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Tue Mar 19 08:51:09 MDT 2024
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
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
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
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
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
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
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
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
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
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
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
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 . . . . . . . . . . . . . . ??
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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 . . . . . . . . . . . ??
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Juan A. Gomez-Pulido and
Bertil Schmidt and
Wu-chun Feng Accelerating bioinformatics applications
via emerging parallel computing systems 971--972
Edward B. Fernandez and
Jason Villarreal and
Stefano Lonardi and
Walid A. Najjar FHAST: FPGA-Based Acceleration of Bowtie
in Hardware . . . . . . . . . . . . . . 973--981
Jorge Gonzalez-Dominguez and
Lars Wienbrandt and
Jan Christian Kassens and
David Ellinghaus and
Manfred Schimmler and
Bertil Schmidt Parallelizing Epistasis Detection in
GWAS on FPGA and GPU-Accelerated
Computing Systems . . . . . . . . . . . 982--994
Hector Martinez and
Joaquin Tarraga and
Ignacio Medina and
Sergio Barrachina and
Maribel Castillo and
Joaquin Dopazo and
Enrique S. Quintana-Orti Concurrent and Accurate Short Read
Mapping on Multicore Processors . . . . 995--1007
Sanchit Misra and
Kiran Pamnany and
Srinivas Aluru Parallel Mutual Information Based
Construction of Genome-Scale Networks on
the Intel Xeon Phi Coprocessor . . . . . 1008--1020
Anne Jeannin-Girardon and
Pascal Ballet and
Vincent Rodin Large Scale Tissue Morphogenesis
Simulation on Heterogeneous Systems
Based on a Flexible Biomechanical Cell
Model . . . . . . . . . . . . . . . . . 1021--1033
Yao Xin and
Will X. Y. Li and
Zhaorui Zhang and
Ray C. C. Cheung and
Dong Song and
Theodore W. Berger An Application Specific Instruction Set
Processor (ASIP) for Adaptive Filters in
Neural Prosthetics . . . . . . . . . . . 1034--1047
Alejandro Chacon and
Santiago Marco-Sola and
Antonio Espinosa and
Paolo Ribeca and
Juan Carlos Moure Boosting the FM-Index on the GPU:
Effective Techniques to Mitigate Random
Memory Access . . . . . . . . . . . . . 1048--1059
Thuy-Diem Nguyen and
Bertil Schmidt and
Zejun Zheng and
Chee-Keong Kwoh Efficient and Accurate OTU Clustering
with GPU-Based Sequence Alignment and
Dynamic Dendrogram Cutting . . . . . . . 1060--1073
Shihua Zhang and
Luonan Chen Guest Editorial for Special Section on
ISB/TBC 2014 . . . . . . . . . . . . . . 1074--1075
H. Robert Frost and
Zhigang Li and
Folkert W. Asselbergs and
Jason H. Moore An Independent Filter for Gene Set
Testing Based on Spectral Enrichment . . 1076--1086
Dominique Chu and
Anton Salykin Evolutionary Pressures on the Yeast
Transcriptome . . . . . . . . . . . . . 1087--1093
Hao Kang and
Kwang-Hyun Cho and
Xiaohua Douglas Zhang and
Tao Zeng and
Luonan Chen Inferring Sequential Order of Somatic
Mutations during Tumorgenesis based on
Markov Chain Model . . . . . . . . . . . 1094--1103
Nan Meng and
Raghu Machiraju and
Kun Huang Identify Critical Genes in Development
with Consistent H3K4me2 Patterns across
Multiple Tissues . . . . . . . . . . . . 1104--1111
Yu-Qing Qiu and
Xue Tian and
Shihua Zhang Infer Metagenomic Abundance and Reveal
Homologous Genomes Based on the
Structure of Taxonomy Tree . . . . . . . 1112--1122
Mauro Leoncini and
Manuela Montangero and
Marco Pellegrini and
Karina Panucia Tillan CMStalker: a Combinatorial Tool for
Composite Motif Discovery . . . . . . . 1123--1136
Jan Zrimec and
Ales Lapanje Fast Prediction of DNA Melting Bubbles
Using DNA Thermodynamic Stability . . . 1137--1145
Shuqin Zhang and
Hongyu Zhao and
Michael K. Ng Functional Module Analysis for Gene
Coexpression Networks with Network
Integration . . . . . . . . . . . . . . 1146--1160
Jeong-Rae Kim and
Sang-Mok Choo and
Hyung-Seok Choi and
Kwang-Hyun Cho Identification of Gene Networks with
Time Delayed Regulation Based on
Temporal Expression Profiles . . . . . . 1161--1168
Leung-Yau Lo and
Kwong-Sak Leung and
Kin-Hong Lee Inferring Time-Delayed Causal Gene
Network Using Time-Series Expression
Data . . . . . . . . . . . . . . . . . . 1169--1182
Dimitrios Kleftogiannis and
Konstantinos Theofilatos and
Spiros Likothanassis and
Seferina Mavroudi YamiPred: a Novel Evolutionary Method
for Predicting Pre-miRNAs and Selecting
Relevant Features . . . . . . . . . . . 1183--1192
Pietro Lovato and
Alejandro Giorgetti and
Manuele Bicego A Multimodal Approach for Protein Remote
Homology Detection . . . . . . . . . . . 1193--1198
Jure Bordon and
Miha Moskon and
Nikolaj Zimic and
Miha Mraz Fuzzy Logic as a Computational Tool for
Quantitative Modelling of Biological
Systems with Uncertain Kinetic Data . . 1199--1205
Po-Kuei Chen and
Chun-Liang Lin Synthesis of Genetic Clock with
Combinational Biologic Circuits . . . . 1206--1212
Emmanouil I. Athanasiadis and
Marilena M. Bourdakou and
George M. Spyrou ZoomOut: Analyzing Multiple Networks as
Single Nodes . . . . . . . . . . . . . . 1213--1216
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
T. M. Murali Guest Editorial . . . . . . . . . . . . 1036--1036
Asish Ghoshal and
Jinyi Zhang and
Michael A. Roth and
Kevin Muyuan Xia and
Ananth Y. Grama and
Somali Chaterji A Distributed Classifier for MicroRNA
Target Prediction with Validation
Through TCGA Expression Data . . . . . . 1037--1051
Shi Qiao and
Mehmet Koyutürk and
Meral Z. Özsoyo\uglu Querying of Disparate Association and
Interaction Data in Biomedical
Applications . . . . . . . . . . . . . . 1052--1065
Alexej Gossmann and
Shaolong Cao and
Damian Brzyski and
Lan-Juan Zhao and
Hong-Wen Deng and
Yu-Ping Wang A Sparse Regression Method for
Group-Wise Feature Selection with False
Discovery Rate Control . . . . . . . . . 1066--1078
Md Abdul Alim and
Ahmet Ay and
Md Mahmudul Hasan and
My T. Thai and
Tamer Kahveci Construction of Signaling Pathways with
RNAi Data and Multiple Reference
Networks . . . . . . . . . . . . . . . . 1079--1091
Xiaodan Fan and
Xinglai Ji and
Rui Jiang Guest Editorial for Special Section on
the Sixth National Conference on
Bioinformatics and System Biology of
China . . . . . . . . . . . . . . . . . 1092--1092
Mahdi Zamanighomi and
Mostafa Zamanian and
Michael Kimber and
Zhengdao Wang Gene Regulatory Network Inference from
Perturbed Time-Series Expression Data
via Ordered Dynamical Expansion of
Non-Steady State Actors . . . . . . . . 1093--1106
Ke Liu and
Sha Hou and
Junbiao Dai and
Zhirong Sun PyMut: a Web Tool for Overlapping Gene
Loss-of-Function Mutation Design . . . . 1107--1110
Xiangfei Cheng and
Yue Hou and
Yumin Nie and
Yiru Zhang and
Huan Huang and
Hongde Liu and
Xiao Sun Nucleosome Positioning of Intronless
Genes in the Human Genome . . . . . . . 1111--1121
Ezio Bartocci and
Pietro Lio and
Nicola Paoletti Guest Editors' Introduction to the
Special Section on the 14th
International Conference on
Computational Methods in Systems Biology
CMSB 2016 . . . . . . . . . . . . . . . 1122--1123
Jerome Feret and
Kim Quyen Ly Local Traces: an Over-Approximation of
the Behavior of the Proteins in
Rule-Based Models . . . . . . . . . . . 1124--1137
François Fages and
Thierry Martinez and
David A. Rosenblueth and
Sylvain Soliman Influence Networks Compared with
Reaction Networks: Semantics,
Expressivity and Attractors . . . . . . 1138--1151
Chunyan Mu and
Peter Dittrich and
David Parker and
Jonathan E. Rowe Organisation-Oriented Coarse Graining
and Refinement of Stochastic Reaction
Networks . . . . . . . . . . . . . . . . 1152--1166
Loic Pauleve Reduction of Qualitative Models of
Biological Networks for Transient
Dynamics Analysis . . . . . . . . . . . 1167--1179
Michael Backenkohler and
Luca Bortolussi and
Verena Wolf Moment-Based Parameter Estimation for
Stochastic Reaction Networks in
Equilibrium . . . . . . . . . . . . . . 1180--1192
Alejandro F. Villaverde and
Kolja Becker and
Julio R. Banga PREMER: a Tool to Infer Biological
Networks . . . . . . . . . . . . . . . . 1193--1202
Andrzej Mizera and
Jun Pang and
Cui Su and
Qixia Yuan \sf ASSA-PBN: a Toolbox for
Probabilistic Boolean Networks . . . . . 1203--1216
Eugen Czeizler and
Kai-Chiu Wu and
Cristian Gratie and
Krishna Kanhaiya and
Ion Petre Structural Target Controllability of
Linear Networks . . . . . . . . . . . . 1217--1228
Tijana Milenkovic and
Sarath Chandra Janga Great Lakes Bioinformatics Conference
GLBIO 2015 Special Section Editorial . . 1229--1230
James B. Pease and
Benjamin K. Rosenzweig Encoding Data Using Biological
Principles: The Multisample Variant
Format for Phylogenomics and Population
Genomics . . . . . . . . . . . . . . . . 1231--1238
Adam Roth and
Sandeep Subramanian and
Madhavi K. Ganapathiraju Towards Extracting Supporting
Information About Predicted
Protein-Protein Interactions . . . . . . 1239--1246
Satwica Yerneni and
Ishita K. Khan and
Qing Wei and
Daisuke Kihara IAS: Interaction Specific GO Term
Associations for Predicting
Protein-Protein Interaction Networks . . 1247--1258
Seyedsasan Hashemikhabir and
Ran Xia and
Yang Xiang and
Sarath Chandra Janga A Framework for Identifying Genotypic
Information from Clinical Records:
Exploiting Integrated Ontology
Structures to Transfer Annotations
between ICD Codes and Gene Ontologies 1259--1269
Pranjal Patra and
Tatsuo Izawa and
Lourdes Pena-Castillo REPA: Applying Pathway Analysis to
Genome-Wide Transcription Factor Binding
Data . . . . . . . . . . . . . . . . . . 1270--1283
Rodrigo F. Ramalho and
Sujun Li and
Predrag Radivojac and
Matthew W. Hahn Proteomic Evidence for In-Frame and
Out-of-Frame Alternatively Spliced
Isoforms in Human and Mouse . . . . . . 1284--1289
Rami Al-Ouran and
Robert Schmidt and
Ashwini Naik and
Jeffrey Jones and
Frank Drews and
David Juedes and
Laura Elnitski and
Lonnie Welch Discovering Gene Regulatory Elements
Using Coverage-Based Heuristics . . . . 1290--1300
Liliana Ironi and
Ettore Lanzarone A Model-Based Tool for the Analysis and
Design of Gene Regulatory Networks . . . 1301--1314
Chun-Qiu Xia and
Ke Han and
Yong Qi and
Yang Zhang and
Dong-Jun Yu A Self-Training Subspace Clustering
Algorithm under Low-Rank Representation
for Cancer Classification on Gene
Expression Data . . . . . . . . . . . . 1315--1324
Xinyu He and
Lishuang Li and
Yang Liu and
Xiaoming Yu and
Jun Meng A Two-Stage Biomedical Event Trigger
Detection Method Integrating Feature
Selection and Word Embeddings . . . . . 1325--1332
Iman Deznabi and
Mohammad Mobayen and
Nazanin Jafari and
Oznur Tastan and
Erman Ayday An Inference Attack on Genomic Data
Using Kinship, Complex Correlations, and
Phenotype Information . . . . . . . . . 1333--1343
Qian Xie and
Xiaoyan He and
Fangji Yang and
Xuling Liu and
Ying Li and
Yujing Liu and
ZhengMeng Yang and
Jianhai Yu and
Bao Zhang and
Wei Zhao Analysis of the Genome Sequence and
Prediction of B-Cell Epitopes of the
Envelope Protein of Middle East
Respiratory Syndrome-Coronavirus . . . . 1344--1350
Yoram Zarai and
Michael Margaliot and
Eduardo D. Sontag and
Tamir Tuller Controllability Analysis and Control
Synthesis for the Ribosome Flow Model 1351--1364
Shangce Gao and
Shuangbao Song and
Jiujun Cheng and
Yuki Todo and
MengChu Zhou Incorporation of Solvent Effect into
Multi-Objective Evolutionary Algorithm
for Improved Protein Structure
Prediction . . . . . . . . . . . . . . . 1365--1378
Karlene Nicole Meyer and
Michelle R. Lacey Modeling Methylation Patterns with Long
Read Sequencing Data . . . . . . . . . . 1379--1389
Guoxian Yu and
Guangyuan Fu and
Jun Wang and
Yingwen Zhao NewGOA: Predicting New GO Annotations of
Proteins by Bi-Random Walks on a Hybrid
Graph . . . . . . . . . . . . . . . . . 1390--1402
Erman Ayday and
Xiaoqian Jiang and
Bradley Malin GenoPri'16: International Workshop on
Genome Privacy and Security . . . . . . 1403--1404
Michael Backes and
Pascal Berrang and
Mathias Humbert and
Xiaoyu Shen and
Verena Wolf Simulating the Large-Scale Erosion of
Genomic Privacy Over Time . . . . . . . 1405--1412
Jean Louis Raisaro and
Gwangbae Choi and
Sylvain Pradervand and
Raphael Colsenet and
Nathalie Jacquemont and
Nicolas Rosat and
Vincent Mooser and
Jean-Pierre Hubaux Protecting Privacy and Security of
Genomic Data in i2b2 with Homomorphic
Encryption and Differential Privacy . . 1413--1426
Dan Bogdanov and
Liina Kamm and
Sven Laur and
Ville Sokk Implementation and Evaluation of an
Algorithm for Cryptographically Private
Principal Component Analysis on Genomic
Data . . . . . . . . . . . . . . . . . . 1427--1432
De-Shuang Huang and
Vitoantonio Bevilacqua and
M. Michael Gromiha Guest Editorial for Special Section on
the 12th International Conference on
Intelligent Computing ICIC . . . . . . . 1433--1435
A. Kulandaisamy and
Ambuj Srivastava and
Pradeep Kumar and
R. Nagarajan and
S. Binny Priya and
M. Michael Gromiha Identification and Analysis of Key
Residues in Protein-RNA Complexes . . . 1436--1444
Hongjie Wu and
Chengyuan Cao and
Xiaoyan Xia and
Qiang Lu Unified Deep Learning Architecture for
Modeling Biology Sequence . . . . . . . 1445--1452
Wenzheng Bao and
Chang-An Yuan and
Youhua Zhang and
Kyungsook Han and
Asoke K. Nandi and
Barry Honig and
De-Shuang Huang Mutli-Features Prediction of Protein
Translational Modification Sites . . . . 1453--1460
Wook Lee and
Byungkyu Park and
Kyungsook Han Sequence-Based Prediction of Putative
Transcription Factor Binding Sites in
DNA Sequences of Any Length . . . . . . 1461--1469
Xiaoli Lin and
Xiaolong Zhang Prediction of Hot Regions in PPIs Based
on Improved Local Community Structure
Detecting . . . . . . . . . . . . . . . 1470--1479
Su-Ping Deng and
Wenxing Hu and
Vince D. Calhoun and
Yu-Ping Wang Integrating Imaging Genomic Data in the
Quest for Biomarkers of Schizophrenia
Disease . . . . . . . . . . . . . . . . 1480--1491
Giulia Russo and
Marzio Pennisi and
Roberta Boscarino and
Francesco Pappalardo Continuous Petri Nets and microRNA
Analysis in Melanoma . . . . . . . . . . 1492--1499
Jian Liu and
Yuhu Cheng and
Xuesong Wang and
Xiaoluo Cui and
Yi Kong and
Junping Du Low Rank Subspace Clustering via
Discrete Constraint and Hypergraph
Regularization for Tumor Molecular
Pattern Discovery . . . . . . . . . . . 1500--1512
Lusheng Wang and
Shuai Cheng Li and
Yi-Ping Phoebe Chen Guest Editorial for the 15th Asia
Pacific Bioinformatics Conference . . . 1513--1514
Jaroslaw Paszek and
Pawel Gorecki Efficient Algorithms for Genomic
Duplication Models . . . . . . . . . . . 1515--1524
Andrzej Mizera and
Jun Pang and
Qixia Yuan Reviving the Two-State Markov Chain
Approach . . . . . . . . . . . . . . . . 1525--1537
Shuai An and
Jun Wang and
Jinmao Wei Local-Nearest-Neighbors-Based Feature
Weighting for Gene Selection . . . . . . 1538--1548
Nan Jiang and
Wenge Rong and
Yifan Nie and
Yikang Shen and
Zhang Xiong Biological Event Trigger Identification
with Noise Contrastive Estimation . . . 1549--1559
Manuel Lafond and
Cedric Chauve and
Nadia El-Mabrouk and
Aida Ouangraoua Gene Tree Construction and Correction
Using SuperTree and Reconciliation . . . 1560--1570
Agnieszka Mykowiecka and
Pawel Szczesny and
Pawel Gorecki Inferring Gene-Species Assignments in
the Presence of Horizontal Gene Transfer 1571--1578
Yue Zhang and
Chunfang Zheng and
David Sankoff Evolutionary Model for the Statistical
Divergence of Paralogous and Orthologous
Gene Pairs Generated by Whole Genome
Duplication and Speciation . . . . . . . 1579--1584
Tom Hartmann and
Nicolas Wieseke and
Roded Sharan and
Martin Middendorf and
Matthias Bernt Genome Rearrangement with ILP . . . . . 1585--1593
Nafiseh Sedaghat and
Mahmood Fathy and
Mohammad Hossein Modarressi and
Ali Shojaie Combining Supervised and Unsupervised
Learning for Improved miRNA Target
Prediction . . . . . . . . . . . . . . . 1594--1604
Safwat Hamad and
Ahmed Elhadad and
Amal Khalifa DNA Watermarking Using Codon Postfix
Technique . . . . . . . . . . . . . . . 1605--1610
Jorge E. Duarte-Sanchez and
Jaime Velasco-Medina and
Pedro A. Moreno Hardware Accelerator for the
Multifractal Analysis of DNA Sequences 1611--1624
Nha Nguyen and
An Vo and
Haibin Sun and
Heng Huang Heavy-Tailed Noise Suppression and
Derivative Wavelet Scalogram for
Detecting DNA Copy Number Aberrations 1625--1635
Xiaoke Ma and
Penggang Sun and
Guimin Qin Identifying Condition-Specific Modules
by Clustering Multiple Networks . . . . 1636--1648
Jin Liu and
Jianxin Wang and
Zhenjun Tang and
Bin Hu and
Fang-Xiang Wu and
Yi Pan Improving Alzheimer's Disease
Classification by Combining Multiple
Measures . . . . . . . . . . . . . . . . 1649--1659
Shuai Ren and
Yan Shi and
Maolin Cai and
Weiqing Xu Influence of Airway Secretion on Airflow
Dynamics of Mechanical Ventilated
Respiratory System . . . . . . . . . . . 1660--1668
Vipin Vijayan and
Tijana Milenkovic Multiple Network Alignment via
MultiMAGNA++ . . . . . . . . . . . . . . 1669--1682
Chunjiang Yu and
Wentao Wu and
Jing Wang and
Yuxin Lin and
Yang and
Jiajia Chen and
Fei Zhu and
Bairong Shen NGS-FC: a Next-Generation Sequencing
Data Format Converter . . . . . . . . . 1683--1691
Hasan M. Jamil Optimizing Phylogenetic Queries for
Performance . . . . . . . . . . . . . . 1692--1705
Min Liu and
Yue He and
Weili Qian and
Yangliu Wei and
Xiaoyan Liu Cell Population Tracking in a Honeycomb
Structure Using an IMM Filter Based $3$D
Local Graph Matching Model . . . . . . . 1706--1717
Shifu Chen and
Ming Liu and
Xiaoni Zhang and
Renwen Long and
Yixing Wang and
Yue Han and
Shiwei Zhang and
Mingyan Xu and
Jia Gu A Study of Cell-Free DNA Fragmentation
Pattern and Its Application in DNA
Sample Type Classification . . . . . . . 1718--1722
Pawel Gorecki and
Oliver Eulenstein Bijective Diameters of Gene Tree
Parsimony Costs . . . . . . . . . . . . 1723--1727
Youyuan Li and
Yingping Zhuang fmpRPMF: a Web Implementation for
Protein Identification by Robust Peptide
Mass Fingerprinting . . . . . . . . . . 1728--1731
Jorge Gonzalez-Dominguez and
Maria J. Martin MPIGeneNet: Parallel Calculation of Gene
Co-Expression Networks on Multicore
Clusters . . . . . . . . . . . . . . . . 1732--1737
Shubhanshu Shekhar and
Sebastien Roch and
Siavash Mirarab Species Tree Estimation Using ASTRAL:
How Many Genes Are Enough? . . . . . . . 1738--1747
Tianhai Tian and
Jingshan Huang Guest Editorial for Special Section on
BIBM 2015 . . . . . . . . . . . . . . . 1752--1753
Yu-Chiao Chiu and
Tzu-Hung Hsiao and
Li-Ju Wang and
Yidong Chen and
Eric Y. Chuang Analyzing Differential Regulatory
Networks Modulated by Continuous-State
Genomic Features in Glioblastoma
Multiforme . . . . . . . . . . . . . . . 1754--1764
Bin Hu and
Yongqiang Dai and
Yun Su and
Philip Moore and
Xiaowei Zhang and
Chengsheng Mao and
Jing Chen and
Lixin Xu Feature Selection for Optimized
High-Dimensional Biomedical Data Using
an Improved Shuffled Frog Leaping
Algorithm . . . . . . . . . . . . . . . 1765--1773
Wei Lan and
Jianxin Wang and
Min Li and
Jin Liu and
Fang-Xiang Wu and
Yi Pan Predicting MicroRNA-Disease Associations
Based on Improved MicroRNA and Disease
Similarities . . . . . . . . . . . . . . 1774--1782
Tatiana Maximova and
Erion Plaku and
Amarda Shehu Structure-Guided Protein Transition
Modeling with a Probabilistic Roadmap
Algorithm . . . . . . . . . . . . . . . 1783--1796
Bo Xu and
Hongfei Lin and
Yuan Lin and
Yunlong Ma and
Liang Yang and
Jian Wang and
Zhihao Yang Improve Biomedical Information Retrieval
Using Modified Learning to Rank Methods 1797--1809
Hongbo Zhang and
Lin Zhu and
De-Shuang Huang DiscMLA: an Efficient Discriminative
Motif Learning Algorithm over
