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


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\reg Xeon Phi\TM 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