                 Xuping Xie and   
                   Yan Wang and   
                  Lan Huang and   
           Shuangquan Zhang and   
                   Ling Gao and   
                       Hao Wang   A Survey of Deep Learning for Detecting
                                  miRNA-Disease Associations: Databases,
                                  Computational Methods, Challenges, and
                                  Future Directions  . . . . . . . . . . . 328--347
                Tara Newman and   
       Hiu Fung Kevin Chang and   
                  Hosna Jabbari   DinoKnot: Duplex Interaction of Nucleic
                                  Acids With PseudoKnots . . . . . . . . . 348--359
                  Juan Wang and   
             Zhenchang Wang and   
                Shasha Yuan and   
              Chunhou Zheng and   
                Jinxing Liu and   
                 Junliang Shang   A Clustering Method for Single-Cell
                                  RNA-Seq Data Based on Automatic
                                  Weighting Penalty and Low-Rank
                                  Representation . . . . . . . . . . . . . 360--371
              Xiao-Hui Yang and   
               Ye-Tong Wang and   
                Ming-Hui Wu and   
                     Fan Li and   
            Cheng-Long Zhou and   
                Li-Jun Yang and   
                 Chen Zheng and   
                    Yong Li and   
                     Zhi Li and   
                  Si-Yi Guo and   
                 Chun-Peng Song   SLPA-Net: a Real-Time Recognition
                                  Network for Intelligent Stomata
                                  Localization and Phenotypic Analysis . . 372--382
                 Shan Zhang and   
                  Yuan Zhou and   
                   Pei Geng and   
                        Qing Lu   Functional Neural Networks for
                                  High-Dimensional Genetic Data Analysis   383--393
                  Cheng Yan and   
                    Guihua Duan   PMDAGS: Predicting miRNA-Disease
                                  Associations With Graph Nonlinear
                                  Diffusion Convolution Network and
                                  Similarities . . . . . . . . . . . . . . 394--404
               Sheena K. S. and   
                  Madhu S. Nair   GenCoder: a Novel Convolutional Neural
                                  Network Based Autoencoder for Genomic
                                  Sequence Data Compression  . . . . . . . 405--415
                   Wei Wang and   
                 Zhenxi Sun and   
                   Dong Liu and   
              Hongjun Zhang and   
                  Juntao Li and   
              Xianfang Wang and   
                       Yun Zhou   MAHyNet: Parallel Hybrid Network for
                                  RNA-Protein Binding Sites Prediction
                                  Based on Multi-Head Attention and
                                  Expectation Pooling  . . . . . . . . . . 416--427
                Sunyong Yoo and   
          Myeonghyeon Jeong and   
              Subhin Seomun and   
                Kiseong Kim and   
                  Youngmahn Han   Interpretable Prediction of SARS-CoV-2
                                  Epitope-Specific TCR Recognition Using a
                                  Pre-Trained Protein Language Model . . . 428--438
      Pallavi M. Shanthappa and   
               Neeraj Verma and   
                 Anu George and   
              Pawan K. Dhar and   
                Prashanth Athri   Computational Prediction of Potential
                                  Vaccine Candidates From tRNA Encoded
                                  peptides (tREP) Using a Bioinformatic
                                  Workflow and Molecular Dynamics
                                  Validations  . . . . . . . . . . . . . . 439--449
              Arnav Solanki and   
             James Cornette and   
                Julia Udell and   
           George Vasmatzis and   
                    Marc Riedel   Evasive Spike Variants Elucidate the
                                  Preservation of T Cell Immune Response
                                  to the SARS-CoV-2 Omicron Variant  . . . 450--460
                 Yuhang Jia and   
                    Siyu Li and   
                  Rui Jiang and   
                 Shengquan Chen   Accurate Annotation for Differentiating
                                  and Imbalanced Cell Types in Single-Cell
                                  Chromatin Accessibility Data . . . . . . 461--471
                 Minglie Li and   
                Shusen Zhou and   
                   Tong Liu and   
               Chanjuan Liu and   
                 Mujun Zang and   
                   Qingjun Wang   TSVM: Transfer Support Vector Machine
                                  for Predicting MPRA Validated Regulatory
                                  Variants . . . . . . . . . . . . . . . . 472--479
                      Ke Ma and   
                  Jiawei Li and   
              Mengyuan Zhao and   
              Ibrahim Zamit and   
                    Bin Lin and   
                    Fei Guo and   
                     Jijun Tang   PPRTGI: a Personalized PageRank Graph
                                  Neural Network for TF-Target Gene
                                  Interaction Detection  . . . . . . . . . 480--491
                 Weiling Li and   
            Raunaq Malhotra and   
                  Steven Wu and   
                Manjari Jha and   
              Allen Rodrigo and   
                  Mary Poss and   
                    Raj Acharya   ViPRA-Haplo: \em De Novo Reconstruction
                                  of Viral Populations Using Paired End
                                  Sequencing Data  . . . . . . . . . . . . 492--500
            Gabriel Cardona and   
           Joan Carles Pons and   
               Gerard Ribas and   
Tomás Martínez Coronado