High-Throughput Datasets . . . . . . . . 1810--1820
Sun Kim Editorial for Selected Papers of a Joint
Conferences, Genome Informatics
Workshop/International Conference on
Bioinformatics GIW/InCoB 2015 . . . . . 1821--1821
Osamu Hirose and
Shotaro Kawaguchi and
Terumasa Tokunaga and
Yu Toyoshima and
Takayuki Teramoto and
Sayuri Kuge and
Takeshi Ishihara and
Yuichi Iino and
Ryo Yoshida SPF-CellTracker: Tracking Multiple Cells
with Strongly-Correlated Moves Using a
Spatial Particle Filter . . . . . . . . 1822--1831
Zhanzhan Cheng and
Shuigeng Zhou and
Yang Wang and
Hui Liu and
Jihong Guan and
Yi-Ping Phoebe Chen Effectively Identifying Compound-Protein
Interactions by Learning from Positive
and Unlabeled Examples . . . . . . . . . 1832--1843
Hamid D. Ismail and
Hiroto Saigo and
Dukka B. KC RF-NR: Random Forest Based Approach for
Improved Classification of Nuclear
Receptors . . . . . . . . . . . . . . . 1844--1852
Takeyuki Tamura and
Wei Lu and
Jiangning Song and
Tatsuya Akutsu Computing Minimum Reaction Modifications
in a Boolean Metabolic Network . . . . . 1853--1862
Ying Tan and
Yuhui Shi Special Section on Swarm-Based
Algorithms and Applications in
Computational Biology and Bioinformatics 1863--1864
Ben Niu and
Jing Liu and
Teresa Wu and
Xianghua Chu and
Zhengxu Wang and
Yanmin Liu Coevolutionary
Structure-Redesigned-Based Bacterial
Foraging Optimization . . . . . . . . . 1865--1876
Biao Xu and
Yong Zhang and
Dunwei Gong and
Yinan Guo and
Miao Rong Environment Sensitivity-Based
Cooperative Co-Evolutionary Algorithms
for Dynamic Multi-Objective Optimization 1877--1890
Yi-Nan Guo and
Jian Cheng and
Sha Luo and
Dunwei Gong and
Yu Xue Robust Dynamic Multi-Objective Vehicle
Routing Optimization Method . . . . . . 1891--1903
Weian Guo and
Chengyong Si and
Yu Xue and
Yanfen Mao and
Lei Wang and
Qidi Wu A Grouping Particle Swarm Optimizer with
Personal-Best-Position Guidance for
Large Scale Optimization . . . . . . . . 1904--1915
Chao Gao and
Mingxin Liang and
Xianghua Li and
Zili Zhang and
Zhen Wang and
Zhili Zhou Network Community Detection Based on the
Physarum-Inspired Computational
Framework . . . . . . . . . . . . . . . 1916--1928
Andres Iglesias and
Akemi Galvez and
Andreina Avila Immunological Approach for Full NURBS
Reconstruction of Outline Curves from
Noisy Data Points in Medical Imaging . . 1929--1942
Qirong Tang and
Lu Ding and
Fangchao Yu and
Yuan Zhang and
Yinghao Li and
Haibo Tu Swarm Robots Search for Multiple Targets
Based on an Improved Grouping Strategy 1943--1950
Xin Gao and
Jake Y. Chen and
Mohammed J. Zaki Multiscale and Multimodal Analysis for
Computational Biology . . . . . . . . . 1951--1952
Miguel Monteiro and
Ana Catarina Fonseca and
Ana Teresa Freitas and
Teresa Pinho e Melo and
Alexandre P. Francisco and
Jose M. Ferro and
Arlindo L. Oliveira Using Machine Learning to Improve the
Prediction of Functional Outcome in
Ischemic Stroke Patients . . . . . . . . 1953--1959
Annie Wang and
Hansaim Lim and
Shu-Yuan Cheng and
Lei Xie ANTENNA, a Multi-Rank, Multi-Layered
Recommender System for Inferring
Reliable Drug-Gene-Disease Associations:
Repurposing Diazoxide as a Targeted
Anti-Cancer Therapy . . . . . . . . . . 1960--1967
Haishuai Wang and
Zhicheng Cui and
Yixin Chen and
Michael Avidan and
Arbi Ben Abdallah and
Alexander Kronzer Predicting Hospital Readmission via
Cost-Sensitive Deep Learning . . . . . . 1968--1978
Ahmed Halioui and
Petko Valtchev and
Abdoulaye Banire Diallo Bioinformatic Workflow Extraction from
Scientific Texts based on Word Sense
Disambiguation . . . . . . . . . . . . . 1979--1990
Zongliang Yue and
Michael T. Neylon and
Thanh Nguyen and
Timothy Ratliff and
Jake Y. Chen ``Super Gene Set'' Causal Relationship
Discovery from Functional Genomics Data 1991--1998
Meshari Alazmi and
Ahmed Abbas and
Xianrong Guo and
Ming Fan and
Lihua Li and
Xin Gao A Slice-based $^{13}$C-detected NMR Spin
System Forming and Resonance Assignment
Method . . . . . . . . . . . . . . . . . 1999--2008
Kavitha Mukund and
Samuel R. Ward and
Richard L. Lieber and
Shankar Subramaniam Co-Expression Network Approach to
Studying the Effects of Botulinum
Neurotoxin-A . . . . . . . . . . . . . . 2009--2016
Daniel P. Martins and
Michael Taynnan Barros and
Massimiliano Pierobon and
Meenakshisundaram Kandhavelu and
Pietro Lio' and
Sasitharan Balasubramaniam Computational Models for Trapping Ebola
Virus Using Engineered Bacteria . . . . 2017--2027
Juntao Li and
Wenpeng Dong and
Deyuan Meng Grouped Gene Selection of Cancer via
Adaptive Sparse Group Lasso Based on
Conditional Mutual Information . . . . . 2028--2038
Ho-Chun Wu and
Xi-Guang Wei and
Shing-Chow Chan Novel Consensus Gene Selection Criteria
for Distributed GPU Partial Least
Squares-Based Gene Microarray Analysis
in Diffused Large B Cell Lymphoma DLBCL
and Related Findings . . . . . . . . . . 2039--2052
Surama Biswas and
Sriyankar Acharyya A Bi-Objective RNN Model to Reconstruct
Gene Regulatory Network: a Modified
Multi-Objective Simulated Annealing
Approach . . . . . . . . . . . . . . . . 2053--2059
Warith Eddine Djeddi and
Sadok Ben Yahia and
Engelbert Mephu Nguifo A Novel Computational Approach for
Global Alignment for Multiple Biological
Networks . . . . . . . . . . . . . . . . 2060--2066
Martin C. Frith and
Anish M. S. Shrestha A Simplified Description of Child Tables
for Sequence Similarity Search . . . . . 2067--2073
Xizhe Zhang Altering Indispensable Proteins in
Controlling Directed Human Protein
Interaction Network . . . . . . . . . . 2074--2078
Ting Xu and
Le Ou-Yang and
Xiaohua Hu and
Xiao-Fei Zhang Identifying Gene Network Rewiring by
Integrating Gene Expression and Gene
Network Data . . . . . . . . . . . . . . 2079--2085
Hongmei Jiao and
Liping Zhang and
Qikun Shen and
Junwu Zhu and
Peng Shi Robust Gene Circuit Control Design for
Time-Delayed Genetic Regulatory Networks
Without SUM Regulatory Logic . . . . . . 2086--2093
Nina Luhmann and
Cedric Chauve and
Jens Stoye and
Roland Wittler Scaffolding of Ancient Contigs and
Ancestral Reconstruction in a
Phylogenetic Framework . . . . . . . . . 2094--2100
Yoshihiro Yamanishi and
Yasubumi Sakakibara and
Yi-Ping Phoebe Chen Guest Editorial for the 16th Asia
Pacific Bioinformatics Conference . . . 1--2
Kouichi Kimura and
Asako Koike Parallel Computation of the
Burrows--Wheeler Transform of Short
Reads Using Prefix Parallelism . . . . . 3--13
Jordan Haack and
Eli Zupke and
Andrew Ramirez and
Yi-Chieh Wu and
Ran Libeskind-Hadas Computing the Diameter of the Space of
Maximum Parsimony Reconciliations in the
Duplication--Transfer--Loss Model . . . 14--22
Romeo Rizzi and
Massimo Cairo and
Veli Makinen and
Alexandru I. Tomescu and
Daniel Valenzuela Hardness of Covering Alignment: Phase
Transition in Post-Sequence Genomics . . 23--30
Andrzej Mizera and
Jun Pang and
Hongyang Qu and
Qixia Yuan Taming Asynchrony for Attractor
Detection in Large Boolean Networks . . 31--42
Tiancong Wang and
Bin Ma Adjacent Y-Ion Ratio Distributions and
Its Application in Peptide Sequencing 43--51
Tom Hartmann and
Matthias Bernt and
Martin Middendorf An Exact Algorithm for Sorting by
Weighted Preserving Genome
Rearrangements . . . . . . . . . . . . . 52--62
Lei Li and
Mukul S. Bansal An Integrated Reconciliation Framework
for Domain, Gene, and Species Level
Evolution . . . . . . . . . . . . . . . 63--76
Yuhei Nishiyama and
Aleksandar Shurbevski and
Hiroshi Nagamochi and
Tatsuya Akutsu Resource Cut, a New Bounding Procedure
to Algorithms for Enumerating Tree-Like
Chemical Graphs . . . . . . . . . . . . 77--90
Bairong Shen and
Xiaoqian Jiang and
Xingming Zhao Modeling and Simulation Studies of
Complex Biological Systems for Precision
Medicine and Healthcare . . . . . . . . 91--92
Md Nazmus Sadat and
Md Momin Al Aziz and
Noman Mohammed and
Feng Chen and
Xiaoqian Jiang and
Shuang Wang SAFETY: Secure gwAs in Federated
Environment through a hYbrid Solution 93--102
Chengsheng Mao and
Yuan Zhao and
Mengxin Sun and
Yuan Luo Are My EHRs Private Enough? Event-Level
Privacy Protection . . . . . . . . . . . 103--112
Yichen Jiang and
Jenny Hamer and
Chenghong Wang and
Xiaoqian Jiang and
Miran Kim and
Yongsoo Song and
Yuhou Xia and
Noman Mohammed and
Md Nazmus Sadat and
Shuang Wang SecureLR: Secure Logistic Regression
Model via a Hybrid Cryptographic
Protocol . . . . . . . . . . . . . . . . 113--123
Mengmeng Sun and
Tao Ding and
Xu-Qing Tang and
Yu Keming An Efficient Mixed-Model for Screening
Differentially Expressed Genes of Breast
Cancer Based on LR--RF . . . . . . . . . 124--130
Wenliang Zhu and
Xiaohe Chen and
Yan Wang and
Lirong Wang Arrhythmia Recognition and
Classification Using ECG Morphology and
Segment Feature Analysis . . . . . . . . 131--138
Zexian Zeng and
Yu Deng and
Xiaoyu Li and
Tristan Naumann and
Yuan Luo Natural Language Processing for
EHR-Based Computational Phenotyping . . 139--153
Yin-Ying Wang and
Chunfeng Cui and
Liqun Qi and
Hong Yan and
Xing-Ming Zhao DrPOCS: Drug Repositioning Based on
Projection Onto Convex Sets . . . . . . 154--162
Dewu Ding and
Xiao Sun A Comparative Study of Network Motifs in
the Integrated Transcriptional
Regulation and Protein Interaction
Networks of \bionameShewanella . . . . . 163--171
Juan Wang and
Jin-Xing Liu and
Chun-Hou Zheng and
Ya-Xuan Wang and
Xiang-Zhen Kong and
Chang-Gang Wen A Mixed-Norm Laplacian Regularized
Low-Rank Representation Method for Tumor
Samples Clustering . . . . . . . . . . . 172--182
Sushmita Paul and
Dhanajit Brahma An Integrated Approach for
Identification of Functionally Similar
MicroRNAs in Colorectal Cancer . . . . . 183--192
Alireza Karbalayghareh and
Ulisses Braga-Neto and
Edward R. Dougherty Classification of Single-Cell Gene
Expression Trajectories from Incomplete
and Noisy Data . . . . . . . . . . . . . 193--207
Kin-On Cheng and
Ngai-Fong Law and
Wan-Chi Siu Clustering-Based Compression for
Population DNA Sequences . . . . . . . . 208--221
Ping Luo and
Li-Ping Tian and
Jishou Ruan and
Fang-Xiang Wu Disease Gene Prediction by Integrating
PPI Networks, Clinical RNA-Seq Data and
OMIM Data . . . . . . . . . . . . . . . 222--232
Cheng Yan and
Jianxin Wang and
Peng Ni and
Wei Lan and
Fang-Xiang Wu and
Yi Pan DNRLMF--MDA: Predicting microRNA-Disease
Associations Based on Similarities of
microRNAs and Diseases . . . . . . . . . 233--243
Ronghui Ju and
Chenhui Hu and
Pan Zhou and
Quanzheng Li Early Diagnosis of Alzheimer's Disease
Based on Resting-State Brain Networks
and Deep Learning . . . . . . . . . . . 244--257
Paola Pesantez-Cabrera and
Ananth Kalyanaraman Efficient Detection of Communities in
Biological Bipartite Networks . . . . . 258--271
Xiangtao Li and
Ka-Chun Wong Elucidating Genome-Wide Protein-RNA
Interactions Using Differential
Evolution . . . . . . . . . . . . . . . 272--282
Xuan Zhang and
Quan Zou and
Alfonso Rodriguez-Paton and
Xiangxiang Zeng Meta-Path Methods for Prioritizing
Candidate Disease miRNAs . . . . . . . . 283--291
Bin Liu and
Junjie Chen and
Mingyue Guo and
Xiaolong Wang Protein Remote Homology Detection and
Fold Recognition Based on Sequence-Order
Frequency Matrix . . . . . . . . . . . . 292--300
Minghan Chen and
Brandon D. Amos and
Layne T. Watson and
John J. Tyson and
Young Cao and
Clifford A. Shaffer and
Michael W. Trosset and
Cihan Oguz and
Gisella Kakoti Quasi-Newton Stochastic Optimization
Algorithm for Parameter Estimation of a
Stochastic Model of the Budding Yeast
Cell Cycle . . . . . . . . . . . . . . . 301--311
Cheng Liu and
Hau San Wong Structured Penalized Logistic Regression
for Gene Selection in Gene Expression
Data Analysis . . . . . . . . . . . . . 312--321
Andres F. Lopez-Lopera and
Mauricio A. Alvarez Switched Latent Force Models for
Reverse-Engineering Transcriptional
Regulation in Gene Expression Data . . . 322--335
Jiao Zhang and
Sam Kwong and
Ka-Chun Wong ToBio: Global Pathway Similarity Search
Based on Topological and Biological
Features . . . . . . . . . . . . . . . . 336--349
Shuigeng Zhou and
Yi-Ping Phoebe Chen and
Hiroshi Mamitsuka Editorial . . . . . . . . . . . . . . . 350--351
Xiaojun Chen and
Joshua Z. Huang and
Qingyao Wu and
Min Yang Subspace Weighting Co-Clustering of Gene
Expression Data . . . . . . . . . . . . 352--364
Bo Tian and
Qiong Duan and
Can Zhao and
Ben Teng and
Zengyou He Reinforce: an Ensemble Approach for
Inferring PPI Network from AP--MS Data 365--376
Bin Xu and
Jihong Guan and
Yang Wang and
Zewei Wang Essential Protein Detection by Random
Walk on Weighted Protein--Protein
Interaction Networks . . . . . . . . . . 377--387
Weiping Sun and
Yi Liu and
Gills A. Lajoie and
Bin Ma and
Kaizhong Zhang An Improved Approach for $N$-Linked
Glycan Structure Identification from HCD
MS/MS Spectra . . . . . . . . . . . . . 388--395
Jingpu Zhang and
Zuping Zhang and
Zhigang Chen and
Lei Deng Integrating Multiple Heterogeneous
Networks for Novel LncRNA-Disease
Association Inference . . . . . . . . . 396--406
Zuping Zhang and
Jingpu Zhang and
Chao Fan and
Yongjun Tang and
Lei Deng KATZLGO: Large-Scale Prediction of
LncRNA Functions by Using the KATZ
Measure Based on Multiple Networks . . . 407--416
Min Li and
Ruiqing Zheng and
Yaohang Li and
Fang-Xiang Wu and
Jianxin Wang MGT--SM: a Method for Constructing
Cellular Signal Transduction Networks 417--424
Shaoliang Peng and
Yingbo Cui and
Shunyun Yang and
Wenhe Su and
Xiaoyu Zhang and
Tenglilang Zhang and
Weiguo Liu and
Xing-Ming Zhao A CPU--MIC Collaborated Parallel
Framework for GROMACS on Tianhe-2
Supercomputer . . . . . . . . . . . . . 425--433
Jie Zhang and
Zhigen Zhao and
Kai Zhang and
Zhi Wei A Feature Sampling Strategy for Analysis
of High Dimensional Genomic Data . . . . 434--441
Kefei Liu and
Jieping Ye and
Yang Yang and
Li Shen and
Hui Jiang A Unified Model for Joint Normalization
and Differential Gene Expression
Detection in RNA-Seq Data . . . . . . . 442--454
Wei Zhang and
Shu-Lin Wang An Integrated Framework for Identifying
Mutated Driver Pathway and Cancer
Progression . . . . . . . . . . . . . . 455--464
Tim Michels and
Dimitri Berh and
Xiaoyi Jiang An RJMCMC-Based Method for Tracking and
Resolving Collisions of
\bionameDrosophila Larvae . . . . . . . 465--474
Lu Zhang and
Qiuping Pan and
Yue Wang and
Xintao Wu and
Xinghua Shi Bayesian Network Construction and
Genotype-Phenotype Inference Using GWAS
Statistics . . . . . . . . . . . . . . . 475--489
Koyel Mandal and
Rosy Sarmah and
Dhruba Kumar Bhattacharyya Biomarker Identification for Cancer
Disease Using Biclustering Approach: an
Empirical Study . . . . . . . . . . . . 490--509
Jakob L. Andersen and
Christoph Flamm and
Daniel Merkle and
Peter F. Stadler Chemical Transformation Motifs ---
Modelling Pathways as Integer Hyperflows 510--523
Shahin Boluki and
Mohammad Shahrokh Esfahani and
Xiaoning Qian and
Edward R. Dougherty Constructing Pathway-Based Priors within
a Gaussian Mixture Model for Bayesian
Regression and Classification . . . . . 524--537
Huanan Zhang and
David Roe and
Rui Kuang Detecting Population-Differentiation
Copy Number Variants in Human Population
Tree by Sparse Group Selection . . . . . 538--549
Claudia Caudai and
Emanuele Salerno and
Monica Zopp\`e and
Anna Tonazzini Estimation of the Spatial Chromatin
Structure Based on a Multiresolution
Bead-Chain Model . . . . . . . . . . . . 550--559
Bilal Nizami and
Elham Mousavinezhad Sarasia and
Mehbub I. K. Momin and
Bahareh Honarparvar Estrogenic Active Stilbene Derivatives
as Anti-Cancer Agents: a DFT and QSAR
Study . . . . . . . . . . . . . . . . . 560--568
Biing-Feng Wang and
Chih-Yu Li Fast Algorithms for Computing
Path-Difference Distances . . . . . . . 569--582
Mathias Foo and
Jongrae Kim and
Declan G. Bates Modelling and Control of Gene Regulatory
Networks for Perturbation Mitigation . . 583--595
Son P. Nguyen and
Zhaoyu Li and
Dong Xu and
Yi Shang New Deep Learning Methods for Protein
Loop Modeling . . . . . . . . . . . . . 596--606
Yun Niu and
Hongmei Wu and
Yuwei Wang Protein-Protein Interaction
Identification Using a
Similarity-Constrained Graph Model . . . 607--616
Leena Salmela and
Alexandru I. Tomescu Safely Filling Gaps with Partial
Solutions Common to All Solutions . . . 617--626
Fernando López-Caamal and
Heinrich J. Huber Stable IL-$ 1 \beta 1 \beta $-Activation
in an Inflammasome Signalling Model
Depends on Positive and Negative
Feedbacks and Tight Regulation of
Protein Production . . . . . . . . . . . 627--637
Amir Najafi and
Sepehr Janghorbani and
Seyed Abolfazl Motahari and
Emad Fatemizadeh Statistical Association Mapping of
Population-Structured Genetic Data . . . 638--649
Xiaohui Lin and
Xin Huang and
Lina Zhou and
Weijie Ren and
Jun Zeng and
Weihong Yao and
Xingyuan Wang The Robust Classification Model Based on
Combinatorial Features . . . . . . . . . 650--657
Mingfu Shao and
Carl Kingsford Theory and A Heuristic for the Minimum
Path Flow Decomposition Problem . . . . 658--670
Florian Kaiser and
Dirk Labudde Unsupervised Discovery of Geometrically
Common Structural Motifs and Long-Range
Contacts in Protein $3$D Structures . . 671--680
Carlos Martin-Vide and
Miguel A. Vega-Rodriguez Algorithms for Computational Biology:
Third Edition . . . . . . . . . . . . . 701--702
Syed Ali Ahmed and
Saad Mneimneh Gibbs/MCMC Sampling for Multiple RNA
Interaction with Sub-Optimal Solutions 703--712
Agnieszka Mykowiecka and
Pawel Gorecki Credibility of Evolutionary Events in
Gene Trees . . . . . . . . . . . . . . . 713--726
David Sankoff and
Chunfang Zheng and
Yue Zhang and
Joao Meidanis and
Eric Lyons and
Haibao Tang Models for Similarity Distributions of
Syntenic Homologs and Applications to
Phylogenomics . . . . . . . . . . . . . 727--737
Laura Urbini and
Blerina Sinaimeri and
Catherine Matias and
Marie-France Sagot Exploring the Robustness of the
Parsimonious Reconciliation Method in
Host-Symbiont Cophylogeny . . . . . . . 738--748
De-Shuang Huang and
Vitoantonio Bevilacqua and
M. Michael Gromiha Guest Editorial for Special Section on
the 13th International Conference on
Intelligent Computing ICIC . . . . . . . 749--750
Jyotsna Talreja Wassan and
Haiying Wang and
Fiona Browne and
Huiru Zheng A Comprehensive Study on Predicting
Functional Role of Metagenomes Using
Machine Learning Methods . . . . . . . . 751--763
Min Li and
Li Tang and
Zhongxiang Liao and
Junwei Luo and
Fang-Xiang Wu and
Yi Pan and
Jianxin Wang A Novel Scaffolding Algorithm Based on
Contig Error Correction and Path
Extension . . . . . . . . . . . . . . . 764--773
Xiaolong Zhang and
Xiaoli Lin and
Jiafu Zhao and
Qianqian Huang and
Xin Xu Efficiently Predicting Hot Spots in PPIs
by Combining Random Forest and Synthetic
Minority Over-Sampling Technique . . . . 774--781
Lin Yuan and
Le-Hang Guo and
Chang-An Yuan and
Youhua Zhang and
Kyungsook Han and
Asoke K. Nandi and
Barry Honig and
De-Shuang Huang Integration of Multi-Omics Data for Gene
Regulatory Network Inference and
Application to Breast Cancer . . . . . . 782--791
Su-Ping Deng and
Wei-Li Guo Identifying Key Genes of Liver Cancer by
Networking of Multiple Data Sets . . . . 792--800
Peng Wu and
Dong Wang Classification of a DNA Microarray for
Diagnosing Cancer Using a Complex
Network Based Method . . . . . . . . . . 801--808
Zhu-Hong You and
Wen-Zhun Huang and
Shanwen Zhang and
Yu-An Huang and
Chang-Qing Yu and
Li-Ping Li An Efficient Ensemble Learning Approach
for Predicting Protein-Protein
Interactions by Integrating Protein
Primary Sequence and Evolutionary
Information . . . . . . . . . . . . . . 809--817
Hua Zhong and
Mingzhou Song A Fast Exact Functional Test for
Directional Association and Cancer
Biology Applications . . . . . . . . . . 818--826
Sandip Samaddar and
Rituparna Sinha and
Rajat K. De A Model for Distributed Processing and
Analyses of NGS Data under Map-Reduce
Paradigm . . . . . . . . . . . . . . . . 827--840
Dongdong Sun and
Minghui Wang and
Ao Li A Multimodal Deep Neural Network for
Human Breast Cancer Prognosis Prediction
by Integrating Multi-Dimensional Data 841--850
Michiel Van Dyck and
Xavier Woot de Trixhe and
An Vermeulen and
Wim Vanroose A Robust Simulator for Physiologically
Structured Population Models . . . . . . 851--864
Maryam Sharifi and
Arta A. Jamshidi and
Nazanin Namazi Sarvestani An Adaptive Robust Control Strategy in a
Cancer Tumor-Immune System Under
Uncertainties . . . . . . . . . . . . . 865--873
Loris Nanni and
Sheryl Brahnam and
Stefano Ghidoni and
Alessandra Lumini Bioimage Classification with Handcrafted
and Learned Features . . . . . . . . . . 874--885
Haoyu Cheng and
Yong Zhang and
Yun Xu BitMapper2: a GPU-Accelerated All-Mapper
Based on the Sparse $q$-Gram Index . . . 886--897
Chris Whidden and
Frederick A. Matsen Calculating the Unrooted Subtree
Prune-and-Regraft Distance . . . . . . . 898--911
Pei Wang and
Daojie Wang and
Jinhu Lu Controllability Analysis of a Gene
Network for \bionameArabidopsis thaliana
Reveals Characteristics of Functional
Gene Families . . . . . . . . . . . . . 912--924
Sven Thiele and
Sandra Heise and
Wiebke Hessenkemper and
Hannes Bongartz and
Melissa Fensky and
Fred Schaper and
Steffen Klamt Designing Optimal Experiments to
Discriminate Interaction Graph Models 925--935
Yi-Yan Zhang and
Qin Li and
Yi Xin and
Wei-Qi Lv Differentiating Prostate Cancer from
Benign Prostatic Hyperplasia Using PSAD
Based on Machine Learning: Single-Center
Retrospective Study in China . . . . . . 936--941
Dimitrios Kaloudas and
Nikolet Pavlova and
Robert Penchovsky EBWS: Essential Bioinformatics Web
Services for Sequence Analyses . . . . . 942--953
Bo Xu and
Hongfei Lin and
Yuan Lin Learning to Refine Expansion Terms for
Biomedical Information Retrieval Using
Semantic Resources . . . . . . . . . . . 954--966
Tiantian He and
Keith C. C. Chan Measuring Boundedness for Protein
Complex Identification in PPI Networks 967--979
Aiguo Wang and
Ye Chen and
Ning An and
Jing Yang and
Lian Li and
Lili Jiang Microarray Missing Value Imputation: a
Regularized Local Learning Method . . . 980--993
You Song and
Siyu Yang and
Jinzhi Lei ParaCells: a GPU Architecture for
Cell-Centered Models in Computational
Biology . . . . . . . . . . . . . . . . 994--1006
Mohammad Nazrul Ishlam Patoary and
Carl Tropper and
Robert A. McDougal and
Zhongwei Lin and
William W. Lytton Parallel Stochastic Discrete Event
Simulation of Calcium Dynamics in Neuron 1007--1019
Chao Fang and
Yi Shang and
Dong Xu Prediction of Protein Backbone Torsion
Angles Using Deep Residual Inception
Neural Networks . . . . . . . . . . . . 1020--1028
Gregor Urban and
Kevin Bache and
Duc T. T. Phan and
Agua Sobrino and
Alexander K. Shmakov and
Stephanie J. Hachey and
Christopher C. W. Hughes and
Pierre Baldi Deep Learning for Drug Discovery and
Cancer Research: Automated Analysis of
Vascularization Images . . . . . . . . . 1029--1035
Kumar Saurabh Singh and
Bartlomiej J. Troczka and
Katherine Beadle and
Linda M. Field and
T. G. Emyr Davies and
Martin S. Williamson and
Ralf Nauen and
Chris Bass Extension of Partial Gene Transcripts by
Iterative Mapping of RNA-Seq Raw Reads 1036--1041
Jia-Juan Tu and
Le Ou-Yang and
Xiaohua Hu and
Xiao-Fei Zhang Inferring Gene Network Rewiring by
Combining Gene Expression and Gene
Mutation Data . . . . . . . . . . . . . 1042--1048
Aisharjya Sarkar and
Yuanfang Ren and
Rasha Elhesha and
Tamer Kahveci A New Algorithm for Counting Independent
Motifs in Probabilistic Networks . . . . 1049--1062
Alexey Markin and
Oliver Eulenstein Computing Manhattan Path-Difference
Median Trees: a Practical Local Search
Approach . . . . . . . . . . . . . . . . 1063--1076
Misagh Kordi and
Mukul S. Bansal Exact Algorithms for
Duplication-Transfer-Loss Reconciliation
with Non-Binary Gene Trees . . . . . . . 1077--1090
Priyanka Ghosh and
Ananth Kalyanaraman FastEtch: a Fast Sketch-Based Assembler
for Genomes . . . . . . . . . . . . . . 1091--1106
Olivia Choudhury and
Ankush Chakrabarty and
Scott J. Emrich Highly Accurate and Efficient
Data-Driven Methods for Genotype
Imputation . . . . . . . . . . . . . . . 1107--1116
Tony Pan and
Patrick Flick and
Chirag Jain and
Yongchao Liu and
Srinivas Aluru Kmerind: a Flexible Parallel Library for
$K$-mer Indexing of Biological Sequences
on Distributed Memory Systems . . . . . 1117--1131
Enrico Siragusa and
Niina Haiminen and
Filippo Utro and
Laxmi Parida Linear Time Algorithms to Construct
Populations Fitting Multiple Constraint
Distributions at Genomic Scales . . . . 1132--1142
Deeptak Verma and
Gevorg Grigoryan and
Chris Bailey-Kellogg Pareto Optimization of Combinatorial
Mutagenesis Libraries . . . . . . . . . 1143--1153
Muhibur Rasheed and
Nathan Clement and
Abhishek Bhowmick and
Chandrajit L. Bajaj Statistical Framework for Uncertainty
Quantification in Computational
Molecular Modeling . . . . . . . . . . . 1154--1167
Wenruo Bai and
Jeffrey Bilmes and
William S. Noble Submodular Generalized Matching for
Peptide Identification in Tandem Mass
Spectrometry . . . . . . . . . . . . . . 1168--1181
Quan Zou and
Qi Liu Advanced Machine Learning Techniques for
Bioinformatics . . . . . . . . . . . . . 1182--1183
Qinhu Zhang and
Lin Zhu and
De-Shuang Huang High-Order Convolutional Neural Network
Architecture for Predicting DNA-Protein
Binding Sites . . . . . . . . . . . . . 1184--1192
Min Li and
Zhihui Fei and
Min Zeng and
Fang-Xiang Wu and
Yaohang Li and
Yi Pan and
Jianxin Wang Automated ICD-9 Coding via A Deep
Learning Approach . . . . . . . . . . . 1193--1202
Bin Liu and
Shumin Li ProtDet-CCH: Protein Remote Homology
Detection by Combining Long Short-Term
Memory and Ranking Methods . . . . . . . 1203--1210
Bingqiang Liu and
Ling Han and
Xiangrong Liu and
Jichang Wu and
Qin Ma Computational Prediction of Sigma-54
Promoters in Bacterial Genomes by
Integrating Motif Finding and Machine
Learning Strategies . . . . . . . . . . 1211--1218
Hongyu Liu and
Qinmin Vivian Hu and
Liang He Term-Based Personalization for Feature
Selection in Clinical Handover Form
Auto-Filling . . . . . . . . . . . . . . 1219--1230
Ran Su and
Huichen Wu and
Bo Xu and
Xiaofeng Liu and
Leyi Wei Developing a Multi-Dose Computational
Model for Drug-Induced Hepatotoxicity
Prediction Based on Toxicogenomics Data 1231--1239
Liang Yu and
Lin Gao Human Pathway-Based Disease Network . . 1240--1249
Mahdi Imani and
Ulisses M. Braga-Neto Control of Gene Regulatory Networks
Using Bayesian Inverse Reinforcement
Learning . . . . . . . . . . . . . . . . 1250--1261
Feng-Biao Guo and
Xinglai Ji and
Jian Huang Guest Editorial for Special Section on
the 7th National Conference on
Bioinformatics and Systems Biology of
China . . . . . . . . . . . . . . . . . 1262--1263
Leyi Wei and
Pengwei Xing and
Gaotao Shi and
Zhiliang Ji and
Quan Zou Fast Prediction of Protein Methylation
Sites Using a Sequence-Based Feature
Selection Technique . . . . . . . . . . 1264--1273
Yan Lin and
Fa-Zhan Zhang and
Kai Xue and
Yi-Zhou Gao and
Feng-Biao Guo Identifying Bacterial Essential Genes
Based on a Feature-Integrated Method . . 1274--1279
Yan Shi and
Bolun Zhang and
Maolin Cai and
Weiqing Xu Coupling Effect of Double Lungs on a VCV
Ventilator with Automatic Secretion
Clearance Function . . . . . . . . . . . 1280--1287
Ying Li and
Ye He and
Siyu Han and
Yanchun Liang Identification and Functional Inference
for Tumor-Associated Long Non-Coding RNA 1288--1301
Jun-Ping Zhang and
Yi Liu and
Wei Sun and
Xiao-Yang Zhao and
La Ta and
Wei-Sheng Guo Characteristics of Myosin V Processivity 1302--1308
Pengmian Feng and
Zhenyi Wang and
Xiaoyu Yu Predicting Antimicrobial Peptides by
Using Increment of Diversity with
Quadratic Discriminant Analysis Method 1309--1312
Guoshi Chai and
Min Yu and
Lixu Jiang and
Yaocong Duan and
Jian Huang HMMCAS: a Web Tool for the
Identification and Domain Annotations of
CAS Proteins . . . . . . . . . . . . . . 1313--1315
Hao Lin and
Zhi-Yong Liang and
Hua Tang and
Wei Chen Identifying Sigma70 Promoters with Novel
Pseudo Nucleotide Composition . . . . . 1316--1321
Erman Ayday and
Muhammad Naveed and
Haixu Tang GenoPri'17: International Workshop on
Genome Privacy and Security . . . . . . 1322--1323
Alexander Senf End-to-End Security for Local and Remote
Human Genetic Data Applications at the
EGA . . . . . . . . . . . . . . . . . . 1324--1327
Jean Louis Raisaro and
Juan Ramon Troncoso-Pastoriza and
Mickael Misbach and
Joao Sa Sousa and
Sylvain Pradervand and
Edoardo Missiaglia and
Olivier Michielin and
Bryan Ford and
Jean-Pierre Hubaux MedCo: Enabling Secure and
Privacy-Preserving Exploration of
Distributed Clinical and Genomic Data 1328--1341
Dixie B. Baker and
Bartha M. Knoppers and
Mark Phillips and
David van Enckevort and
Petra Kaufmann and
Hanns Lochmuller and
Domenica Taruscio Privacy-Preserving Linkage of Genomic
and Clinical Data Sets . . . . . . . . . 1342--1348
Jake Weidman and
William Aurite and
Jens Grossklags On Sharing Intentions, and Personal and
Interdependent Privacy Considerations
for Genetic Data: a Vignette Study . . . 1349--1361
Ion I. Mandoiu and
Pavel Skums and
Alexander Zelikovsky Guest Editors' Introduction to the
Special Section on Bioinformatics
Research and Applications . . . . . . . 1362--1363
Nina Luhmann and
Manuel Lafond and
Annelyse Thevenin and
Aida Ouangraoua and
Roland Wittler and
Cedric Chauve The SCJ Small Parsimony Problem for
Weighted Gene Adjacencies . . . . . . . 1364--1373
Alexey Markin and
Oliver Eulenstein Efficient Local Search for Euclidean
Path-Difference Median Trees . . . . . . 1374--1385
Min Li and
Peng Ni and
Xiaopei Chen and
Jianxin Wang and
Fang-Xiang Wu and
Yi Pan Construction of Refined Protein
Interaction Network for Predicting
Essential Proteins . . . . . . . . . . . 1386--1397
Roman Sergeevich Sergeev and
Ivan S. Kavaliou and
Uladzislau V. Sataneuski and
Andrei Gabrielian and
Alex Rosenthal and
Michael Tartakovsky and
Alexander V. Tuzikov Genome-Wide Analysis of MDR and XDR
Tuberculosis from Belarus:
Machine-Learning Approach . . . . . . . 1398--1408
Amarda Shehu and
Giuseppe Pozzi and
Tamer Kahveci Guest Editorial for the ACM
International Conference on
Bioinformatics, Computational Biology,
and Health Informatics . . . . . . . . . 1409--1409
Paola Bonizzoni and
Simone Ciccolella and
Gianluca Della Vedova and
Mauricio Soto Does Relaxing the Infinite Sites
Assumption Give Better Tumor
Phylogenies? An ILP-Based Comparative
Approach . . . . . . . . . . . . . . . . 1410--1423
Alan Cleary and
Thiruvarangan Ramaraj and
Indika Kahanda and
Joann Mudge and
Brendan Mumey Exploring Frequented Regions in
Pan-Genomic Graphs . . . . . . . . . . . 1424--1435
Sunyoung Kwon and
Sungroh Yoon End-to-End Representation Learning for
Chemical-Chemical Interaction Prediction 1436--1447
Laraib Malik and
Rob Patro Rich Chromatin Structure Prediction from
Hi-C Data . . . . . . . . . . . . . . . 1448--1458
Alexey Markin and
Oliver Eulenstein Cophenetic Median Trees . . . . . . . . 1459--1470
Lu Zhu and
Ralf Hofestadt and
Martin Ester Tissue-Specific Subcellular Localization
Prediction Using Multi-Label Markov
Random Fields . . . . . . . . . . . . . 1471--1482
Thuc Duy Le and
Tao Hoang and
Jiuyong Li and
Lin Liu and
Huawen Liu and
Shu Hu A Fast PC Algorithm for High Dimensional
Causal Discovery with Multi-Core PCs . . 1483--1495
Pieter Meysman and
Yvan Saeys and
Ehsan Sabaghian and
Wout Bittremieux and
Yves Van de Peer and
Bart Goethals and
Kris Laukens Mining the Enriched Subgraphs for
Specific Vertices in a Biological Graph 1496--1507
Neda Jahanshad and
Joshua Faskowitz and
Gennady Roshchupkin and
Derrek P. Hibar and
Boris A. Gutman and
Nicholas J. Tustison and
Hieab H. H. Adams and
Wiro J. Niessen and
Meike W. Vernooij and
M. Arfan Ikram and
Marcel P. Zwiers and
Alejandro Arias Vasquez and
Barbara Franke and
Jennifer L. Kroll and
Benson Mwangi and
Jair C. Soares and
Alex Ing and
Sylvane Desrivieres and
Gunter Schumann and
Narelle K. Hansell and
Greig I. de Zubicaray and
Katie L. McMahon and
Nicholas G. Martin and
Margaret J. Wright and
Paul M. Thompson Multi-Site Meta-Analysis of Morphometry 1508--1514
Shokoufeh Mirzaei and
Tomer Sidi and
Chen Keasar and
Silvia Crivelli Purely Structural Protein Scoring
Functions Using Support Vector Machine
and Ensemble Learning . . . . . . . . . 1515--1523
Ritambhara Singh and
Jack Lanchantin and
Gabriel Robins and
Yanjun Qi Transfer String Kernel for Cross-Context
DNA--Protein Binding Prediction . . . . 1524--1536
Tanay Kumar Saha and
Ataur Katebi and
Wajdi Dhifli and
Mohammad Al Hasan Discovery of Functional Motifs from the
Interface Region of Oligomeric Proteins
Using Frequent Subgraph Mining . . . . . 1537--1549
Marco Frasca and
Nicolo Cesa Bianchi Multitask Protein Function Prediction
through Task Dissimilarity . . . . . . . 1550--1560
Jerome Feret and
Heinz Koeppl Editorial . . . . . . . . . . . . . . . 1561--1561
Russ Harmer and
Yves-Stan Le Cornec and
Sebastien Legare and
Eugenia Oshurko Bio-Curation for Cellular Signalling:
The KAMI Project . . . . . . . . . . . . 1562--1573
Celia Biane and
Franck Delaplace Causal Reasoning on Boolean Control
Networks Based on Abduction: Theory and
Application to Cancer Drug Discovery . . 1574--1585
Houssam Abbas and
Alena Rodionova and
Konstantinos Mamouras and
Ezio Bartocci and
Scott A. Smolka and
Radu Grosu Quantitative Regular Expressions for
Arrhythmia Detection . . . . . . . . . . 1586--1597
Alexander Luck and
Pascal Giehr and
Karl Nordstrom and
Jorn Walter and
Verena Wolf Hidden Markov Modelling Reveals
Neighborhood Dependence of Dnmt3a and 3b
Activity . . . . . . . . . . . . . . . . 1598--1609
Hugues Mandon and
Cui Su and
Jun Pang and
Soumya Paul and
Stefan Haar and
Loic Pauleve Algorithms for the Sequential
Reprogramming of Boolean Networks . . . 1610--1619
Viacheslav Kapilevich and
Shigeto Seno and
Hideo Matsuda and
Yoichi Takenaka Chromatin $3$D Reconstruction from
Chromosomal Contacts Using a Genetic
Algorithm . . . . . . . . . . . . . . . 1620--1626
Jong Ho Jhee and
Sunjoo Bang and
Dong-gi Lee and
Hyunjung Shin Comorbidity Scoring with Causal Disease
Networks . . . . . . . . . . . . . . . . 1627--1634
Donghe Li and
Wonji Kim and
Longfei Wang and
Kyong-Ah Yoon and
Boyoung Park and
Charny Park and
Sun-Young Kong and
Yongdeuk Hwang and
Daehyun Baek and
Eun Sook Lee and
Sungho Won Comparison of INDEL Calling Tools with
Simulation Data and Real Short-Read Data 1635--1644
Shimpei Nishida and
Shun Sakuraba and
Kiyoshi Asai and
Michiaki Hamada Estimating Energy Parameters for RNA
Secondary Structure Predictions Using
Both Experimental and Computational Data 1645--1655
Je-Keun Rhee and
Jinseon Yoo and
Kyu Ryung Kim and
Jeeyoon Kim and
Yong-Jae Lee and
Byoung Chul Cho and
Tae-Min Kim Identification of Local Clusters of
Mutation Hotspots in Cancer-Related
Genes and Their Biological Relevance . . 1656--1662
Shailima Rampogu and
Ayoung Baek and
Rohit Bavi and
Minky Son and
Guang Ping Cao and
Raj Kumar and
Chanin Park and
Amir Zeb and
Rabia Mukthar Rana and
Seok Ju Park and
Keun Woo Lee Identification of Novel Scaffolds with
Dual Role as Antiepileptic and
Anti-Breast Cancer . . . . . . . . . . . 1663--1674
Hiroki Sudo and
Masanobu Jimbo and
Koji Nuida and
Kana Shimizu Secure Wavelet Matrix: Alphabet-Friendly
Privacy-Preserving String Search for
Bioinformatics . . . . . . . . . . . . . 1675--1684
Man-Sun Kim and
Dongsan Kim and
Jeong-Rae Kim Stage-Dependent Gene Expression
Profiling in Colorectal Cancer . . . . . 1685--1692
SeongRyeol Moon and
Curt Balch and
Sungjin Park and
Jinhyuk Lee and
Jiyong Sung and
Seungyoon Nam Systematic Inspection of the Clinical
Relevance of TP53 Missense Mutations in
Gastric Cancer . . . . . . . . . . . . . 1693--1701
FanChang Hao and
Melvin Zhang and
Hon Wai Leong A $2$-Approximation Scheme for Sorting
Signed Permutations by Reversals,
Transpositions, Transreversals, and
Block-Interchanges . . . . . . . . . . . 1702--1711
Limin Li and
Menglan Cai Drug Target Prediction by Multi-View Low
Rank Embedding . . . . . . . . . . . . . 1712--1721
Wen-Bin Xie and
Hong Yan and
Xing-Ming Zhao EmDL: Extracting miRNA--Drug
Interactions from Literature . . . . . . 1722--1728
Yanbo Wang and
Quan Liu and
Shan Huang and
Bo Yuan Learning a Structural and Functional
Representation for Gene Expressions: To
Systematically Dissect Complex Cancer
Phenotypes . . . . . . . . . . . . . . . 1729--1742
Yishu Wang and
Huaying Fang and
Dejie Yang and
Hongyu Zhao and
Minghua Deng Network Clustering Analysis Using
Mixture Exponential-Family Random Graph
Models and Its Application in Genetic
Interaction Data . . . . . . . . . . . . 1743--1752
Zhenni Zhao and
Xinqi Gong Protein--Protein Interaction Interface
Residue Pair Prediction Based on Deep
Learning Architecture . . . . . . . . . 1753--1759
Xi Yang and
Guoqiang Han and
Hongmin Cai and
Yan Song Recovering Hidden Diagonal Structures
via Non-Negative Matrix Factorization
with Multiple Constraints . . . . . . . 1760--1772
Anup Kumar Halder and
Piyali Chatterjee and
Mita Nasipuri and
Dariusz Plewczynski and
Subhadip Basu 3gClust: Human Protein Cluster Analysis 1773--1784
Aurpan Majumder and
Mrityunjay Sarkar and
Prolay Sharma A Composite Mode Differential Gene
Regulatory Architecture based on
Temporal Expression Profiles . . . . . . 1785--1793
Yujie Feng and
Fan Yang and
Xichuan Zhou and
Yanli Guo and
Fang Tang and
Fengbo Ren and
Jishun Guo and
Shuiwang Ji A Deep Learning Approach for Targeted
Contrast-Enhanced Ultrasound Based
Prostate Cancer Detection . . . . . . . 1794--1801
Aida Brankovic and
Marjan Hosseini and
Luigi Piroddi A Distributed Feature Selection
Algorithm Based on Distance Correlation
with an Application to Microarrays . . . 1802--1815
Li Zhang and
Ho-Chun Wu and
Cheuk-Hei Ho and
Shing-Chow Chan A Multi-Laplacian Prior and Augmented
Lagrangian Approach to the Exploratory
Analysis of Time-Varying Gene and
Transcriptional Regulatory Networks for
Gene Microarray Data . . . . . . . . . . 1816--1829
Anvita Gupta Malhotra and
Sudha Singh and
Mohit Jha and
Khushhali M. Pandey A Parametric Targetability Evaluation
Approach for Vitiligo Proteome Extracted
through Integration of Gene Ontologies
and Protein Interaction Topologies . . . 1830--1842
Juho Timonen and
Henrik Mannerström and
Harri Lähdesmäki and
Jukka Intosalmi A Probabilistic Framework for Molecular
Network Structure Inference by Means of
Mechanistic Modeling . . . . . . . . . . 1843--1854
Xiaoke Ma and
Penggang Sun and
Zhong-Yuan Zhang An Integrative Framework for Protein
Interaction Network and Methylation Data
to Discover Epigenetic Modules . . . . . 1855--1866
Claudia Caudai and
Emanuele Salerno and
Monica Zopp\`e and
Ivan Merelli and
Anna Tonazzini ChromStruct 4: a Python Code to Estimate
the Chromatin Structure from Hi-C Data 1867--1878
Huiwei Zhou and
Yunlong Yang and
Shixian Ning and
Zhuang Liu and
Chengkun Lang and
Yingyu Lin and
Degen Huang Combining Context and Knowledge
Representations for Chemical-Disease
Relation Extraction . . . . . . . . . . 1879--1889
Huimin Luo and
Jianxin Wang and
Min Li and
Junwei Luo and
Peng Ni and
Kaijie Zhao and
Fang-Xiang Wu and
Yi Pan Computational Drug Repositioning with
Random Walk on a Heterogeneous Network 1890--1900
Sabrina Stella and
Roberto Chignola and
Edoardo Milotti Dynamical Detection of Boundaries and
Cavities in Biophysical Cell-Based
Simulations of Growing Tumor Tissues . . 1901--1911
Xingyu Cai and
Abdullah-Al Mamun and
Sanguthevar Rajasekaran Efficient Algorithms for Finding the
Closest $ \ell 1$-Mers in Biological
Data . . . . . . . . . . . . . . . . . . 1912--1921
Lun Hu and
Xiaohui Yuan and
Xing Liu and
Shengwu Xiong and
Xin Luo Efficiently Detecting Protein Complexes
from Protein Interaction Networks via
Alternating Direction Method of
Multipliers . . . . . . . . . . . . . . 1922--1935
Toktam Dehghani and
Mahmoud Naghibzadeh and
Javad Sadri Enhancement of Protein $ \beta $-Sheet
Topology Prediction Using Maximum Weight
Disjoint Path Cover . . . . . . . . . . 1936--1947
Xue Jiang and
Han Zhang and
Zhao Zhang and
Xiongwen Quan Flexible Non-Negative Matrix
Factorization to Unravel Disease-Related
Genes . . . . . . . . . . . . . . . . . 1948--1957
Marianna Milano and
Pietro Hiram Guzzi and
Mario Cannataro GLAlign: a Novel Algorithm for Local
Network Alignment . . . . . . . . . . . 1958--1969
Amit Paul and
Jaya Sil Identification of Differentially
Expressed Genes to Establish New
Biomarker for Cancer Prediction . . . . 1970--1985
Xiaoke Hao and
Xiaohui Yao and
Shannon L. Risacher and
Andrew J. Saykin and
Jintai Yu and
Huifu Wang and
Lan Tan and
Li Shen and
Daoqiang Zhang Identifying Candidate Genetic
Associations with MRI-Derived AD-Related
ROI via Tree-Guided Sparse Learning . . 1986--1996
Anjing Fan and
Haitao Wang and
Hua Xiang and
Xiufen Zou Inferring Large-Scale Gene Regulatory
Networks Using a Randomized Algorithm
Based on Singular Value Decomposition 1997--2008
Ayan Chaudhury and
Christopher Ward and
Ali Talasaz and
Alexander G. Ivanov and
Mark Brophy and
Bernard Grodzinski and
Norman P. A. Hüner and
Rajnikant V. Patel and
John L. Barron Machine Vision System for $3$D Plant
Phenotyping . . . . . . . . . . . . . . 2009--2022
O. Ufuk Nalbantoglu and
Khalid Sayood MIMOSA: Algorithms for Microbial
Profiling . . . . . . . . . . . . . . . 2023--2034
Michail-Antisthenis Tsompanas and
Andrew Adamatzky and
Ioannis Ieropoulos and
Neil William Phillips and
Georgios Ch. Sirakoulis and
John Greenman Modelling Microbial Fuel Cells Using
Lattice Boltzmann Methods . . . . . . . 2035--2045
Runtao Yang and
Chengjin Zhang and
Rui Gao and
Lina Zhang and
Qing Song Predicting FAD Interacting Residues with
Feature Selection and Comprehensive
Sequence Descriptors . . . . . . . . . . 2046--2056
MD Aksam V. K. and
V. M. Chandrasekaran and
Sundaramurthy Pandurangan Protein Domain Level Cancer Drug Targets
in the Network of MAPK Pathways . . . . 2057--2065
Ashis Kumer Biswas and
Dong-Chul Kim and
Mingon Kang and
Jean X. Gao Robust Inductive Matrix Completion
Strategy to Explore Associations Between
LincRNAs and Human Disease Phenotypes 2066--2077
Benjamin Wingfield and
Sonya Coleman and
TM McGinnity and
AJ Bjourson Robust Microbial Markers for
Non-Invasive Inflammatory Bowel Disease
Identification . . . . . . . . . . . . . 2078--2088
Rahul K. Sevakula and
Vikas Singh and
Nishchal K. Verma and
Chandan Kumar and
Yan Cui Transfer Learning for Molecular Cancer
Classification Using Deep Neural
Networks . . . . . . . . . . . . . . . . 2089--2100
Carlos Martín-Vide and
Miguel A. Vega-Rodríguez Algorithms for Computational Biology:
Fifth Edition . . . . . . . . . . . . . 1--1
Klairton Lima Brito and
Andre Rodrigues Oliveira and
Ulisses Dias and
Zanoni Dias Heuristics for the Reversal and
Transposition Distance Problem . . . . . 2--13
Leo van Iersel and
Remie Janssen and
Mark Jones and
Yukihiro Murakami and
Norbert Zeh Polynomial-Time Algorithms for
Phylogenetic Inference Problems
Involving Duplication and Reticulation 14--26
Atsuko Miyawaki-Kuwakado and
Soichiro Komori and
Fumihide Shiraishi A Promising Method for Calculating True
Steady-State Metabolite Concentrations
in Large-Scale Metabolic Reaction
Network Models . . . . . . . . . . . . . 27--36
Ranjan Kumar Maji and
Sunirmal Khatua and
Zhumur Ghosh A Supervised Ensemble Approach for
Sensitive microRNA Target Prediction . . 37--46
Mehmet Kocak and
Khyobeni Mozhui An Application of the Bayesian
Periodicity Test to Identify Diurnal
Rhythm Genes in the Brain . . . . . . . 47--55
Syed Sazzad Ahmed and
Swarup Roy and
Jugal Kalita Assessing the Effectiveness of Causality
Inference Methods for Gene Regulatory
Networks . . . . . . . . . . . . . . . . 56--70
Cheng-Hong Yang and
Yu-Da Lin and
Li-Yeh Chuang Class Balanced Multifactor
Dimensionality Reduction to Detect
Gene--Gene Interactions . . . . . . . . 71--81
Jing wei Tan and
Siow-Wee Chang and
Sameem Abdul-Kareem and
Hwa Jen Yap and
Kien-Thai Yong Deep Learning for Plant Species
Classification Using Leaf Vein
Morphometric . . . . . . . . . . . . . . 82--90
Yangqin Feng and
Lei Zhang and
Juan Mo Deep Manifold Preserving Autoencoder for
Classifying Breast Cancer
Histopathological Images . . . . . . . . 91--101
Mahnaz Habibi and
Pegah Khosravi Disruption of Protein Complexes from
Weighted Complex Networks . . . . . . . 102--109
Yicheng He and
Junfeng Liu and
Xia Ning Drug Selection via Joint Push and
Learning to Rank . . . . . . . . . . . . 110--123
Jiyun Zhou and
Qin Lu and
Ruifeng Xu and
Lin Gui and
Hongpeng Wang EL\_LSTM: Prediction of DNA-Binding
Residue from Protein Sequence by
Combining Long Short-Term Memory and
Ensemble Learning . . . . . . . . . . . 124--135
Tony Pan and
Rahul Nihalani and
Srinivas Aluru Fast de Bruijn Graph Compaction in
Distributed Memory Environments . . . . 136--148
Michal Marczyk and
Roman Jaksik and
Andrzej Polanski and
Joanna Polanska GaMRed-Adaptive Filtering of
High-Throughput Biological Data . . . . 149--157
Joan Carles Pons and
Celine Scornavacca and
Gabriel Cardona Generation of Level-$k$ k LGT Networks 158--164
Jiulun Cai and
Hongmin Cai and
Jiazhou Chen and
Xi Yang Identifying ``Many-to--Many''
Relationships between Gene-Expression
Data and Drug-Response Data via Sparse
Binary Matching . . . . . . . . . . . . 165--176
Xingyu Liao and
Min Li and
Junwei Luo and
You Zou and
Fang-Xiang Wu and
Yi Pan and
Feng Luo and
Jianxin Wang Improving de novo Assembly Based on
Read Classification . . . . . . . . . . 177--188
Tianyi Zhang and
Minghui Wang and
Jianing Xi and
Ao Li LPGNMF: Predicting Long Non-Coding RNA
and Protein Interaction Using Graph
Regularized Nonnegative Matrix
Factorization . . . . . . . . . . . . . 189--197
Patricia Carvajal-López and
Fernando D. Von Borstel and
Amada Torres and
Gabriella Rustici and
Joaquín Gutiérrez and
Eduardo Romero-Vivas Microarray-Based Quality Assessment as a
Supporting Criterion for de novo
Transcriptome Assembly Selection . . . . 198--206
Sudipta Acharya and
Sriparna Saha and
Prasanna Pradhan Multi-Factored Gene-Gene Proximity
Measures Exploiting Biological Knowledge
Extracted from Gene Ontology:
Application in Gene Clustering . . . . . 207--219
Tao Li and
Xiankai Zhang and
Feng Luo and
Fang-Xiang Wu and
Jianxin Wang MultiMotifMaker: a Multi-Thread Tool for
Identifying DNA Methylation Motifs from
Pacbio Reads . . . . . . . . . . . . . . 220--225
Xiangtao Li and
Shixiong Zhang and
Ka-Chun Wong Nature-Inspired Multiobjective Epistasis
Elucidation from Genome-Wide Association
Studies . . . . . . . . . . . . . . . . 226--237
Guoxian Yu and
Keyao Wang and
Guangyuan Fu and
Maozu Guo and
Jun Wang NMFGO: Gene Function Prediction via
Nonnegative Matrix Factorization with
Gene Ontology . . . . . . . . . . . . . 238--249
Ali Foroughi pour and
Lori A. Dalton Optimal Bayesian Filtering for Biomarker
Discovery: Performance and Robustness 250--263
Sepideh Mazrouee and
Wei Wang PolyCluster: Minimum Fragment
Disagreement Clustering for Polyploid
Phasing . . . . . . . . . . . . . . . . 264--277
Saptarshi Pyne and
Alok Ranjan Kumar and
Ashish Anand Rapid Reconstruction of Time-Varying
Gene Regulatory Networks . . . . . . . . 278--291
Ramón A. Delgado and
Zhiyong Chen and
Richard H. Middleton Stepwise Tikhonov Regularisation:
Application to the Prediction of HIV-1
Drug Resistance . . . . . . . . . . . . 292--301
Kieran Alden and
Jason Cosgrove and
Mark Coles and
Jon Timmis Using Emulation to Engineer and
Understand Simulations of Biological
Systems . . . . . . . . . . . . . . . . 302--315
Dor Ganor and
Ron Y. Pinter and
Meirav Zehavi A Note on GRegNetSim: a Tool for the
Discrete Simulation and Analysis of
Genetic Regulatory Networks . . . . . . 316--320
Ziwei Chen and
Xiangqi Bai and
Liang Ma and
Xiawei Wang and
Xiuqin Liu and
Yuting Liu and
Luonan Chen and
Lin Wan A Branch Point on Differentiation
Trajectory is the Bifurcating Event
Revealed by Dynamical Network Biomarker
Analysis of Single-Cell Data . . . . . . 366--375
Lihua Zhang and
Shihua Zhang Comparison of Computational Methods for
Imputing Single-Cell RNA-Sequencing Data 376--389
Feng Li and
Lin Gao and
Bingbo Wang Detection of Driver Modules with Rarely
Mutated Genes in Cancers . . . . . . . . 390--401
Hao Jiang and
Yushan Qiu and
Wenpin Hou and
Xiaoqing Cheng and
Man Yi Yim and
Wai-Ki Ching Drug Side-Effect Profiles Prediction:
From Empirical to Structural Risk
Minimization . . . . . . . . . . . . . . 402--410
Zhan-Ying Feng and
Yong Wang ELF: Extract Landmark Features By
Optimizing Topology Maintenance,
Redundancy, and Specificity . . . . . . 411--421
Jianing Xi and
Ao Li and
Minghui Wang HetRCNA: a Novel Method to Identify
Recurrent Copy Number Alternations from
Heterogeneous Tumor Samples Based on
Matrix Decomposition Framework . . . . . 422--434
Ye Liu and
Michael K. Ng and
Stephen Wu Multi-Domain Networks Association for
Biological Data Using Block Signed Graph
Clustering . . . . . . . . . . . . . . . 435--448
Jifan Shi and
Juan Zhao and
Xiaoping Liu and
Luonan Chen and
Tiejun Li Quantifying Direct Dependencies in
Biological Networks by Multiscale
Association Analysis . . . . . . . . . . 449--458
Rajan Kapoor and
Aniruddha Datta and
Chao Sima and
Jianping Hua and
Rosana Lopes and
Michael L. Bittner A Gaussian Mixture-Model Exploiting
Pathway Knowledge for Dissecting Cancer
Heterogeneity . . . . . . . . . . . . . 459--468
Paola Lecca and
Angela Re A Reaction-Based Model of the State
Space of Chemical Reaction Systems
Enables Efficient Simulations . . . . . 469--482
Kaspar Riesen and
Miquel Ferrer and
Horst Bunke Approximate Graph Edit Distance in
Quadratic Time . . . . . . . . . . . . . 483--494
Xiujuan Lei and
Xiaoqin Yang and
Fang-Xiang Wu Artificial Fish Swarm Optimization Based
Method to Identify Essential Proteins 495--505
Rishika Sen and
Somnath Tagore and
Rajat K. De ASAPP: Architectural Similarity-Based
Automated Pathway Prediction System and
Its Application in Host-Pathogen
Interactions . . . . . . . . . . . . . . 506--515
Haifen Chen and
D. A. K. Maduranga and
Piyushkumar A. Mundra and
Jie Zheng Bayesian Data Fusion of Gene Expression
and Histone Modification Profiles for
Inference of Gene Regulatory Network . . 516--525
Hossein Yazdani and
Leo L. Cheng and
David C. Christiani and
Azam Yazdani Bounded Fuzzy Possibilistic Method
Reveals Information about Lung Cancer
through Analysis of Metabolomics . . . . 526--535
Yujie Li and
Heng Huang and
Hanbo Chen and
Tianming Liu Deep Neural Networks for \em In Situ
Hybridization Grid Completion and
Clustering . . . . . . . . . . . . . . . 536--546
Abazar Arabameri and
Davud Asemani and
Pegah Teymourpour Detection of Colorectal Carcinoma Based
on Microbiota Analysis Using Generalized
Regression Neural Networks and Nonlinear
Feature Selection . . . . . . . . . . . 547--557
Shengping Yang and
Mitchell S. Wachtel and
Jiangrong Wu DFseq: Distribution-Free Method to
Detect Differential Gene Expression for
RNA-Sequencing Data . . . . . . . . . . 558--565
Hussain Ahmed Chowdhury and
Dhruba Kumar Bhattacharyya and
Jugal Kumar Kalita Differential Expression Analysis of
RNA-seq Reads: Overview, Taxonomy, and
Tools . . . . . . . . . . . . . . . . . 566--586
Hang Wang and
Jianing Xi and
Minghui Wang and
Ao Li Dual-Layer Strengthened Collaborative
Topic Regression Modeling for Predicting
Drug Sensitivity . . . . . . . . . . . . 587--598
Lishuang Li and
Yang Liu and
Meiyue Qin Extracting Biomedical Events with
Parallel Multi-Pooling Convolutional
Neural Networks . . . . . . . . . . . . 599--607
Aydin Saribudak and
Adarsha A. Subick and
Na Hyun Kim and
Joshua A. Rutta and
M. Ümit Uyar Gene Expressions, Hippocampal Volume
Loss, and MMSE Scores in Computation of
Progression and Pharmacologic Therapy
Effects for Alzheimer's Disease . . . . 608--622
Qiu Xiao and
Jiawei Luo and
Cheng Liang and
Guanghui Li and
Jie Cai and
Pingjian Ding and
Ying Liu Identifying lncRNA and mRNA
Co-Expression Modules from Matched
Expression Data in Ovarian Cancer . . . 623--634
Ali Karimnezhad and
David R. Bickel Incorporating Prior Knowledge about
Genetic Variants into the Analysis of
Genetic Association Data: an Empirical
Bayes Approach . . . . . . . . . . . . . 635--646
Rongrong Zhang and
Ming Hu and
Yu Zhu and
Zhaohui Qin and
Ke Deng and
Jun S. Liu Inferring Spatial Organization of
Individual Topologically Associated
Domains via Piecewise Helical Model . . 647--656
Zhen Cao and
Shihua Zhang Probe Efficient Feature Representation
of Gapped $K$-mer Frequency Vectors from
Sequences Using Deep Neural Networks . . 657--667
Paul Fergus and
Casimiro Curbelo Montañez and
Basma Abdulaimma and
Paulo Lisboa and
Carl Chalmers and
Beth Pineles Utilizing Deep Learning and Genome Wide
Association Studies for Epistatic-Driven
Preterm Birth Classification in
African--American Women . . . . . . . . 668--678
Qinhu Zhang and
Lin Zhu and
Wenzheng Bao and
De-Shuang Huang Weakly-Supervised Convolutional Neural
Network Architecture for Predicting
Protein--DNA Binding . . . . . . . . . . 679--689
Saurav Mallik and
Sanghamitra Bandyopadhyay WeCoMXP: Weighted Connectivity Measure
Integrating Co-Methylation,
Co-Expression and Protein-Protein
Interactions for Gene-Module Detection 690--703
Samah J. Fodeh and
Taihua Li and
Haya Jarad and
Basmah Safdar Classification of Patients with Coronary
Microvascular Dysfunction . . . . . . . 704--711
Jie Zheng and
Jinyan Li and
Yun Zheng Guest Editorial for the 29th
International Conference on Genome
Informatics (GIW 2018) . . . . . . . . . 726--727
Xingyu Liao and
Min Li and
You Zou and
Fang-Xiang Wu and
Yi Pan and
Jianxin Wang An Efficient Trimming Algorithm based on
Multi-Feature Fusion Scoring Model for
NGS Data . . . . . . . . . . . . . . . . 728--738
Shunfang Wang and
Zicheng Cao and
Mingyuan Li and
Yaoting Yue G-DipC: an Improved Feature
Representation Method for Short
Sequences to Predict the Type of Cargo
in Cell-Penetrating Peptides . . . . . . 739--747
Yong Liu and
Min Wu and
Chenghao Liu and
Xiao-Li Li and
Jie Zheng SL$^2$MF: Predicting Synthetic Lethality
in Human Cancers via Logistic Matrix
Factorization . . . . . . . . . . . . . 748--757
Junrong Song and
Wei Peng and
Feng Wang An Entropy-Based Method for Identifying
Mutual Exclusive Driver Genes in Cancer 758--768
Jiajie Peng and
Linjiao Zhu and
Yadong Wang and
Jin Chen Mining Relationships among Multiple
Entities in Biological Networks . . . . 769--776
Heng Yao and
Yunjia Shi and
Jihong Guan and
Shuigeng Zhou Accurately Detecting Protein Complexes
by Graph Embedding and Combining
Functions with Interactions . . . . . . 777--787
Yuanyuan Ma and
Xiaohua Hu and
Tingting He and
Xingpeng Jiang Clustering and Integrating of
Heterogeneous Microbiome Data by Joint
Symmetric Nonnegative Matrix
Factorization with Laplacian
Regularization . . . . . . . . . . . . . 788--795
Renjie Tan and
Jixuan Wang and
Xiaoliang Wu and
Liran Juan and
Tianjiao Zhang and
Rui Ma and
Qing Zhan and
Tao Wang and
Shuilin Jin and
Qinghua Jiang and
Yadong Wang ERDS-Exome: a Hybrid Approach for Copy
Number Variant Detection from
Whole-Exome Sequencing Data . . . . . . 796--803
Shaoliang Peng and
Xiaoyu Zhang and
Wenhe Su and
Dong Dong and
Yutong Lu and
Xiangke Liao and
Kai Lu and
Canqun Yang and
Jie Liu and
Weiliang Zhu and
Dongqing Wei High-Scalable Collaborated Parallel
Framework for Large-Scale Molecular
Dynamic Simulation on Tianhe-2
Supercomputer . . . . . . . . . . . . . 804--816
Min Li and
Xiangmao Meng and
Ruiqing Zheng and
Fang-Xiang Wu and
Yaohang Li and
Yi Pan and
Jianxin Wang Identification of Protein Complexes by
Using a Spatial and Temporal Active
Protein Interaction Network . . . . . . 817--827
Mohammad Arifur Rahman and
Nathan LaPierre and
Huzefa Rangwala Phenotype Prediction from Metagenomic
Data Using Clustering and Assembly with
Multiple Instance Learning (CAMIL) . . . 828--840
Lishuang Li and
Yuxin Jiang Integrating Language Model and Reading
Control Gate in BLSTM-CRF for Biomedical
Named Entity Recognition . . . . . . . . 841--846
Binbin Wu and
Min Li and
Xingyu Liao and
Junwei Luo and
Fang-Xiang Wu and
Yi Pan and
Jianxin Wang MEC: Misassembly Error Correction in
Contigs based on Distribution of
Paired-End Reads and Statistics of
GC-contents . . . . . . . . . . . . . . 847--857
Huiru Zheng and
Haiying Wang and
Richard J. Dewhurst and
Rainer Roehe Improving the Inference of Co-Occurrence
Networks in the Bovine Rumen Microbiome 858--867
Fatima Zare and
Sardar Ansari and
Kayvan Najarian and
Sheida Nabavi Preprocessing Sequence Coverage Data for
More Precise Detection of Copy Number
Variations . . . . . . . . . . . . . . . 868--876
Junwei Luo and
Jianxin Wang and
Juan Shang and
Huimin Luo and
Min Li and
Fang-Xiang Wu and
Yi Pan GapReduce: a Gap Filling Algorithm Based
on Partitioned Read Sets . . . . . . . . 877--886
Haigen Hu and
Qiu Guan and
Shengyong Chen and
Zhiwei Ji and
Yao Lin Detection and Recognition for Life State
of Cell Cancer Using Two-Stage Cascade
CNNs . . . . . . . . . . . . . . . . . . 887--898
Yuansheng Liu and
Chaowang Lan and
Michael Blumenstein and
Jinyan Li Bi-Level Error Correction for PacBio
Long Reads . . . . . . . . . . . . . . . 899--905
Peng Ni and
Jianxin Wang and
Ping Zhong and
Yaohang Li and
Fang-Xiang Wu and
Yi Pan Constructing Disease Similarity Networks
Based on Disease Module Theory . . . . . 906--915
Zhi-Zhong Chen and
Youta Harada and
Yuna Nakamura and
Lusheng Wang Faster Exact Computation of rSPR
Distance via Better Approximation . . . 916--929
Zaobo He and
Jiguo Yu and
Ji Li and
Qilong Han and
Guangchun Luo and
Yingshu Li Inference Attacks and Controls on
Genotypes and Phenotypes for Individual
Genomic Data . . . . . . . . . . . . . . 930--937
Jin Zhao and
Haodi Feng and
Daming Zhu and
Chi Zhang and
Ying Xu IsoTree: a New Framework for de novo
Transcriptome Assembly from RNA-seq
Reads . . . . . . . . . . . . . . . . . 938--948
Jingsong Zhang and
Jianmei Guo and
Ming Zhang and
Xiangtian Yu and
Xiaoqing Yu and
Weifeng Guo and
Tao Zeng and
Luonan Chen Efficient Mining Multi-Mers in a Variety
of Biological Sequences . . . . . . . . 949--958
Fatima Boukari and
Sokratis Makrogiannis Automated Cell Tracking Using Motion
Prediction-Based Matching and Event
Handling . . . . . . . . . . . . . . . . 959--971
Lei Wang and
Zhu-Hong You and
De-Shuang Huang and
Fengfeng Zhou Combining High Speed ELM Learning with a
Deep Convolutional Neural Network
Feature Encoding for Predicting
Protein-RNA Interactions . . . . . . . . 972--980
Qiwen Kang and
Neil Moore and
Christopher L. Schardl and
Ruriko Yoshida CURatio: Genome-Wide Phylogenomic
Analysis Method Using Ratios of Total
Branch Lengths . . . . . . . . . . . . . 981--989
Sarawoot Som-In and
Warangkhana Kimpan Enhancing of Particle Swarm Optimization
Based Method for Multiple Motifs
Detection in DNA Sequences Collections 990--998
Somayeh Bakhteh and
Alireza Ghaffari-Hadigheh and
Nader Chaparzadeh Identification of Minimum Set of Master
Regulatory Genes in Gene Regulatory
Networks . . . . . . . . . . . . . . . . 999--1009
Haswanth Vundavilli and
Aniruddha Datta and
Chao Sima and
Jianping Hua and
Rosana Lopes and
Michael Bittner In Silico Design and Experimental
Validation of Combination Therapy for
Pancreatic Cancer . . . . . . . . . . . 1010--1018
De-Shuang Huang and
Vitoantonio Bevilacqua and
Michael Gromiha Guest Editorial for Special Section on
the 14th International Conference on
Intelligent Computing (ICIC) . . . . . . 1474--1475
Wook Lee and
Kyungsook Han Constructive Prediction of Potential RNA
Aptamers for a Protein Target . . . . . 1476--1482
Zhen Shen and
Su-Ping Deng and
De-Shuang Huang Capsule Network for Predicting
RNA--Protein Binding Preferences Using
Hybrid Feature . . . . . . . . . . . . . 1483--1492
Huiqiang Jia and
Haichao Wei and
Daming Zhu and
Jingjing Ma and
Hai Yang and
Ruizhi Wang and
Xianzhong Feng PASA: Identifying More Credible
Structural Variants of Hedou12 . . . . . 1493--1503
Jian Liu and
Zhi Qu and
Mo Yang and
Jialiang Sun and
Shuhui Su and
Lei Zhang Jointly Integrating VCF-Based Variants
and OWL-Based Biomedical Ontologies in
MongoDB . . . . . . . . . . . . . . . . 1504--1515
Pengwei Hu and
Yu-An Huang and
Keith C. C. Chan and
Zhu-Hong You Learning Multimodal Networks From
Heterogeneous Data for Prediction of
lncRNA--miRNA Interactions . . . . . . . 1516--1524
Xiaoli Lin and
Xiaolong Zhang and
Xin Xu Efficient Classification of Hot Spots
and Hub Protein Interfaces by Recursive
Feature Elimination and Gradient
Boosting . . . . . . . . . . . . . . . . 1525--1534
Jade Hind and
Paulo Lisboa and
Abir J. Hussain and
Dhiya Al-Jumeily A Novel Approach to Detecting Epistasis
using Random Sampling Regularisation . . 1535--1545
Jianqiang Li and
Xiaofeng Shi and
Zhu-Hong You and
Hai-Cheng Yi and
Zhuangzhuang Chen and
Qiuzhen Lin and
Min Fang Using Weighted Extreme Learning Machine
Combined With Scale-Invariant Feature
Transform to Predict Protein-Protein
Interactions From Protein Evolutionary
Information . . . . . . . . . . . . . . 1546--1554
Maryam Shahdoust and
Hossein Mahjub and
Hamid Pezeshk and
Mehdi Sadeghi A Network-Based Comparison Between
Molecular Apocrine Breast Cancer Tumor
and Basal and Luminal Tumors by Joint
Graphical Lasso . . . . . . . . . . . . 1555--1562
Qian Guo and
Tianhong Pan and
Shan Chen and
Xiaobo Zou and
Dorothy Yu Huang A Novel Edge Effect Detection Method for
Real-Time Cellular Analyzer Using
Functional Principal Component Analysis 1563--1572
Nirmala Sharma and
Harish Sharma and
Ajay Sharma An Effective Solution for Large Scale
Single Machine Total Weighted Tardiness
Problem using Lunar Cycle Inspired
Artificial Bee Colony Algorithm . . . . 1573--1581
Aisharjya Sarkar and
Yilmaz Atay and
Alana Lorraine Erickson and
Ivan Arisi and
Cesare Saltini and
Tamer Kahveci An Efficient Algorithm for Identifying
Mutated Subnetworks Associated with
Survival in Cancer . . . . . . . . . . . 1582--1594
Cheng Yan and
Guihua Duan and
Fang-Xiang Wu and
Yi Pan and
Jianxin Wang BRWMDA:Predicting Microbe-Disease
Associations Based on Similarities and
Bi-Random Walk on Disease and Microbe
Networks . . . . . . . . . . . . . . . . 1595--1604
Chen Peng and
Yang Zheng and
De-Shuang Huang Capsule Network Based Modeling of
Multi-omics Data for Discovery of Breast
Cancer-Related Genes . . . . . . . . . . 1605--1612
Pourya Naderi Yeganeh and
M. Taghi Mostafavi Causal Disturbance Analysis: a Novel
Graph Centrality Based Method for
Pathway Enrichment Analysis . . . . . . 1613--1624
Jirí Filipovic and
Ondrej Vávra and
Jan Plhák and
David Bednár and
Sérgio M. Marques and
Jan Brezovský and
Ludek Matyska and
Jirí Damborský CaverDock: a Novel Method for the Fast
Analysis of Ligand Transport . . . . . . 1625--1638
Xiangxiang Zeng and
Yinglai Lin and
Yuying He and
Linyuan Lü and
Xiaoping Min and
Alfonso Rodríguez-Patón Deep Collaborative Filtering for
Prediction of Disease Genes . . . . . . 1639--1647
Ashish Ranjan and
Md Shah Fahad and
David Fernández-Baca and
Akshay Deepak and
Sudhakar Tripathi Deep Robust Framework for Protein
Function Prediction Using
Variable-Length Protein Sequences . . . 1648--1659
Sunildatt Sharma and
Sanjeev Narayan Sharma and
Rajiv Saxena Identification of Short Exons Disunited
by a Short Intron in Eukaryotic DNA
Regions . . . . . . . . . . . . . . . . 1660--1670
Min Wang and
Ting-Zhu Huang and
Jian Fang and
Vince D. Calhoun and
Yu-Ping Wang Integration of Imaging (epi)Genomics
Data for the Study of Schizophrenia
Using Group Sparse Joint Nonnegative
Matrix Factorization . . . . . . . . . . 1671--1681
Lan Zhao and
Hong Yan MCNF: a Novel Method for Cancer
Subtyping by Integrating Multi-Omics and
Clinical Data . . . . . . . . . . . . . 1682--1690
Matthieu Pichené and
Sucheendra K. Palaniappan and
Eric Fabre and
Blaise Genest Modeling Variability in Populations of
Cells Using Approximated Multivariate
Distributions . . . . . . . . . . . . . 1691--1702
Yuan Zhang and
Haihong Liu and
Zhouhong Li and
Zhonghua Miao and
Jin Zhou Oscillatory Dynamics of p53-Mdm2 Circuit
in Response to DNA Damage Caused by
Ionizing Radiation . . . . . . . . . . . 1703--1713
Sijia Wu and
Xiaoming Wu and
Jie Tian and
Xiaobo Zhou and
Liyu Huang PredictFP2: a New Computational Model to
Predict Fusion Peptide Domain in All
Retroviruses . . . . . . . . . . . . . . 1714--1720
Laiyi Fu and
Qinke Peng and
Ling Chai Predicting DNA Methylation States with
Hybrid Information Based Deep-Learning
Model . . . . . . . . . . . . . . . . . 1721--1728
Sushmita Paul and
Madhumita RFCM$^3$: Computational Method for
Identification of miRNA--mRNA Regulatory
Modules in Cervical Cancer . . . . . . . 1729--1740
Zhen Shen and
Su-Ping Deng and
De-Shuang Huang RNA-Protein Binding Sites Prediction via
Multi Scale Convolutional Gated
Recurrent Unit Networks . . . . . . . . 1741--1750
Saad Raza and
Ghulam Abbas and
Syed Sikander Azam Screening Pipeline for Flavivirus Based
Inhibitors for Zika Virus NS1 . . . . . 1751--1761
Keisuke Kawano and
Satoshi Koide and
Chie Imamura Seq2seq Fingerprint with Byte-Pair
Encoding for Predicting Changes in
Protein Stability upon Single Point
Mutation . . . . . . . . . . . . . . . . 1762--1772
Da Yan and
Xin Gao and
Samah J. Fodeh and
Jake Y. Chen Guest Editorial for Selected Papers from
BIOKDD 2018 and DMBIH 2018 . . . . . . . 1832--1834
Michael Sokolovsky and
Francisco Guerrero and
Sarun Paisarnsrisomsuk and
Carolina Ruiz and
Sergio A. Alvarez Deep Learning for Automated Feature
Discovery and Classification of Sleep
Stages . . . . . . . . . . . . . . . . . 1835--1845
Matthew B. A. McDermott and
Jennifer Wang and
Wen-Ning Zhao and
Steven D. Sheridan and
Peter Szolovits and
Isaac Kohane and
Stephen J. Haggarty and
Roy H. Perlis Deep Learning Benchmarks on L1000 Gene
Expression Data . . . . . . . . . . . . 1846--1857
Jingyi Zheng and
Fushing Hsieh and
Linqiang Ge A Data-Driven Approach to Predict and
Classify Epileptic Seizures from
Brain-Wide Calcium Imaging Video Data 1858--1870
Hongming Xu and
Sunho Park and
Tae Hyun Hwang Computerized Classification of Prostate
Cancer Gleason Scores from Whole Slide
Images . . . . . . . . . . . . . . . . . 1871--1882
Shreyasi Pathak and
Jorit van Rossen and
Onno Vijlbrief and
Jeroen Geerdink and
Christin Seifert and
Maurice van Keulen Post-Structuring Radiology Reports of
Breast Cancer Patients for Clinical
Quality Assurance . . . . . . . . . . . 1883--1894
Enrique Noriega-Atala and
Paul D. Hein and
Shraddha S. Thumsi and
Zechy Wong and
Xia Wang and
Sean M. Hendryx and
Clayton T. Morrison Extracting Inter-Sentence Relations for
Associating Biological Context with
Events in Biomedical Texts . . . . . . . 1895--1906
Jonathon A. Gibbs and
Michael P. Pound and
Andrew P. French and
Darren M. Wells and
Erik H. Murchie and
Tony P. Pridmore Active Vision and Surface Reconstruction
for $3$D Plant Shoot Modelling . . . . . 1907--1917
Xiaoyang Jing and
Qiwen Dong and
Daocheng Hong and
Ruqian Lu Amino Acid Encoding Methods for Protein
Sequences: a Comprehensive Review and
Assessment . . . . . . . . . . . . . . . 1918--1931
Soumya Paul and
Cui Su and
Jun Pang and
Andrzej Mizera An Efficient Approach Towards the
Source-Target Control of Boolean
Networks . . . . . . . . . . . . . . . . 1932--1945
Letu Qingge and
Killian Smith and
Sean Jungst and
Baihui Wang and
Qing Yang and
Binhai Zhu Approaching the One-Sided Exemplar
Adjacency Number Problem . . . . . . . . 1946--1954
Mohammad Bozlul Karim and
Ming Huang and
Naoaki Ono and
Shigehiko Kanaya and
Md. Altaf-Ul-Amin BiClusO: a Novel Biclustering Approach
and Its Application to Species-VOC
Relational Data . . . . . . . . . . . . 1955--1965
Guang-Hui Liu and
Bei-Wei Zhang and
Gang Qian and
Bin Wang and
Bo Mao and
Isabelle Bichindaritz Bioimage-Based Prediction of Protein
Subcellular Location in Human Tissue
with Ensemble Features and Deep Networks 1966--1980
Nicola Paoletti and
Kin Sum Liu and
Hongkai Chen and
Scott A. Smolka and
Shan Lin Data-Driven Robust Control for a
Closed-Loop Artificial Pancreas . . . . 1981--1993
Jian Liu and
Qiuru Liu and
Lei Zhang and
Shuhui Su and
Yongzhuang Liu Enabling Massive XML-Based Biological
Data Management in HBase . . . . . . . . 1994--2004
Pratik Dutta and
Sriparna Saha and
Saraansh Chopra and
Varnika Miglani Ensembling of Gene Clusters Utilizing
Deep Learning and Protein-Protein
Interaction Information . . . . . . . . 2005--2016
Lun Hu and
Pengwei Hu and
Xin Luo and
Xiaohui Yuan and
Zhu-Hong You Incorporating the Coevolving Information
of Substrates in Predicting HIV-1
Protease Cleavage Sites . . . . . . . . 2017--2028
Xinyi Yu and
Wenge Rong and
Jingshuang Liu and
Deyu Zhou and
Yuanxin Ouyang and
Zhang Xiong LSTM-Based End-to-End Framework for
Biomedical Event Extraction . . . . . . 2029--2039
Ehsan Kazemi and
Matthias Grossglauser MPGM: Scalable and Accurate Multiple
Network Alignment . . . . . . . . . . . 2040--2052
Wei Zhang and
Jia Xu and
Xiufen Zou Predicting Essential Proteins by
Integrating Network Topology,
Subcellular Localization Information,
Gene Expression Profile and GO
Annotation Data . . . . . . . . . . . . 2053--2061
Zengyou He and
Can Zhao and
Hao Liang and
Bo Xu and
Quan Zou Protein Complexes Identification with
Family-Wise Error Rate Control . . . . . 2062--2073
Midusha Shrestha and
Truong X. Tran and
Bidhan Bhattarai and
Marc L. Pusey and
Ramazan S. Aygun Schema Matching and Data Integration
with Consistent Naming on Protein
Crystallization Screens . . . . . . . . 2074--2085
Thomas C. Carroll and
Jude-Thaddeus Ojiaku and
Prudence W. H. Wong Semiglobal Sequence Alignment with Gaps
Using GPU . . . . . . . . . . . . . . . 2086--2097
Shun-Ichi Azuma and
Toshimitsu Kure and
Toshiharu Sugie Structural Bistability Analysis of
Flower-Shaped and Chain-Shaped Boolean
Networks . . . . . . . . . . . . . . . . 2098--2106
John A. Rhodes Topological Metrizations of Trees, and
New Quartet Methods of Tree Inference 2107--2118
Gui-Jun Zhang and
Xiao-Qi Wang and
Lai-Fa Ma and
Liu-Jing Wang and
Jun Hu and
Xiao-Gen Zhou Two-Stage Distance Feature-based
Optimization Algorithm for \em De novo
Protein Structure Prediction . . . . . . 2119--2130
Adeola Ogunleye and
Qing-Guo Wang XGBoost Model for Chronic Kidney Disease
Diagnosis . . . . . . . . . . . . . . . 2131--2140
Matteo Manica and
Raphael Polig and
Mitra Purandare and
Roland Mathis and
Christoph Hagleitner and
María Rodríguez Martínez FPGA Accelerated Analysis of Boolean
Gene Regulatory Networks . . . . . . . . 2141--2147
Ming Xiao and
Xiangyu Yang and
Jun Yu and
Le Zhang CGIDLA: Developing the Web Server for
CpG Island Related Density and LAUPs
(Lineage-Associated Underrepresented
Permutations) Study . . . . . . . . . . 2148--2154
Manuela Petti and
Daniele Bizzarri and
Antonella Verrienti and
Rosa Falcone and
Lorenzo Farina Connectivity Significance for Disease
Gene Prioritization in an Expanding
Universe . . . . . . . . . . . . . . . . 2155--2161
Carlos Martín-Vide and
Miguel A. Vega-Rodríguez \booktitleAlgorithms for Computational
Biology: Sixth Edition . . . . . . . . . 1--1
Thien Le and
Aaron Sy and
Erin K. Molloy and
Qiuyi Zhang and
Satish Rao and
Tandy Warnow Using Constrained-INC for Large-Scale
Gene Tree and Species Tree Estimation 2--15
Sridevi Maharaj and
Taotao Qian and
Zarin Ohiba and
Wayne Hayes Common Neighbors Extension of the Sticky
Model for PPI Networks Evaluated by
Global and Local Graphlet Similarity . . 16--26
Peng Xiao and
Xingyu Cai and
Sanguthevar Rajasekaran EMS3: an Improved Algorithm for Finding
Edit-Distance Based Motifs . . . . . . . 27--37
Liu Liu and
Reza Zare and
Shuihua Wang Guest Editorial: Transfer Learning
Methods Used in Medical Imaging and
Health Informatics . . . . . . . . . . . 38--39
Yizhang Jiang and
Xiaoqing Gu and
Dongrui Wu and
Wenlong Hang and
Jing Xue and
Shi Qiu and
Chin-Teng Lin A Novel Negative-Transfer-Resistant
Fuzzy Clustering Model With a Shared
Cross-Domain Transfer Latent Space and
its Application to Brain CT Image
Segmentation . . . . . . . . . . . . . . 40--52
Kaijian Xia and
TongGuang Ni and
Hongsheng Yin and
Bo Chen Cross-Domain Classification Model With
Knowledge Utilization Maximization for
Recognition of Epileptic EEG Signals . . 53--61
Chenxi Huang and
Yisha Lan and
Gaowei Xu and
Xiaojun Zhai and
Jipeng Wu and
Fan Lin and
Nianyin Zeng and
Qingqi Hong and
E. Y. K. Ng and
Yonghong Peng and
Fei Chen and
Guokai Zhang A Deep Segmentation Network of
Multi-Scale Feature Fusion Based on
Attention Mechanism for IVOCT Lumen
Contour . . . . . . . . . . . . . . . . 62--69
Pengjiang Qian and
Jiamin Zheng and
Qiankun Zheng and
Yuan Liu and
Tingyu Wang and
Rose Al Helo and
Atallah Baydoun and
Norbert Avril and
Rodney J. Ellis and
Harry Friel and
Melanie S. Traughber and
Ajit Devaraj and
Bryan Traughber and
Raymond F. Muzic Transforming UTE-mDixon MR
Abdomen--Pelvis Images Into CT by
Jointly Leveraging Prior Knowledge and
Partial Supervision . . . . . . . . . . 70--82
Rishav Singh and
Tanveer Ahmed and
Abhinav Kumar and
Amit Kumar Singh and
Anil Kumar Pandey and
Sanjay Kumar Singh Imbalanced Breast Cancer Classification
Using Transfer Learning . . . . . . . . 83--93
Xiang Yu and
Cheng Kang and
David S. Guttery and
Seifedine Kadry and
Yang Chen and
Yu-Dong Zhang ResNet--SCDA--50 for Breast Abnormality
Classification . . . . . . . . . . . . . 94--102
Jintai Chen and
Haochao Ying and
Xuechen Liu and
Jingjing Gu and
Ruiwei Feng and
Tingting Chen and
Honghao Gao and
Jian Wu A Transfer Learning Based
Super-Resolution Microscopy for Biopsy
Slice Images: The Joint Methods
Perspective . . . . . . . . . . . . . . 103--113
Yong Jin and
Zhenjiang Qian and
Shengrong Gong and
Weiyong Yang Learning Transferable Driven and Drone
Assisted Sustainable and Robust Regional
Disease Surveillance for Smart
Healthcare . . . . . . . . . . . . . . . 114--125
Hansaim Lim and
Lei Xie A New Weighted Imputed
Neighborhood-Regularized
Tri-Factorization One-Class
Collaborative Filtering Algorithm:
Application to Target Gene Prediction of
Transcription Factors . . . . . . . . . 126--137
Daniel R. Allen and
Sharma V. Thankachan and
Bojian Xu An Ultra-Fast and Parallelizable
Algorithm for Finding $k$-Mismatch
Shortest Unique Substrings . . . . . . . 138--148
P. Tabaszewski and
P. Górecki and
A. Markin and
T. Anderson and
O. Eulenstein Consensus of All Solutions for
Intractable Phylogenetic Tree Inference 149--161
Srilakshmi Pattabiraman and
Tandy Warnow Profile Hidden Markov Models Are Not
Identifiable . . . . . . . . . . . . . . 162--172
Jiaqi Guan and
Runzhe Li and
Sheng Yu and
Xuegong Zhang A Method for Generating Synthetic
Electronic Medical Record Text . . . . . 173--182
Ruiqi Qin and
Lei Duan and
Huiru Zheng and
Jesse Li-Ling and
Kaiwen Song and
Yidan Zhang An Ontology-Independent Representation
Learning for Similar Disease Detection
Based on Multi-Layer Similarity Network 183--193
Wei Long and
Tiange Li and
Yang Yang and
Hong-Bin Shen FlyIT: \bionameDrosophila Embryogenesis
Image Annotation based on Image Tiling
and Convolutional Neural Networks . . . 194--204
Suyang Dai and
Yuxia Ding and
Zihan Zhang and
Wenxuan Zuo and
Xiaodi Huang and
Shanfeng Zhu GrantExtractor: Accurate Grant Support
Information Extraction from Biomedical
Fulltext Based on Bi-LSTM-CRF . . . . . 205--215
Bo Yang and
Yupei Zhang and
Shanmin Pang and
Xuequn Shang and
Xueqing Zhao and
Minghui Han Integrating Multi-Omic Data With Deep
Subspace Fusion Clustering for Cancer
Subtype Prediction . . . . . . . . . . . 216--226
Lei Du and
Kefei Liu and
Xiaohui Yao and
Shannon L. Risacher and
Junwei Han and
Andrew J. Saykin and
Lei Guo and
Li Shen Multi-Task Sparse Canonical Correlation
Analysis with Application to Multi-Modal
Brain Imaging Genetics . . . . . . . . . 227--239
Jianliang Gao and
Ling Tian and
Tengfei Lv and
Jianxin Wang and
Bo Song and
Xiaohua Hu Protein2Vec: Aligning Multiple PPI
Networks with Representation Learning 240--249
Cameron Chalk and
Niels Kornerup and
Wyatt Reeves and
David Soloveichik Composable Rate-Independent Computation
in Continuous Chemical Reaction Networks 250--260
Sara-Jane Dunn and
Hillel Kugler and
Boyan Yordanov Formal Analysis of Network Motifs Links
Structure to Function in Biological
Programs . . . . . . . . . . . . . . . . 261--271
Pavol Bokes and
Michal Hojcka and
Abhyudai Singh MicroRNA Based Feedforward Control of
Intrinsic Gene Expression Noise . . . . 272--282
Keenan Breik and
Cameron Chalk and
David Doty and
David Haley and
David Soloveichik Programming Substrate-Independent
Kinetic Barriers With Thermodynamic
Binding Networks . . . . . . . . . . . . 283--295
Min Zeng and
Min Li and
Zhihui Fei and
Fang-Xiang Wu and
Yaohang Li and
Yi Pan and
Jianxin Wang A Deep Learning Framework for
Identifying Essential Proteins by
Integrating Multiple Types of Biological
Information . . . . . . . . . . . . . . 296--305
Quanhua Mu and
Jiguang Wang CNAPE: a Machine Learning Method for
Copy Number Alteration Prediction from
Gene Expression . . . . . . . . . . . . 306--311
Titinunt Kitrungrotsakul and
Xian-Hau Han and
Yutaro Iwamoto and
Satoko Takemoto and
Hideo Yokota and
Sari Ipponjima and
Tomomi Nemoto and
Wei Xiong and
Yen-Wei Chen A Cascade of 2.5D CNN and Bidirectional
CLSTM Network for Mitotic Cell Detection
in $4$D Microscopy Image . . . . . . . . 396--404
Wen Zhang and
Zhishuai Li and
Wenzheng Guo and
Weitai Yang and
Feng Huang A Fast Linear Neighborhood
Similarity-Based Network Link Inference
Method to Predict MicroRNA--Disease
Associations . . . . . . . . . . . . . . 405--415
Biing-Feng Wang and
Krister M. Swenson A Faster Algorithm for Computing the
Kernel of Maximum Agreement Subtrees . . 416--430
Yunpei Xu and
Hong-Dong Li and
Yi Pan and
Feng Luo and
Fang-Xiang Wu and
Jianxin Wang A Gene Rank Based Approach for Single
Cell Similarity Assessment and
Clustering . . . . . . . . . . . . . . . 431--442
Sahar Araghi and
Thanh Nguyen A Hybrid Supervised Approach to Human
Population Identification Using Genomics
Data . . . . . . . . . . . . . . . . . . 443--454
Hsin-Hung Chou and
Ching-Tien Hsu and
Li-Hsuan Chen and
Yue-Cheng Lin and
Sun-Yuan Hsieh A Novel Branch-and-Bound Algorithm for
the Protein Folding Problem in the $3$D
HP Model . . . . . . . . . . . . . . . . 455--462
Huimin Luo and
Jianxin Wang and
Cheng Yan and
Min Li and
Fang-Xiang Wu and
Yi Pan A Novel Drug Repositioning Approach
Based on Collaborative Metric Learning 463--471
Seyedeh Shaghayegh Sadeghi and
Mohammad Reza Keyvanpour An Analytical Review of Computational
Drug Repurposing . . . . . . . . . . . . 472--488
Anupam Banerjee and
Kuntal Pal and
Pralay Mitra An Evolutionary Profile Guided Greedy
Parallel Replica-Exchange Monte Carlo
Search Algorithm for Rapid Convergence
in Protein Design . . . . . . . . . . . 489--499
Wanrong Gu and
Ziye Zhang and
Xianfen Xie and
Yichen He An Improved Muti-Task Learning Algorithm
for Analyzing Cancer Survival Data . . . 500--511
Kevin Chow and
Aisharjya Sarkar and
Rasha Elhesha and
Pietro Cinaglia and
Ahmet Ay and
Tamer Kahveci \pkgANCA: Alignment-Based Network
Construction Algorithm . . . . . . . . . 512--524
Miguel González and
Cristina Gutiérrez and
Rodrigo Martínez Bayesian Inference in Y-Linked Two-Sex
Branching Processes with Mutations: ABC
Approach . . . . . . . . . . . . . . . . 525--538
Xiguo Yuan and
Jiaao Yu and
Jianing Xi and
Liying Yang and
Junliang Shang and
Zhe Li and
Junbo Duan \pkgCNV\_IFTV: an Isolation Forest and
Total Variation-Based Detection of CNVs
from Short-Read Sequencing Data . . . . 539--549
Sourav Biswas and
Sumanta Ray and
Sanghamitra Bandyopadhyay Colored Network Motif Analysis by
Dynamic Programming Approach: an
Application in Host Pathogen Interaction
Network . . . . . . . . . . . . . . . . 550--561
Jacob C. Kimmel and
Andrew S. Brack and
Wallace F. Marshall Deep Convolutional and Recurrent Neural
Networks for Cell Motility
Discrimination and Prediction . . . . . 562--574
Min Li and
Yake Wang and
Ruiqing Zheng and
Xinghua Shi and
Yaohang Li and
Fang-Xiang Wu and
Jianxin Wang DeepDSC: a Deep Learning Method to
Predict Drug Sensitivity of Cancer Cell
Lines . . . . . . . . . . . . . . . . . 575--582
Jingrong Zhang and
Zihao Wang and
Zhiyong Liu and
Fa Zhang Improve the Resolution and Parallel
Performance of the Three-Dimensional
Refine Algorithm in RELION Using CUDA
and MPI . . . . . . . . . . . . . . . . 583--595
Muhammad Awais and
Waqar Hussain and
Yaser Daanial Khan and
Nouman Rasool and
Sher Afzal Khan and
Kuo-Chen Chou \pkgiPhosH-PseAAC: Identify
Phosphohistidine Sites in Proteins by
Blending Statistical Moments and
Position Relative Features According to
the Chou's 5-Step Rule and General
Pseudo Amino Acid Composition . . . . . 596--610
Cheng Yan and
Guihua Duan and
Fang-Xiang Wu and
Yi Pan and
Jianxin Wang \pkgMCHMDA: Predicting Microbe-Disease
Associations Based on Similarities and
Low-Rank Matrix Completion . . . . . . . 611--620
Cheng Peng and
Xinyu Wu and
Wen Yuan and
Xinran Zhang and
Yu Zhang and
Ying Li \pkgMGRFE: Multilayer Recursive Feature
Elimination Based on an Embedded Genetic
Algorithm for Cancer Classification . . 621--632
Alexandre Gondeau and
Zahia Aouabed and
Mohamed Hijri and
Pedro R. Peres-Neto and
Vladimir Makarenkov Object Weighting: a New Clustering
Approach to Deal with Outliers and
Cluster Overlap in Computational Biology 633--643
Alireza Karbalayghareh and
Xiaoning Qian and
Edward R. Dougherty Optimal Bayesian Transfer Learning for
Count Data . . . . . . . . . . . . . . . 644--655
Andrés F. López-Lopera and
Nicolas Durrande and
Mauricio A. Álvarez Physically-Inspired Gaussian Process
Models for Post-Transcriptional
Regulation in \bionameDrosophila . . . . 656--666
Qinhu Zhang and
Zhen Shen and
De-Shuang Huang Predicting in-vitro Transcription
Factor Binding Sites Using DNA Sequence
$+$ Shape . . . . . . . . . . . . . . . 667--676
Jingxuan Qiu and
Tianyi Qiu and
Qingli Dong and
Dongpo Xu and
Xiang Wang and
Qi Zhang and
Jing Pan and
Qing Liu Predicting the Antigenic Relationship of
Foot-and-Mouth Disease Virus for Vaccine
Selection Through a Computational Model 677--685
Chen Zhang and
Yanrui Ding Probing the Relation Between Community
Evolution in Dynamic Residue Interaction
Networks and Xylanase Thermostability 686--696
Gui-Jun Zhang and
Teng-Yu Xie and
Xiao-Gen Zhou and
Liu-Jing Wang and
Jun Hu Protein Structure Prediction Using
Population-Based Algorithm Guided by
Information Entropy . . . . . . . . . . 697--707
Saikat Biswas and
Pabitra Mitra and
Krothapalli Sreenivasa Rao Relation Prediction of Co-Morbid
Diseases Using Knowledge Graph
Completion . . . . . . . . . . . . . . . 708--717
Xiaona Song and
Mi Wang and
Shuai Song and
Choon Ki Ahn Sampled-Data State Estimation of
Reaction Diffusion Genetic Regulatory
Networks via Space-Dividing Approaches 718--730
Guimu Guo and
Hongzhi Chen and
Da Yan and
James Cheng and
Jake Y. Chen and
Zechen Chong Scalable De Novo Genome Assembly Using a
Pregel-Like Graph-Parallel System . . . 731--744
Da Yan and
Sharma Thankachan and
Jake Y. Chen Guest Editorial for Selected Papers From
BIOKDD 2019 . . . . . . . . . . . . . . 809--810
Vineet K. Raghu and
Xiaoyu Ge and
Arun Balajiee and
Daniel J. Shirer and
Isha Das and
Panayiotis V. Benos and
Panos K. Chrysanthis A Pipeline for Integrated Theory and
Data-Driven Modeling of Biomedical Data 811--822
Tianwen Jiang and
Qingkai Zeng and
Tong Zhao and
Bing Qin and
Ting Liu and
Nitesh V. Chawla and
Meng Jiang Biomedical Knowledge Graphs Construction
From Conditional Statements . . . . . . 823--835
Jithin K. Sreedharan and
Krzysztof Turowski and
Wojciech Szpankowski Revisiting Parameter Estimation in
Biological Networks: Influence of
Symmetries . . . . . . . . . . . . . . . 836--849
Ke Yan and
Zhiwei Ji and
Qun Jin and
Qing-Guo Wang Guest Editorial: Machine Learning for
AI-Enhanced Healthcare and Medical
Services: New Development and Promising
Solution . . . . . . . . . . . . . . . . 850--851
Sheng Lian and
Lei Li and
Guiren Lian and
Xiao Xiao and
Zhiming Luo and
Shaozi Li A Global and Local Enhanced Residual
U-Net for Accurate Retinal Vessel
Segmentation . . . . . . . . . . . . . . 852--862
Huijuan Lu and
Huiyun Gao and
Minchao Ye and
Xiuhui Wang A Hybrid Ensemble Algorithm Combining
AdaBoost and Genetic Algorithm for
Cancer Classification with Gene
Expression Data . . . . . . . . . . . . 863--870
Xiaodan Yan and
Baojiang Cui and
Yang Xu and
Peilin Shi and
Ziqi Wang A Method of Information Protection for
Collaborative Deep Learning under GAN
Model Attack . . . . . . . . . . . . . . 871--881
Qingchen Zhang and
Changchuan Bai and
Laurence T. Yang and
Zhikui Chen and
Peng Li and
Hang Yu A Unified Smart Chinese Medicine
Framework for Healthcare and Medical
Services . . . . . . . . . . . . . . . . 882--890
Dehua Chen and
Meihua Huang and
Weimin Li Knowledge-Powered Deep Breast Tumor
Classification With Multiple Medical
Reports . . . . . . . . . . . . . . . . 891--901
Yiyuan Chen and
Yufeng Wang and
Liang Cao and
Qun Jin CCFS: a Confidence-Based Cost-Effective
Feature Selection Scheme for Healthcare
Data Classification . . . . . . . . . . 902--911
Xiaokang Zhou and
Yue Li and
Wei Liang CNN-RNN Based Intelligent Recommendation
for Online Medical Pre-Diagnosis Support 912--921
Lu Yan and
Weihong Huang and
Liming Wang and
Song Feng and
Yonghong Peng and
Jie Peng Data-Enabled Digestive Medicine: a New
Big Data Analytics Platform . . . . . . 922--931
Mauricio Guevara Souza and
Edgar E. Vallejo and
Karol Estrada Detecting Clustered Independent Rare
Variant Associations Using Genetic
Algorithms . . . . . . . . . . . . . . . 932--939
Yongjin Zhou and
Weijian Huang and
Pei Dong and
Yong Xia and
Shanshan Wang D-UNet: a Dimension-Fusion U Shape
Network for Chronic Stroke Lesion
Segmentation . . . . . . . . . . . . . . 940--950
Yaqi Wang and
Lingling Sun and
Qun Jin Enhanced Diagnosis of Pneumothorax with
an Improved Real-Time Augmentation for
Imbalanced Chest X-rays Data Based on
DCNN . . . . . . . . . . . . . . . . . . 951--962
Xiuhui Wang and
Shiling Feng and
Wei Qi Yan Human Gait Recognition Based on
Self-Adaptive Hidden Markov Model . . . 963--972
Jayanta Kumar Pal and
Shubhra Sankar Ray and
Sankar K. Pal Identifying Drug Resistant miRNAs Using
Entropy Based Ranking . . . . . . . . . 973--984
Bing Wang and
Changqing Mei and
Yuanyuan Wang and
Yuming Zhou and
Mu-Tian Cheng and
Chun-Hou Zheng and
Lei Wang and
Jun Zhang and
Peng Chen and
Yan Xiong Imbalance Data Processing Strategy for
Protein Interaction Sites Prediction . . 985--994
Xiran Jiang and
Jiaxin Li and
Yangyang Kan and
Tao Yu and
Shijie Chang and
Xianzheng Sha and
Hairong Zheng and
Yahong Luo and
Shanshan Wang MRI Based Radiomics Approach With Deep
Learning for Prediction of Vessel
Invasion in Early-Stage Cervical Cancer 995--1002
Cheng Li and
Jingxu Xu and
Qiegen Liu and
Yongjin Zhou and
Lisha Mou and
Zuhui Pu and
Yong Xia and
Hairong Zheng and
Shanshan Wang Multi-View Mammographic Density
Classification by Dilated and
Attention-Guided Residual Learning . . . 1003--1013
Ali Cakmak and
M. Hasan Celik Personalized Metabolic Analysis of
Diseases . . . . . . . . . . . . . . . . 1014--1025
Wenyan Wang and
Yuming Zhou and
Mu-Tian Cheng and
Yan Wang and
Chun-Hou Zheng and
Yan Xiong and
Peng Chen and
Zhiwei Ji and
Bing Wang Potential Pathogenic Genes
Prioritization Based on Protein Domain
Interaction Network Analysis . . . . . . 1026--1034
Souad Bouasker and
Wissem Inoubli and
Sadok Ben Yahia and
Gayo Diallo Pregnancy Associated Breast Cancer Gene
Expressions: New Insights on Their
Regulation Based on Rare Correlated
Patterns . . . . . . . . . . . . . . . . 1035--1048
Jiechen Li and
Haochen Zhao and
Zhanwei Xuan and
Jingwen Yu and
Xiang Feng and
Bo Liao and
Lei Wang A Novel Approach for Potential Human
LncRNA-Disease Association Prediction
Based on Local Random Walk . . . . . . . 1049--1059
Min Liu and
Yalan Liu and
Weili Qian and
Yaonan Wang DeepSeed Local Graph Matching for
Densely Packed Cells Tracking . . . . . 1060--1069
Zhen Zhang and
Junwei Luo and
Juan Shang and
Min Li and
Fang-Xiang Wu and
Yi Pan and
Jianxin Wang Deletion Detection Method Using the
Distribution of Insert Size and a
Precise Alignment Strategy . . . . . . . 1070--1081
Tingting Yu and
Jianxing Liu and
Qingshuang Zeng and
Ligang Wu Dissipativity-Based Filtering for
Switched Genetic Regulatory Networks
with Stochastic Disturbances and
Time-Varying Delays . . . . . . . . . . 1082--1092
Ying An and
Nengjun Huang and
Xianlai Chen and
Fangxiang Wu and
Jianxin Wang High-Risk Prediction of Cardiovascular
Diseases via Attention-Based Deep Neural
Networks . . . . . . . . . . . . . . . . 1093--1105
Qingfeng Chen and
Dehuan Lai and
Wei Lan and
Ximin Wu and
Baoshan Chen and
Jin Liu and
Yi-Ping Phoebe Chen and
Jianxin Wang ILDMSF: Inferring Associations Between
Long Non-Coding RNA and Disease Based on
Multi-Similarity Fusion . . . . . . . . 1106--1112
Dong-Qing Wei and
Aman Chandra Kaushik and
Gurudeeban Selvaraj and
Yi Pan Editorial: Computational Genomics and
Molecular Medicine for Emerging COVID-19 1227--1229
Chunmei Cui and
Chuanbo Huang and
Wanlu Zhou and
Xiangwen Ji and
Fenghong Zhang and
Liang Wang and
Yuan Zhou and
Qinghua Cui \geneAGTR2, One Possible Novel Key Gene
for the Entry of SARS-CoV-2 Into Human
Cells . . . . . . . . . . . . . . . . . 1230--1233
Yadunath Pathak and
Piyush Kumar Shukla and
K. V. Arya Deep Bidirectional Classification Model
for COVID-19 Disease Infected Patients 1234--1241
Jinxiong Lv and
Shikui Tu and
Lei Xu Detection of Phenotype-Related Mutations
of COVID-19 via the Whole Genomic Data 1242--1249
Ming Xiao and
Guangdi Liu and
Jianghang Xie and
Zichun Dai and
Zihao Wei and
Ziyao Ren and
Jun Yu and
Le Zhang 2019nCoVAS: Developing the Web Service
for Epidemic Transmission Prediction,
Genome Analysis, and Psychological
Stress Assessment for 2019-nCoV . . . . 1250--1261
Chandrabose Selvaraj and
Dhurvas Chandrasekaran Dinesh and
Umesh Panwar and
Evzen Boura and
Sanjeev Kumar Singh High-Throughput Screening and Quantum
Mechanics for Identifying Potent
Inhibitors Against Mac1 Domain of
SARS-CoV-2 Nsp3 . . . . . . . . . . . . 1262--1270
Broto Chakrabarty and
Dibyajyoti Das and
Gopalakrishnan Bulusu and
Arijit Roy Network-Based Analysis of Fatal
Comorbidities of COVID-19 and Potential
Therapeutics . . . . . . . . . . . . . . 1271--1280
Elmeri M. Jokinen and
Krishnasamy Gopinath and
Sami T. Kurkinen and
Olli T. Pentikäinen Detection of Binding Sites on SARS-CoV-2
Spike Protein Receptor-Binding Domain by
Molecular Dynamics Simulations in Mixed
Solvents . . . . . . . . . . . . . . . . 1281--1289
Deshan Zhou and
Shaoliang Peng and
Dong-Qing Wei and
Wu Zhong and
Yutao Dou and
Xiaolan Xie LUNAR: Drug Screening for Novel
Coronavirus Based on Representation
Learning Graph Convolutional Network . . 1290--1298
Aman Chandra Kaushik and
Aamir Mehmood and
Gurudeeban Selvaraj and
Xiaofeng Dai and
Yi Pan and
Dong-Qing Wei CoronaPep: an Anti-Coronavirus Peptide
Generation Tool . . . . . . . . . . . . 1299--1304
Zhimiao Yu and
Jiarui Lu and
Yuan Jin and
Yang Yang KenDTI: an Ensemble Model for Predicting
Drug-Target Interaction by Integrating
Multi-Source Information . . . . . . . . 1305--1314
ShanShan Hu and
DeNan Xia and
Benyue Su and
Peng Chen and
Bing Wang and
Jinyan Li A Convolutional Neural Network System to
Discriminate Drug-Target Interactions 1315--1324
Enze Liu and
Jin Li and
Garrett H. Kinnebrew and
Pengyue Zhang and
Yan Zhang and
Lijun Cheng and
Lang Li A Fast and Furious Bayesian Network and
Its Application of Identifying Colon
Cancer to Liver Metastasis Gene
Regulatory Networks . . . . . . . . . . 1325--1335
Hector Carrillo-Cabada and
Jeremy Benson and
Asghar M. Razavi and
Brianna Mulligan and
Michel A. Cuendet and
Harel Weinstein and
Michela Taufer and
Trilce Estrada A Graphic Encoding Method for
Quantitative Classification of Protein
Structure and Representation of
Conformational Changes . . . . . . . . . 1336--1349
Aiying Zhang and
Jian Fang and
Wenxing Hu and
Vince D. Calhoun and
Yu-Ping Wang A Latent Gaussian Copula Model for Mixed
Data Analysis in Brain Imaging Genetics 1350--1360
Ulavappa B. Angadi and
Krishna Kumar Chaturvedi and
Sudhir Srivastava and
Anil Rai A Novel Way of Comparing Protein $3$D
Structure Using Graph Partitioning
Approach . . . . . . . . . . . . . . . . 1361--1368
Liguang Wang and
Yujia Wang and
Yi Fu and
Yunge Gao and
Jiawei Du and
Chen Yang and
Jianxiao Liu AFSBN: a Method of Artificial Fish Swarm
Optimizing Bayesian Network for
Epistasis Detection . . . . . . . . . . 1369--1383
Ziying Yang and
Guoxian Yu and
Maozu Guo and
Jiantao Yu and
Xiangliang Zhang and
Jun Wang CDPath: Cooperative Driver Pathways
Discovery Using Integer Linear
Programming and Markov Clustering . . . 1384--1395
Bing Nan Li and
Xinle Wang and
Rong Wang and
Teng Zhou and
Rongke Gao and
Edward J. Ciaccio and
Peter H. Green Celiac Disease Detection From
Videocapsule Endoscopy Images Using
Strip Principal Component Analysis . . . 1396--1404
Yan Ge and
Philipp Rosendahl and
Claudio Durán and
Nicole Töpfner and
Sara Ciucci and
Jochen Guck and
Carlo Vittorio Cannistraci Cell Mechanics Based Computational
Classification of Red Blood Cells Via
Machine Intelligence Applied to
Morpho-Rheological Markers . . . . . . . 1405--1415
Wenju Zhang and
Zhewei Liang and
Xin Chen and
Lei Xin and
Baozhen Shan and
Zhigang Luo and
Ming Li ChimST: an Efficient Spectral Library
Search Tool for Peptide Identification
from Chimeric Spectra in Data-Dependent
Acquisition . . . . . . . . . . . . . . 1416--1425
Sidharth Maheshwari and
Venkateshwarlu Y. Gudur and
Rishad Shafik and
Ian Wilson and
Alex Yakovlev and
Amit Acharyya CORAL: Verification-Aware OpenCL Based
Read Mapper for Heterogeneous Systems 1426--1438
Yingwen Zhao and
Jun Wang and
Maozu Guo and
Xiangliang Zhang and
Guoxian Yu Cross-Species Protein Function
Prediction with Asynchronous-Random Walk 1439--1450
Jun Zhang and
Qingcai Chen and
Bin Liu DeepDRBP-2L: a New Genome Annotation
Predictor for Identifying DNA-Binding
Proteins and RNA-Binding Proteins Using
Convolutional Neural Network and Long
Short-Term Memory . . . . . . . . . . . 1451--1463
Shaoliang Peng and
Yaning Yang and
Wei Liu and
Fei Li and
Xiangke Liao Discriminant Projection Shared
Dictionary Learning for Classification
of Tumors Using Gene Expression Data . . 1464--1473
Furkan Ozden and
Metin Can Siper and
Necmi Acarsoy and
Tugrulcan Elmas and
Bryan Marty and
Xinjian Qi and
A. Ercument Cicek DORMAN: Database of Reconstructed
MetAbolic Networks . . . . . . . . . . . 1474--1480
Yue Hu and
Jin-Xing Liu and
Ying-Lian Gao and
Junliang Shang DSTPCA: Double-Sparse Constrained Tensor
Principal Component Analysis Method for
Feature Selection . . . . . . . . . . . 1481--1491
Xingyu Liao and
Min Li and
Junwei Luo and
You Zou and
Fang-Xiang Wu and
Yi-Pan and
Feng Luo and
Jianxin Wang EPGA-SC: a Framework for \em de novo
Assembly of Single-Cell Sequencing Reads 1492--1503
Afsaneh Javadi and
Faezeh Keighobadi and
Vahab Nekoukar and
Marzieh Ebrahimi Finite-Set Model Predictive Control of
Melanoma Cancer Treatment Using
Signaling Pathway Inhibitor of Cancer
Stem Cell . . . . . . . . . . . . . . . 1504--1511
Chao Wang and
Lei Gong and
Shiming Lei and
Haijie Fang and
Xi Li and
Aili Wang and
Xuehai Zhou GenSeq+: a Scalable High-Performance
Accelerator for Genome Sequencing . . . 1512--1523
Kaijian Xia and
Yizhang Jiang and
Yudong Zhang and
Wen Si Guest Editorial: Advanced
Machine-Learning Methods for
Brain-Machine Interfacing or
Brain-Computer Interfacing . . . . . . . 1643--1644
Xiaotong Gu and
Zehong Cao and
Alireza Jolfaei and
Peng Xu and
Dongrui Wu and
Tzyy-Ping Jung and
Chin-Teng Lin EEG-Based Brain-Computer Interfaces
(BCIs): a Survey of Recent Studies on
Signal Sensing Technologies and
Computational Intelligence Approaches
and Their Applications . . . . . . . . . 1645--1666
Yuanpeng Zhang and
Ziyuan Zhou and
Wenjie Pan and
Heming Bai and
Wei Liu and
Li Wang and
Chuang Lin Epilepsy Signal Recognition Using Online
Transfer TSK Fuzzy Classifier Underlying
Classification Error and Joint
Distribution Consensus Regularization 1667--1678
Xiaoqing Gu and
Cong Zhang and
TongGuang Ni A Hierarchical Discriminative Sparse
Representation Classifier for EEG Signal
Detection . . . . . . . . . . . . . . . 1679--1687
Zhihan Lv and
Liang Qiao and
Qingjun Wang and
Francesco Piccialli Advanced Machine-Learning Methods for
Brain-Computer Interfacing . . . . . . . 1688--1698
Bo Lin and
Shuiguang Deng and
Honghao Gao and
Jianwei Yin A Multi-Scale Activity Transition
Network for Data Translation in EEG
Signals Decoding . . . . . . . . . . . . 1699--1709
Shuaiqi Liu and
Xu Wang and
Ling Zhao and
Jie Zhao and
Qi Xin and
Shui-Hua Wang Subject-Independent Emotion Recognition
of EEG Signals Based on Dynamic
Empirical Convolutional Neural Network 1710--1721
Chenxi Huang and
Yutian Xiao and
Gaowei Xu Predicting Human Intention-Behavior
Through EEG Signal Analysis Using
Multi-Scale CNN . . . . . . . . . . . . 1722--1729
De-Shuang Huang and
Vitoantonio Bevilacqua and
M. Michael Gromiha Guest Editorial for Special Section on
the 15th International Conference on
Intelligent Computing (ICIC) . . . . . . 1730--1732
Kai Zheng and
Zhu-Hong You and
Lei Wang and
Yi-Ran Li and
Ji-Ren Zhou and
Hai-Tao Zeng MISSIM: an Incremental Learning-Based
Model With Applications to the
Prediction of miRNA-Disease Association 1733--1742
Qinhu Zhang and
Dailun Wang and
Kyungsook Han and
De-Shuang Huang Predicting TF-DNA Binding Motifs from
ChIP-seq Datasets Using the Bag-Based
Classifier Combined With a Multi-Fold
Learning Scheme . . . . . . . . . . . . 1743--1751
Hongjie Wu and
Huajing Ling and
Lei Gao and
Qiming Fu and
Weizhong Lu and
Yijie Ding and
Min Jiang and
Haiou Li Empirical Potential Energy Function
Toward ab Initio Folding G
Protein-Coupled Receptors . . . . . . . 1752--1762
Yue Liu and
Shu-Lin Wang and
Jun-Feng Zhang and
Wei Zhang and
Su Zhou and
Wen Li DMFMDA: Prediction of Microbe-Disease
Associations Based on Deep Matrix
Factorization Using Bayesian
Personalized Ranking . . . . . . . . . . 1763--1772
Xinguo Lu and
Xinyu Wang and
Li Ding and
Jinxin Li and
Yan Gao and
Keren He frDriver: a Functional Region Driver
Identification for Protein Sequence . . 1773--1783
Jiang Xie and
Chang Zhao and
Jiamin Sun and
Jiaxin Li and
Fuzhang Yang and
Jiao Wang and
Qing Nie Prediction of Essential Genes in
Comparison States Using Machine Learning 1784--1792
Qinhu Zhang and
Wenbo Yu and
Kyungsook Han and
Asoke K. Nandi and
De-Shuang Huang Multi-Scale Capsule Network for
Predicting DNA-Protein Binding Sites . . 1793--1800
Menglu Li and
Yanan Wang and
Fuyi Li and
Yun Zhao and
Mengya Liu and
Sijia Zhang and
Yannan Bin and
A. Ian Smith and
Geoffrey I. Webb and
Jian Li and
Jiangning Song and
Junfeng Xia A Deep Learning-Based Method for
Identification of Bacteriophage-Host
Interaction . . . . . . . . . . . . . . 1801--1810
Xiguo Yuan and
Junping Li and
Jun Bai and
Jianing Xi A Local Outlier Factor-Based Detection
of Copy Number Variations From NGS Data 1811--1820
Hai-Hui Huang and
Yong Liang A Novel Cox Proportional Hazards Model
for High-Dimensional Genomic Data in
Cancer Prognosis . . . . . . . . . . . . 1821--1830
Jinhao Zhang and
Zehua Zhang and
Lianrong Pu and
Jijun Tang and
Fei Guo AIEpred: an Ensemble Predictive Model of
Classifier Chain to Identify
Anti-Inflammatory Peptides . . . . . . . 1831--1840
Ying Qian and
Yu Zhang and
Jiongmin Zhang Alignment-Free Sequence Comparison With
Multiple $k$ Values . . . . . . . . . . 1841--1849
Benlian Xu and
Jian Shi and
Mingli Lu and
Jinliang Cong and
Ling Wang and
Brett Nener An Automated Cell Tracking Approach With
Multi-Bernoulli Filtering and Ant Colony
Labor Division . . . . . . . . . . . . . 1850--1863
Gautam Kumar and
Rajnish Kumar and
Manoj Kumar Pal and
Nilotpal Pramanik and
Tapobrata Lahiri and
Ankita Gupta and
Saket Pandey APT: an Automated Probe Tracker From
Gene Expression Data . . . . . . . . . . 1864--1874
Yue Zhang and
Chunfang Zheng and
Sindeed Islam and
Yong-Min Kim and
David Sankoff Branching Out to Speciation in a Model
of Fractionation: The Malvaceae . . . . 1875--1884
Atefeh Ghasemnejad and
Samira Bazmara and
Mahsa Shadmani and
Kamran Pooshang Bagheri Designing a New Multi-Epitope Pertussis
Vaccine with Highly Population Coverage
Based on a Novel Sequence and Structural
Filtration Algorithm . . . . . . . . . . 1885--1892
Xiguo Yuan and
Xiangyan Xu and
Haiyong Zhao and
Junbo Duan ERINS: Novel Sequence Insertion
Detection by Constructing an Extended
Reference . . . . . . . . . . . . . . . 1893--1901
Chetna Kumari and
Muhammad Abulaish and
Naidu Subbarao Exploring Molecular Descriptors and
Fingerprints to Predict mTOR Kinase
Inhibitors using Machine Learning
Techniques . . . . . . . . . . . . . . . 1902--1913
Jiaojiao Chen and
Jianbo Jiao and
Shengfeng He and
Guoqiang Han and
Jing Qin Few-Shot Breast Cancer Metastases
Classification via Unsupervised Cell
Ranking . . . . . . . . . . . . . . . . 1914--1923
Belal Medhat and
Ahmed Shawish FLR: a Revolutionary Alignment-Free
Similarity Analysis Methodology for
DNA-Sequences . . . . . . . . . . . . . 1924--1936
Cangzhi Jia and
Meng Zhang and
Cunshuo Fan and
Fuyi Li and
Jiangning Song Formator: Predicting Lysine Formylation
Sites Based on the Most Distant
Undersampling and Safe-Level Synthetic
Minority Oversampling . . . . . . . . . 1937--1945
Srinivas Aluru Editorial: From the New Editor-in-Chief 2058--2058
Carlos Martín-Vide and
Miguel A. Vega-Rodríguez \booktitleAlgorithms for Computational
Biology: Seventh Edition . . . . . . . . 2059--2060
Tathagata Debnath and
Mingzhou Song Fast Optimal Circular Clustering and
Applications on Round Genomes . . . . . 2061--2071
Shaoheng Liang and
Qingnan Liang and
Rui Chen and
Ken Chen Stratified Test Accurately Identifies
Differentially Expressed Genes Under
Batch Effects in Single-Cell Data . . . 2072--2079
Andre Rodrigues Oliveira and
Géraldine Jean and
Guillaume Fertin and
Klairton Lima Brito and
Ulisses Dias and
Zanoni Dias Sorting Permutations by Intergenic
Operations . . . . . . . . . . . . . . . 2080--2093
Gabriel Siqueira and
Klairton Lima Brito and
Ulisses Dias and
Zanoni Dias Heuristics for Genome Rearrangement
Distance With Replicated Genes . . . . . 2094--2108
Nickolas Steinauer and
Kevin Zhang and
Chun Guo and
Jinsong Zhang Computational Modeling of Gene-Specific
Transcriptional Repression, Activation
and Chromatin Interactions in
Leukemogenesis by LASSO-Regularized
Logistic Regression . . . . . . . . . . 2109--2122
Louxin Zhang and
Shaoliang Peng and
Yi-Ping Phoebe Chen and
David Sankoff and
Guoliang Li and
Hong-Yu Zhang Guest Editorial for the 17th Asia
Pacific Bioinformatics Conference . . . 2123--2124
Pawe\l Górecki and
Oliver Eulenstein and
Jerzy Tiuryn The Unconstrained Diameters of the
Duplication-Loss Cost and the Loss Cost 2125--2135
Melissa Grueter and
Kalani Duran and
Ramya Ramalingam and
Ran Libeskind-Hadas Reconciliation Reconsidered: In Search
of a Most Representative Reconciliation
in the Duplication-Transfer-Loss Model 2136--2143
Haoxing Du and
Yi Sheng Ong and
Marina Knittel and
Ross Mawhorter and
Nuo Liu and
Gianluca Gross and
Reiko Tojo and
Ran Libeskind-Hadas and
Yi-Chieh Wu Multiple Optimal Reconciliations Under
the Duplication-Loss-Coalescence Model 2144--2156
Hongzhe Guo and
Yilei Fu and
Yan Gao and
Junyi Li and
Yadong Wang and
Bo Liu deGSM: Memory Scalable Construction Of
Large Scale de Bruijn Graph . . . . . . 2157--2166
Cui Su and
Jun Pang and
Soumya Paul Towards Optimal Decomposition of Boolean
Networks . . . . . . . . . . . . . . . . 2167--2176
Tom Hartmann and
Max Bannach and
Martin Middendorf Sorting Signed Permutations by Inverse
Tandem Duplication Random Losses . . . . 2177--2188
Nguyen Quoc Khanh Le and
Binh P. Nguyen Prediction of FMN Binding Sites in
Electron Transport Chains Based on $2$-D
CNN and PSSM Profiles . . . . . . . . . 2189--2197
Ozan Firat Özgül and
Batuhan Bardak and
Mehmet Tan A Convolutional Deep Clustering
Framework for Gene Expression Time
Series . . . . . . . . . . . . . . . . . 2198--2207
Fuhao Zhang and
Hong Song and
Min Zeng and
Fang-Xiang Wu and
Yaohang Li and
Yi Pan and
Min Li A Deep Learning Framework for Gene
Ontology Annotations With Sequence- and
Network-Based Information . . . . . . . 2208--2217
Zilu Wang and
Qinghui Hong and
Xiaoping Wang A Memristive Circuit Implementation of
Eyes State Detection in Fatigue Driving
Based on Biological Long Short-Term
Memory Rule . . . . . . . . . . . . . . 2218--2229
Pablo Nascimento da Silva and
Alexandre Plastino and
Fabio Fabris and
Alex A. Freitas A Novel Feature Selection Method for
Uncertain Features: an Application to
the Prediction of Pro-\slash
Anti-Longevity Genes . . . . . . . . . . 2230--2238
Dong Li and
Zhisong Pan and
Guyu Hu and
Graham Anderson and
Shan He Active Module Identification From
Multilayer Weighted Gene Co-Expression
Networks: a Continuous Optimization
Approach . . . . . . . . . . . . . . . . 2239--2248
Qiong Fang and
Dewei Su and
Wilfred Ng and
Jianlin Feng An Effective Biclustering-Based
Framework for Identifying Cell
Subpopulations From scRNA-seq Data . . . 2249--2260
Junyi Chen and
Junhui Hou and
Ka-Chun Wong Categorical Matrix Completion With
Active Learning for High-Throughput
Screening . . . . . . . . . . . . . . . 2261--2270
Oyetunji E. Ogundijo and
Kaiyi Zhu and
Xiaodong Wang and
Dimitris Anastassiou Characterizing Intra-Tumor Heterogeneity
From Somatic Mutations Without
Copy-Neutral Assumption . . . . . . . . 2271--2280
Shaoxun Yuan and
Haitao Li and
Jiansheng Wu and
Xiao Sun Classification of Mild Cognitive
Impairment With Multimodal Data Using
Both Labeled and Unlabeled Samples . . . 2281--2290
Anne-Marie Lyne and
Le\"\ila Perié Comparing Phylogenetic Approaches to
Reconstructing Cell Lineage From
Microsatellites With Missing Data . . . 2291--2301
Guillermo Blanco and
Borja Sánchez and
Lorena Ruiz and
Florentino Fdez-Riverola and
Abelardo Margolles and
Anália Lourenço Computational Approach to the Systematic
Prediction of Glycolytic Abilities:
Looking Into Human Microbiota . . . . . 2302--2313
Eyla Willing and
Jens Stoye and
Marília D. V. Braga Computing the Inversion-Indel Distance 2314--2326
Junzhong Ji and
Yao Yao Convolutional Neural Network With
Graphical Lasso to Extract Sparse
Topological Features for Brain Disease
Classification . . . . . . . . . . . . . 2327--2338
Annalisa Occhipinti and
Youssef Hamadi and
Hillel Kugler and
Christoph M. Wintersteiger and
Boyan Yordanov and
Claudio Angione Discovering Essential Multiple Gene
Effects Through Large Scale
Optimization: an Application to Human
Cancer Metabolism . . . . . . . . . . . 2339--2352
Min Zeng and
Chengqian Lu and
Zhihui Fei and
Fang-Xiang Wu and
Yaohang Li and
Jianxin Wang and
Min Li DMFLDA: a Deep Learning Framework for
Predicting lncRNA--Disease Associations 2353--2363
Sunny Sun and
Yi-Ping Phoebe Chen Editorial . . . . . . . . . . . . . . . 1--2
Hui Bi and
Shumei Cao and
Hanying Yan and
Zhongyi Jiang and
Jun Zhang and
Ling Zou Resting State Functional Connectivity
Analysis During General Anesthesia: a
High-Density EEG Study . . . . . . . . . 3--13
Pierrick Craveur and
Tarun J. Narwani and
Narayanaswamy Srinivasan and
Jean-Christophe Gelly and
Joseph Rebehmed and
Alexandre G. de Brevern Shaking the $ \beta $-Bulges . . . . . . 14--18
Madhusudan Paul and
Ashish Anand A New Family of Similarity Measures for
Scoring Confidence of Protein
Interactions Using Gene Ontology . . . . 19--30
Runhua Huang and
Chengchuang Lin and
Aihua Yin and
Hanbiao Chen and
Li Guo and
Gansen Zhao and
Xiaomao Fan and
Shuangyin Li and
Jinji Yang A Clinical Dataset and Various Baselines
for Chromosome Instance Segmentation . . 31--39
Ying Qian and
Xuelian Li and
Qian Zhang and
Jiongmin Zhang \pkgSPP-CPI: Predicting
Compound--Protein Interactions Based On
Neural Networks . . . . . . . . . . . . 40--47
Jin Zhao and
Haodi Feng and
Daming Zhu and
Yu Lin \pkgMultiTrans: an Algorithm for Path
Extraction Through Mixed Integer Linear
Programming for Transcriptome Assembly 48--56
Anuradha Wickramarachchi and
Yu Lin \pkgGraphPlas: Refined Classification of
Plasmid Sequences Using Assembly Graphs 57--67
Shuai Lu and
Yuguang Li and
Fei Wang and
Xiaofei Nan and
Shoutao Zhang Leveraging Sequential and Spatial
Neighbors Information by Using CNNs
Linked With GCNs for Paratope Prediction 68--74
Tzu-Hsien Yang An Aggregation Method to Identify the
RNA Meta-Stable Secondary Structure and
its Functionally Interpretable Structure
Ensemble . . . . . . . . . . . . . . . . 75--86
Trinh-Trung-Duong Nguyen and
The-Anh Tran and
Nguyen-Quoc-Khanh Le and
Dinh-Minh Pham and
Yu-Yen Ou An Extensive Examination of Discovering
5-Methylcytosine Sites in Genome-Wide
DNA Promoters Using Machine Learning
Based Approaches . . . . . . . . . . . . 87--94
Barbara Di Camillo and
Giuseppe Nicosia Guest Editorial: Deep Learning For
Genomics . . . . . . . . . . . . . . . . 95--96
Jim Clauwaert and
Willem Waegeman Novel Transformer Networks for Improved
Sequence Labeling in genomics . . . . . 97--106
Zhong Chen and
Wensheng Zhang and
Hongwen Deng and
Kun Zhang Effective Cancer Subtype and Stage
Prediction via Dropfeature-DNNs . . . . 107--120
Francisco Cristovao and
Silvia Cascianelli and
Arif Canakoglu and
Mark Carman and
Luca Nanni and
Pietro Pinoli and
Marco Masseroli Investigating Deep Learning Based Breast
Cancer Subtyping Using Pan-Cancer and
Multi-Omic Data . . . . . . . . . . . . 121--134
Gautier Viaud and
Prasanna Mayilvahanan and
Paul-Henry Courn\`ede Representation Learning for the
Clustering of Multi-Omics Data . . . . . 135--145
Tuan Nguyen and
Giang T. T. Nguyen and
Thin Nguyen and
Duc-Hau Le Graph Convolutional Networks for Drug
Response Prediction . . . . . . . . . . 146--154
Satyajit Mahapatra and
Vivek Raj Gupta and
Sitanshu Sekhar Sahu and
Ganapati Panda Deep Neural Network and Extreme Gradient
Boosting Based Hybrid Classifier for
Improved Prediction of Protein-Protein
Interaction . . . . . . . . . . . . . . 155--165
Zhipeng Cai and
Min Li and
Pavel Skums Guest Editors' Introduction to the
Special Section on Bioinformatics
Research and Applications . . . . . . . 166--167
Cheng Yan and
Guihua Duan and
Yayan Zhang and
Fang-Xiang Wu and
Yi Pan and
Jianxin Wang Predicting Drug-Drug Interactions Based
on Integrated Similarity and
Semi-Supervised Learning . . . . . . . . 168--179
Fengpan Zhao and
Pavel Skums and
Alex Zelikovsky and
Eric L. Sevigny and
Monica Haavisto Swahn and
Sheryl M. Strasser and
Yan Huang and
Yubao Wu Computational Approaches to Detect
Illicit Drug Ads and Find Vendor
Communities Within Social Media
Platforms . . . . . . . . . . . . . . . 180--191
Sudipta Acharya and
Laizhong Cui and
Yi Pan A Refined 3-in-1 Fused Protein
Similarity Measure: Application in
Threshold-Free Hub Detection . . . . . . 192--206
Zhipeng Cai and
Giri Narasimhan and
Pavel Skums Guest Editors' Introduction to the
Special Section on Bioinformatics
Research and Applications . . . . . . . 207--208
Shan Gao and
Renmin Han and
Xiangrui Zeng and
Zhiyong Liu and
Min Xu and
Fa Zhang Macromolecules Structural Classification
With a $3$D Dilated Dense Network in
Cryo-Electron Tomography . . . . . . . . 209--219
Davide Storato and
Matteo Comin \pkgK2Mem: Discovering Discriminative
$K$-mers From Sequencing Data for
Metagenomic Reads Classification . . . . 220--229
Saurav Dhar and
Chengchen Zhang and
Ion I. Mandoiu and
Mukul S. Bansal \pkgTNet: Transmission Network Inference
Using Within-Host Strain Diversity and
its Application to Geographical Tracking
of COVID-19 Spread . . . . . . . . . . . 230--242
Jun Wang and
Huiling Zhang and
Wei Ren and
Maozu Guo and
Guoxian Yu \pkgEpiMC: Detecting Epistatic
Interactions Using Multiple Clusterings 243--254
Sunil Kumar P. V. and
Adheeba Thahsin and
Manju M. and
Gopakumar G. A Heterogeneous Information Network
Model for Long Non-Coding RNA Function
Prediction . . . . . . . . . . . . . . . 255--266
Hansheng Li and
JianPing Li and
Yuxin Kang and
Chunbao Wang and
Feihong Liu and
Wenli Hui and
Qirong Bo and
Lei Cui and
Jun Feng and
Lin Yang A Novel Encoding and Decoding
Calibration Guiding Pathway for
Pathological Image Analysis . . . . . . 267--274
Sadaf Gull and
Fayyaz Minhas \pkgAMP$_0$: Species-Specific Prediction
of Anti-microbial Peptides Using Zero
and Few Shot Learning . . . . . . . . . 275--283
Pietro Hiram Guzzi and
Marinka Zitnik Editorial Deep Learning and Graph
Embeddings for Network Biology . . . . . 653--654
Jin Li and
Jingru Wang and
Hao Lv and
Zhuoxuan Zhang and
Zaixia Wang IMCHGAN: Inductive Matrix Completion
With Heterogeneous Graph Attention
Networks for Drug-Target Interactions
Prediction . . . . . . . . . . . . . . . 655--665
Xiaoyong Pan and
Lei Chen and
Min Liu and
Zhibin Niu and
Tao Huang and
Yu-Dong Cai Identifying Protein Subcellular
Locations With Embeddings-Based node2loc 666--675
Kishan KC and
Rui Li and
Feng Cui and
Anne R. Haake Predicting Biomedical Interactions With
Higher-Order Graph Convolutional
Networks . . . . . . . . . . . . . . . . 676--687
Xiujuan Lei and
Jiaojiao Tie and
Yi Pan Inferring Metabolite-Disease Association
Using Graph Convolutional Networks . . . 688--698
Jianliang Gao and
Tengfei Lyu and
Fan Xiong and
Jianxin Wang and
Weimao Ke and
Zhao Li Predicting the Survival of Cancer
Patients With Multimodal Graph Neural
Network . . . . . . . . . . . . . . . . 699--709
Giang T. T. Nguyen and
Hoa D. Vu and
Duc-Hau Le Integrating Molecular Graph Data of
Drugs and Multiple -Omic Data of Cell
Lines for Drug Response Prediction . . . 710--717
Tri Minh Nguyen and
Thin Nguyen and
Thao Minh Le and
Truyen Tran GEFA: Early Fusion Approach in
Drug-Target Affinity Prediction . . . . 718--728
Ichcha Manipur and
Mario Manzo and
Ilaria Granata and
Maurizio Giordano and
Lucia Maddalena and
Mario R. Guarracino Netpro2vec: a Graph Embedding Framework
for Biomedical Applications . . . . . . 729--740
Yuanfang Ren and
Aisharjya Sarkar and
Pierangelo Veltri and
Ahmet Ay and
Alin Dobra and
Tamer Kahveci Pattern Discovery in Multilayer Networks 741--752
Zhen Shen and
Qinhu Zhang and
Kyungsook Han and
De-Shuang Huang A Deep Learning Model for RNA-Protein
Binding Preference Prediction Based on
Hierarchical LSTM and Attention Network 753--762
Zhen Gao and
Yu-Tian Wang and
Qing-Wen Wu and
Lei Li and
Jian-Cheng Ni and
Chun-Hou Zheng A New Method Based on Matrix Completion
and Non-Negative Matrix Factorization
for Predicting Disease-Associated miRNAs 763--772
Koushik Mallick and
Saurav Mallik and
Sanghamitra Bandyopadhyay and
Sikim Chakraborty A Novel Graph Topology-Based
GO-Similarity Measure for Signature
Detection From Multi-Omics Data and its
Application to Other Problems . . . . . 773--785
Xin Huang and
Zhenqian Liao and
Bing Liu and
Fengmei Tao and
Benzhe Su and
Xiaohui Lin A Novel Method for Constructing
Classification Models by Combining
Different Biomarker Patterns . . . . . . 786--794
Shi-Hao Feng and
Chun-Qiu Xia and
Pei-Dong Zhang and
Hong-Bin Shen \em Ab-Initio Membrane Protein
Amphipathic Helix Structure Prediction
Using Deep Neural Networks . . . . . . . 795--805
Trinh Van Giang and
Tatsuya Akutsu and
Kunihiko Hiraishi An FVS-Based Approach to Attractor
Detection in Asynchronous Random Boolean
Networks . . . . . . . . . . . . . . . . 806--818
Yiding Zhang and
Lyujie Chen and
Shao Li CIPHER-SC: Disease-Gene Association
Inference Using Graph Convolution on a
Context-Aware Network With Single-Cell
Data . . . . . . . . . . . . . . . . . . 819--829
Aisharjya Sarkar and
Prabhat Mishra and
Tamer Kahveci Data Perturbation and Recovery of Time
Series Gene Expression Data . . . . . . 830--842
Sachin Bhatt and
Prithvi Singh and
Archana Sharma and
Arpita Rai and
Ravins Dohare and
Shweta Sankhwar and
Akash Sharma and
Mansoor Ali Syed Deciphering Key Genes and miRNAs
Associated With Hepatocellular Carcinoma
via Network-Based Approach . . . . . . . 843--853
Yu-Ting Su and
Yao Lu and
Mei Chen and
An-An Liu Deep Reinforcement Learning-Based
Progressive Sequence Saliency Discovery
Network for Mitosis Detection In
Time-Lapse Phase-Contrast Microscopy
Images . . . . . . . . . . . . . . . . . 854--865
Ben Cao and
Xue Ii and
Xiaokang Zhang and
Bin Wang and
Qiang Zhang and
Xiaopeng Wei Designing Uncorrelated Address Constrain
for DNA Storage by DMVO Algorithm . . . 866--877
Boxin Guan and
Yuhai Zhao and
Ying Yin and
Yuan Li Detecting Disease-Associated SNP--SNP
Interactions Using Progressive Screening
Memetic Algorithm . . . . . . . . . . . 878--887
Ho Bae and
Seonwoo Min and
Hyun-Soo Choi and
Sungroh Yoon DNA Privacy: Analyzing Malicious DNA
Sequences Using Deep Neural Networks . . 888--898
Seonho Kim and
Juntae Yoon Dual Triggered Correspondence Topic
(DTCT) model for MeSH annotation . . . . 899--911
Christian Ponte-Fernández and
Jorge González-Domínguez and
Antonio Carvajal-Rodríguez and
María J. Martín Evaluation of Existing Methods for
High-Order Epistasis Detection . . . . . 912--926
Tapan Chowdhury and
Susanta Chakraborty and
Argha Nandan GPU Accelerated Drug Application on
Signaling Pathways Containing Multiple
Faults Using Boolean Networks . . . . . 927--939
Edward E. Seabolt and
Gowri Nayar and
Harsha Krishnareddy and
Akshay Agarwal and
Kristen L. Beck and
Ignacio Terrizzano and
Eser Kandogan and
Mark Kunitomi and
Mary Roth and
Vandana Mukherjee and
James H. Kaufman Functional Genomics Platform, a
Cloud-Based Platform for Studying
Microbial Life at Scale . . . . . . . . 940--952
Fei Wang and
Yulian Ding and
Xiujuan Lei and
Bo Liao and
Fang-Xiang Wu Identifying Gene Signatures for Cancer
Drug Repositioning Based on Sample
Clustering . . . . . . . . . . . . . . . 953--965
Meshari Alazmi and
Olaa Motwalli Immuno-Informatics Based Peptides: an
Approach for Vaccine Development Against
Outer Membrane Proteins of
\bionamePseudomonas Genus . . . . . . . 966--973
Khalique Newaz and
Tijana Milenkovi\'c Inference of a Dynamic Aging-related
Biological Subnetwork via Network
Propagation . . . . . . . . . . . . . . 974--988
Stephen Kwok-Wing Tsui Editorial . . . . . . . . . . . . . . . 1255--1256
Jiongmin Zhang and
Man Zhu and
Ying Qian protein2vec: Predicting Protein--Protein
Interactions Based on LSTM . . . . . . . 1257--1266
Byungkyu Park and
Wook Lee and
Kyungsook Han A New Approach to Deriving Prognostic
Gene Pairs From Cancer Patient-Specific
Gene Correlation Networks . . . . . . . 1267--1276
Yanbo Li and
Yu Lin DCHap: a Divide-and-Conquer Haplotype
Phasing Algorithm for Third-Generation
Sequences . . . . . . . . . . . . . . . 1277--1284
Chengchuang Lin and
Gansen Zhao and
Zhirong Yang and
Aihua Yin and
Xinming Wang and
Li Guo and
Hanbiao Chen and
Zhaohui Ma and
Lei Zhao and
Haoyu Luo and
Tianxing Wang and
Bichao Ding and
Xiongwen Pang and
Qiren Chen CIR-Net: Automatic Classification of
Human Chromosome Based on
Inception-ResNet Architecture . . . . . 1285--1293
Shengtian Sang and
Xiaoxia Liu and
Xiaoyu Chen and
Di Zhao A Scalable Embedding Based Neural
Network Method for Discovering Knowledge
From Biomedical Literature . . . . . . . 1294--1301
Sun Ah Kim and
Nayeon Kang and
Taesung Park Hierarchical Structured Component
Analysis for Microbiome Data Using
Taxonomy Assignments . . . . . . . . . . 1302--1312
Ken Hung-On Yu and
Xiunan Fang and
Haobin Yao and
Bond Ng and
Tak Kwan Leung and
Ling-Ling Wang and
Chi Ho Lin and
Agnes Sze Wah Chan and
Wai Keung Leung and
Suet Yi Leung and
Joshua Wing Kei Ho Evaluation of Experimental Protocols for
Shotgun Whole-Genome Metagenomic
Discovery of Antibiotic Resistance Genes 1313--1321
Yingjun Ma and
Tingting He and
Yuting Tan and
Xingpeng Jiang Seq-BEL: Sequence-Based Ensemble
Learning for Predicting Virus-Human
Protein--Protein Interaction . . . . . . 1322--1333
Xiuzhen Huang and
Yu Zhang and
Xuan Guo Editorial . . . . . . . . . . . . . . . 1334--1335
Sina Abdollahi and
Peng-Chan Lin and
Jung-Hsien Chiang DiaDeL: an Accurate Deep Learning-Based
Model With Mutational Signatures for
Predicting Metastasis Stage and Cancer
Types . . . . . . . . . . . . . . . . . 1336--1343
Nahim Adnan and
Maryam Zand and
Tim H. M. Huang and
Jianhua Ruan Construction and Evaluation of Robust
Interpretation Models for Breast Cancer
Metastasis Prediction . . . . . . . . . 1344--1353
Tapas Bhadra and
Saurav Mallik and
Amir Sohel and
Zhongming Zhao Unsupervised Feature Selection Using an
Integrated Strategy of Hierarchical
Clustering With Singular Value
Decomposition: an Integrative Biomarker
Discovery Method With Application to
Acute Myeloid Leukemia . . . . . . . . . 1354--1364
Lien A. Bui and
Dacosta Yeboah and
Louis Steinmeister and
Sima Azizi and
Daniel B. Hier and
Donald C. Wunsch and
Gayla R. Olbricht and
Tayo Obafemi-Ajayi Heterogeneity in Blood Biomarker
Trajectories After Mild TBI Revealed by
Unsupervised Learning . . . . . . . . . 1365--1378
Elisabetta Manduchi and
Trang T. Le and
Weixuan Fu and
Jason H. Moore Genetic Analysis of Coronary Artery
Disease Using Tree-Based Automated
Machine Learning Informed By
Biology-Based Feature Selection . . . . 1379--1386
Jason Causey and
Jonathan Stubblefield and
Jake Qualls and
Jennifer Fowler and
Lingrui Cai and
Karl Walker and
Yuanfang Guan and
Xiuzhen Huang An Ensemble of U-Net Models for Kidney
Tumor Segmentation With CT Images . . . 1387--1392
Lechuan Li and
Chonghao Zhang and
Shiyu Liu and
Hannah Guan and
Yu Zhang Age Prediction by DNA Methylation in
Neural Networks . . . . . . . . . . . . 1393--1402
Madhumita and
Sushmita Paul A Feature Weighting-Assisted Approach
for Cancer Subtypes Identification From
Paired Expression Profiles . . . . . . . 1403--1414
Lewei Zhou and
Yucong Tang and
Guiying Yan A New Estimation Method for the
Biological Interaction Predicting
Problems . . . . . . . . . . . . . . . . 1415--1423
Chengye Zou and
Xiaopeng Wei and
Qiang Zhang and
Changjun Zhou A Novel Adaptive Linear Neuron Based on
DNA Strand Displacement Reaction Network 1424--1434
Hao Jiang and
Fei Zhan and
Congtao Wang and
Jianfeng Qiu and
Yansen Su and
Chunhou Zheng and
Xingyi Zhang and
Xiangxiang Zeng A Robust Algorithm Based on Link Label
Propagation for Identifying Functional
Modules From Protein--Protein
Interaction Networks . . . . . . . . . . 1435--1448
Sanjay Bankapur and
Nagamma Patil An Effective Multi-Label Protein
Sub-Chloroplast Localization Prediction
by Skipped-Grams of Evolutionary
Profiles Using Deep Neural Network . . . 1449--1458
Liangliang Liu and
Shaojie Tang and
Fang-Xiang Wu and
Yu-Ping Wang and
Jianxin Wang An Ensemble Hybrid Feature Selection
Method for Neuropsychiatric Disorder
Classification . . . . . . . . . . . . . 1459--1471
Maryam Pouryahya and
Jung Hun Oh and
Pedram Javanmard and
James C. Mathews and
Zehor Belkhatir and
Joseph O. Deasy and
Allen R. Tannenbaum aWCluster: a Novel Integrative
Network-Based Clustering of Multiomics
for Subtype Analysis of Cancer Data . . 1472--1483
Hu Zhang and
Jingsong Chen and
Tianhai Tian Bayesian Inference of Stochastic Dynamic
Models Using Early-Rejection Methods
Based on Sequential Stochastic
Simulations . . . . . . . . . . . . . . 1484--1494
Daiane Aparecida Zuanetti and
Luis Aparecido Milan Bayesian Modeling for Epistasis Analysis
Using Data-Driven Reversible Jump . . . 1495--1506
Alex M. Ascensión and
Marcos J. Araúzo-Bravo BigMPI4py: Python Module for
Parallelization of Big Data Objects
Discloses Germ Layer Specific DNA
Demethylation Motifs . . . . . . . . . . 1507--1522
Conghua Wang and
Haihong Liu and
Zhonghua Miao and
Jin Zhou Circadian Rhythm Regulated by Tumor
Suppressor p53 and Time Delay in
Unstressed Cells . . . . . . . . . . . . 1523--1530
Abhinandan Khan and
Goutam Saha and
Rajat Kumar Pal Controlling the Effects of External
Perturbations on a Gene Regulatory
Network Using
Proportional-Integral-Derivative
Controller . . . . . . . . . . . . . . . 1531--1544
Omid Abbaszadeh and
Ali Azarpeyvand and
Alireza Khanteymoori and
Abbas Bahari Data-Driven and Knowledge-Based
Algorithms for Gene Network
Reconstruction on High-Dimensional Data 1545--1557
Jian Ma Guest Editorial for Selected Papers From
ACM-BCB 2019 . . . . . . . . . . . . . . 1919
Yue Guo and
Oleh Krupa and
Jason Stein and
Guorong Wu and
Ashok Krishnamurthy SAU-Net: a Unified Network for Cell
Counting in $2$D and $3$D Microscopy
Images . . . . . . . . . . . . . . . . . 1920--1932
John Lazarsfeld and
Jonathan Rodríguez and
Mert Erden and
Yuelin Liu and
Lenore J. Cowen Majority Vote Cascading: a
Semi-Supervised Framework for Improving
Protein Function Prediction . . . . . . 1933--1945
Mira Barshai and
Alice Aubert and
Yaron Orenstein G4detector: Convolutional Neural Network
to Predict DNA G-Quadruplexes . . . . . 1946--1955
Pietro Pinoli and
Gaia Ceddia and
Stefano Ceri and
Marco Masseroli Predicting Drug Synergism by Means of
Non-Negative Matrix Tri-Factorization 1956--1967
Yang Qiu and
Yang Zhang and
Yifan Deng and
Shichao Liu and
Wen Zhang A Comprehensive Review of Computational
Methods For Drug-Drug Interaction
Detection . . . . . . . . . . . . . . . 1968--1985
Yuanying Zhuang and
Xiangrong Liu and
Yue Zhong and
Longxin Wu A Deep Ensemble Predictor for
Identifying Anti-Hypertensive Peptides
Using Pretrained Protein Embedding . . . 1986--1992
Xingyi Li and
Ju Xiang and
Fang-Xiang Wu and
Min Li A Dual Ranking Algorithm Based on the
Multiplex Network for Heterogeneous
Complex Disease Analysis . . . . . . . . 1993--2002
Xibin Jia and
Zheng Sun and
Qing Mi and
Zhenghan Yang and
Dawei Yang A Multimodality-Contribution-Aware
TripNet for Histologic Grading of
Hepatocellular Carcinoma . . . . . . . . 2003--2016
Shiming Wang and
Jie Li and
Yadong Wang and
Liran Juan A Neighborhood-Based Global Network
Model to Predict Drug-Target
Interactions . . . . . . . . . . . . . . 2017--2025
Xiaojian Ding and
Fan Yang and
Yaoyi Zhong and
Jie Cao A Novel Recursive Gene Selection Method
Based on Least Square Kernel Extreme
Learning Machine . . . . . . . . . . . . 2026--2038
Anik Chaudhuri and
Anwoy Kumar Mohanty and
Manoranjan Satpathy A Parallelizable Model for Analyzing
Cancer Tissue Heterogeneity . . . . . . 2039--2048
Cunmei Ji and
Yutian Wang and
Zhen Gao and
Lei Li and
Jiancheng Ni and
Chunhou Zheng A Semi-Supervised Learning Method for
MiRNA-Disease Association Prediction
Based on Variational Autoencoder . . . . 2049--2059
Raktim Kumar Mondol and
Nhan Duy Truong and
Mohammad Reza and
Samuel Ippolito and
Esmaeil Ebrahimie and
Omid Kavehei AFExNet: an Adversarial Autoencoder for
Differentiating Breast Cancer Sub-Types
and Extracting Biologically Relevant
Genes . . . . . . . . . . . . . . . . . 2060--2070
Jingjing Ma and
Haitao Jiang and
Daming Zhu and
Runmin Yang Algorithms and Hardness for Scaffold
Filling to Maximize Increased
Duo-Preservations . . . . . . . . . . . 2071--2079
Atheer Matroud and
Christopher Tuffley and
Michael Hendy An Asymmetric Alignment Algorithm for
Estimating Ancestor-Descendant Edit
Distance for Tandem Repeats . . . . . . 2080--2091
Qichang Zhao and
Mengyun Yang and
Zhongjian Cheng and
Yaohang Li and
Jianxin Wang Biomedical Data and Deep Learning
Computational Models for Predicting
Compound-Protein Relations . . . . . . . 2092--2110
Debraj Ghosh and
Rajat K. De Block Search Stochastic Simulation
Algorithm (\em BlSSSA): a Fast
Stochastic Simulation Algorithm for
Modeling Large Biochemical Networks . . 2111--2123
Ritabrata Sanyal and
Devroop Kar and
Ram Sarkar Carcinoma Type Classification From
High-Resolution Breast Microscopy Images
Using a Hybrid Ensemble of Deep
Convolutional Features and Gradient
Boosting Trees Classifiers . . . . . . . 2124--2136
Lopamudra Dey and
Anirban Mukhopadhyay Compact Genetic Algorithm-Based Feature
Selection for Sequence-Based Prediction
of Dengue--Human Protein Interactions 2137--2148
Changli Feng and
Jin Wu and
Haiyan Wei and
Lei Xu and
Quan Zou CRCF: a Method of Identifying Secretory
Proteins of Malaria Parasites . . . . . 2149--2157
Cheng-Hong Yang and
Kuo-Chuan Wu and
Li-Yeh Chuang and
Hsueh-Wei Chang DeepBarcoding: Deep Learning for Species
Classification Using DNA Barcoding . . . 2158--2165
Guoxian Yu and
Yeqian Yang and
Yangyang Yan and
Maozu Guo and
Xiangliang Zhang and
Jun Wang DeepIDA: Predicting Isoform-Disease
Associations by Data Fusion and Deep
Neural Networks . . . . . . . . . . . . 2166--2176
Jun Wang and
Long Zhang and
An Zeng and
Dawen Xia and
Jiantao Yu and
Guoxian Yu DeepIII: Predicting Isoform-Isoform
Interactions by Deep Neural Networks and
Data Fusion . . . . . . . . . . . . . . 2177--2187
Zhonghao Liu and
Jing Jin and
Yuxin Cui and
Zheng Xiong and
Alireza Nasiri and
Yong Zhao and
Jianjun Hu DeepSeqPanII: an Interpretable Recurrent
Neural Network Model With Attention
Mechanism for Peptide-HLA Class II
Binding Prediction . . . . . . . . . . . 2188--2196
Betül Güvenç Paltun and
Samuel Kaski and
Hiroshi Mamitsuka DIVERSE: Bayesian Data IntegratiVE
Learning for Precise Drug ResponSE
Prediction . . . . . . . . . . . . . . . 2197--2207
Zhongjian Cheng and
Cheng Yan and
Fang-Xiang Wu and
Jianxin Wang Drug-Target Interaction Prediction Using
Multi-Head Self-Attention and Graph
Attention Network . . . . . . . . . . . 2208--2218
Dongyuan Li and
Shuyao Zhang and
Xiaoke Ma Dynamic Module Detection in Temporal
Attributed Networks of Cancers . . . . . 2219--2230
Chuang Liu and
Yao Dai and
Keping Yu and
Zi-Ke Zhang Enhancing Cancer Driver Gene Prediction
by Protein--Protein Interaction Network 2231--2240
Yan Wang and
Lei Zhang and
Xin Shu and
Yangqin Feng and
Zhang Yi and
Qing Lv Feature-Sensitive Deep Convolutional
Neural Network for Multi-Instance Breast
Cancer Detection . . . . . . . . . . . . 2241--2251
Da Yan and
Hong Qin and
Hsiang-Yun Wu and
Jake Y. Chen Guest Editorial for Selected Papers From
BIOKDD 2020 . . . . . . . . . . . . . . 2545--2546
Rayol Mendonca-Neto and
Zhi Li and
David Fenyö and
Claudio T. Silva and
Fabíola G. Nakamura and
Eduardo F. Nakamura A Gene Selection Method Based on
Outliers for Breast Cancer Subtype
Classification . . . . . . . . . . . . . 2547--2559
Yuanyuan Jin and
Wendi Ji and
Wei Zhang and
Xiangnan He and
Xinyu Wang and
Xiaoling Wang A KG-Enhanced Multi-Graph Neural Network
for Attentive Herb Recommendation . . . 2560--2571
Andreia S. Martins and
Marta Gromicho and
Susana Pinto and
Mamede de Carvalho and
Sara C. Madeira Learning Prognostic Models Using Disease
Progression Patterns: Predicting the
Need for Non-Invasive Ventilation in
Amyotrophic Lateral Sclerosis . . . . . 2572--2583
Qingyu Chen and
Jingcheng Du and
Alexis Allot and
Zhiyong Lu LitMC-BERT: Transformer-Based
Multi-Label Classification of Biomedical
Literature With An Application on
COVID-19 Literature Curation . . . . . . 2584--2595
Jaswanth K. Yella and
Anil G. Jegga MGATRx: Discovering Drug Repositioning
Candidates Using Multi-View Graph
Attention . . . . . . . . . . . . . . . 2596--2604
Jieli Zhou and
Baoyu Jing and
Zeya Wang and
Hongyi Xin and
Hanghang Tong SODA: Detecting COVID-19 in Chest X-Rays
With Semi-Supervised Open Set Domain
Adaptation . . . . . . . . . . . . . . . 2605--2612
Xiaojuan Guo and
Kewei Chen and
Yinghua Chen and
Chengjie Xiong and
Yi Su and
Li Yao and
Eric M. Reiman A Computational Monte Carlo Simulation
Strategy to Determine the Temporal
Ordering of Abnormal Age Onset Among
Biomarkers of Alzheimer's Disease 2613--2622
Zhankun Xiong and
Feng Huang and
Ziyan Wang and
Shichao Liu and
Wen Zhang A Multimodal Framework for Improving \em
in Silico Drug Repositioning With the
Prior Knowledge From Knowledge Graphs 2623--2631
Qiao Ning and
Xiaowei Zhao and
Zhiqiang Ma A Novel Method for Identification of
Glutarylation Sites Combining
Borderline-SMOTE With Tomek Links
Technique in Imbalanced Data . . . . . . 2632--2641
Matthew LeMay and
Ran Libeskind-Hadas and
Yi-Chieh Wu A Polynomial-Time Algorithm for
Minimizing the Deep Coalescence Cost for
Level-1 Species Networks . . . . . . . . 2642--2653
Xuan Yang and
Chen Yang and
Jimeng Lei and
Jianxiao Liu An Approach of Epistasis Detection Using
Integer Linear Programming Optimizing
Bayesian Network . . . . . . . . . . . . 2654--2671
Chao Li and
Jun Sun and
Li-Wei Li and
Xiaojun Wu and
Vasile Palade An Effective Swarm Intelligence
Optimization Algorithm for Flexible
Ligand Docking . . . . . . . . . . . . . 2672--2684
Ashish Ranjan and
David Fernández-Baca and
Sudhakar Tripathi and
Akshay Deepak An Ensemble Tf-Idf Based Approach to
Protein Function Prediction via Sequence
Segmentation . . . . . . . . . . . . . . 2685--2696
Venkateshwarlu Yellaswamy Gudur and
Sidharth Maheshwari and
Amit Acharyya and
Rishad Shafik An FPGA Based Energy-Efficient Read
Mapper With Parallel Filtering and
In-Situ Verification . . . . . . . . . . 2697--2711
Xinyi Qin and
Lu Zhang and
Min Liu and
Ziwei Xu and
Guangzhong Liu ASFold-DNN: Protein Fold Recognition
Based on Evolutionary Features With
Variable Parameters Using Full Connected
Neural Network . . . . . . . . . . . . . 2712--2722
Jianhong Cheng and
Wei Zhao and
Jin Liu and
Xingzhi Xie and
Shangjie Wu and
Liangliang Liu and
Hailin Yue and
Junjian Li and
Jianxin Wang and
Jun Liu Automated Diagnosis of COVID-19 Using
Deep Supervised Autoencoder With
Multi-View Features From CT Images . . . 2723--2736
Zhihao Huang and
Yan Wang and
Xiaoke Ma Clustering of Cancer Attributed Networks
by Dynamically and Jointly Factorizing
Multi-Layer Graphs . . . . . . . . . . . 2737--2748
Muhammad Arif and
Muhammad Kabir and
Saeed Ahmed and
Abid Khan and
Fang Ge and
Adel Khelifi and
Dong-Jun Yu DeepCPPred: a Deep Learning Framework
for the Discrimination of
Cell-Penetrating Peptides and Their
Uptake Efficiencies . . . . . . . . . . 2749--2759
Yuqian Pu and
Jiawei Li and
Jijun Tang and
Fei Guo DeepFusionDTA: Drug-Target Binding
Affinity Prediction With Information
Fusion and Hybrid Deep-Learning Ensemble
Model . . . . . . . . . . . . . . . . . 2760--2769
Pratik Dutta and
Aditya Prakash Patra and
Sriparna Saha DeePROG: Deep Attention-Based Model for
Diseased Gene Prognosis by Fusing
Multi-Omics Data . . . . . . . . . . . . 2770--2781
Weizhong Zhao and
Jinyong Zhang and
Jincai Yang and
Xingpeng Jiang and
Tingting He Document-Level Chemical-Induced Disease
Relation Extraction via Hierarchical
Representation Learning . . . . . . . . 2782--2793
Hamda B. Ajmal and
Michael G. Madden Dynamic Bayesian Network Learning to
Infer Sparse Models From Time Series
Gene Expression Data . . . . . . . . . . 2794--2805
Jian Liu and
Jialiang Sun and
Yongzhuang Liu Effective Identification of Bacterial
Genomes From Short and Long Read
Sequencing Data . . . . . . . . . . . . 2806--2816
Debopriya Ghosh and
Javier Cabrera Enriched Random Forest for High
Dimensional Genomic Data . . . . . . . . 2817--2828
Pei Wang and
Daojie Wang Gene Differential Co-Expression Networks
Based on RNA-Seq: Construction and Its
Applications . . . . . . . . . . . . . . 2829--2841
Musab Naik and
Luis Rueda and
Akram Vasighizaker Identification of Enriched Regions in
ChIP-Seq Data via a Linear-Time
Multi-Level Thresholding Algorithm . . . 2842--2850
Young-Joon Ko and
Sangsoo Kim and
Cheol-Ho Pan and
Keunwan Park Identification of Functional Microbial
Modules Through Network-Based Analysis
of Meta-Microbial Features Using Matrix
Factorization . . . . . . . . . . . . . 2851--2862
Junrong Song and
Wei Peng and
Feng Wang Identifying Cancer Patient Subgroups by
Finding Co-Modules From the Driver
Mutation Profiles and Downstream Gene
Expression Profiles . . . . . . . . . . 2863--2872
Siyuan Zhao and
Jun Meng and
Qiang Kang and
Yushi Luan Identifying LncRNA-Encoded Short
Peptides Using Optimized Hybrid Features
and Ensemble Learning . . . . . . . . . 2873--2881
Da Yan and
Zhaohui S. Qin and
Debswapna Bhattacharya and
Jake Y. Chen Guest Editorial for Selected Papers From
BIOKDD 2021 . . . . . . . . . . . . . . 3068--3069
Cheng Ye and
Rowan Swiers and
Stephen Bonner and
Ian Barrett A Knowledge Graph-Enhanced Tensor
Factorisation Model for Discovering Drug
Targets . . . . . . . . . . . . . . . . 3070--3080
Ngan Dong and
Stefanie Mücke and
Megha Khosla MuCoMiD: a Multitask Graph Convolutional
Learning Framework for MiRNA-Disease
Association Prediction . . . . . . . . . 3081--3092
Raquel Aoki and
Frederick Tung and
Gabriel L. Oliveira Heterogeneous Multi-Task Learning With
Expert Diversity . . . . . . . . . . . . 3093--3102
Emre Sefer BioCode: a Data-Driven Procedure to
Learn the Growth of Biological Networks 3103--3113
Kingshuk Mukherjee and
Daniel Dole-Muinos and
Massimiliano Rossi and
Ayomide Ajayi and
Mattia Prosperi and
Christina Boucher Finding Overlapping Rmaps via Clustering 3114--3123
De-Shuang Huang and
Kyungsook Han and
Tatsuya Akutsu Guest Editorial for Special Section on
the 16th International Conference on
Intelligent Computing (ICIC) . . . . . . 3124--3125
Tengsheng Jiang and
Yuhui Chen and
Shixuan Guan and
Zhongtian Hu and
Weizhong Lu and
Qiming Fu and
Yijie Ding and
Haiou Li and
Hongjie Wu G Protein-Coupled Receptor Interaction
Prediction Based on Deep Transfer
Learning . . . . . . . . . . . . . . . . 3126--3134
Hsin-Hung Chou and
Ching-Tien Hsu and
Chin-Wei Hsu and
Kai-Hsun Yao and
Hao-Ching Wang and
Sun-Yuan Hsieh Novel Algorithm for Improved Protein
Classification Using Graph Similarity 3135--3143
Qinhu Zhang and
Yindong Zhang and
Siguo Wang and
Zhan-Heng Chen and
Valeriya Gribova and
Vladimir Fedorovich Filaretov and
De-Shuang Huang Predicting In-Vitro DNA--Protein Binding
With a Spatially Aligned Fusion of
Sequence and Shape . . . . . . . . . . . 3144--3153
Min Fang and
Yufeng He and
Zhihua Du and
Vladimir N. Uversky DeepCLD: an Efficient Sequence-Based
Predictor of Intrinsically Disordered
Proteins . . . . . . . . . . . . . . . . 3154--3159
Xinguo Lu and
Jinxin Li and
Zhenghao Zhu and
Yue Yuan and
Guanyuan Chen and
Keren He Predicting miRNA--Disease Associations
via Combining Probability Matrix Feature
Decomposition With Neighbor Learning . . 3160--3170
Qing-Wen Wu and
Rui-Fen Cao and
Jun-Feng Xia and
Jian-Cheng Ni and
Chun-Hou Zheng and
Yan-Sen Su Extra Trees Method for Predicting
LncRNA--Disease Association Based On
Multi-Layer Graph Embedding Aggregation 3171--3178
Bo Li and
Yihui Tian and
Yang Tian and
Shihua Zhang and
Xiaolong Zhang Predicting Cancer Lymph-Node Metastasis
From LncRNA Expression Profiles Using
Local Linear Reconstruction Guided
Distance Metric Learning . . . . . . . . 3179--3189
Wen Li and
Shulin Wang and
Junlin Xu and
Ju Xiang Inferring Latent MicroRNA--Disease
Associations on a Gene-Mediated
Tripartite Heterogeneous Multiplexing
Network . . . . . . . . . . . . . . . . 3190--3201
Yulian Xie and
Min Liu and
Shirui Zhou and
Yaonan Wang A Deep Local Patch Matching Network for
Cell Tracking in Microscopy Image
Sequences Without Registration . . . . . 3202--3212
Huang Zhanpeng and
Wu Jiekang A Multiview Clustering Method With
Low-Rank and Sparsity Constraints for
Cancer Subtyping . . . . . . . . . . . . 3213--3223
Nassima Aleb A Mutual Attention Model for Drug Target
Binding Affinity Prediction . . . . . . 3224--3232
Jianshen Zhu and
Naveed Ahmed Azam and
Fan Zhang and
Aleksandar Shurbevski and
Kazuya Haraguchi and
Liang Zhao and
Hiroshi Nagamochi and
Tatsuya Akutsu A Novel Method for Inferring Chemical
Compounds With Prescribed Topological
Substructures Based on Integer
Programming . . . . . . . . . . . . . . 3233--3245
Yueran Yang and
Yu Zhang and
Shuai Li and
Xubin Zheng and
Man-Hon Wong and
Kwong-Sak Leung and
Lixin Cheng A Robust and Generalizable
Immune-Related Signature for Sepsis
Diagnostics . . . . . . . . . . . . . . 3246--3254
Xinzhe Ni and
Bohao Geng and
Haoyu Zheng and
Jiawei Shi and
Gang Hu and
Jianzhao Gao Accurate Estimation of Single-Cell
Differentiation Potency Based on Network
Topology and Gene Ontology Information 3255--3262
Yiming Li and
Min Zeng and
Yifan Wu and
Yaohang Li and
Min Li Accurate Prediction of Human Essential
Proteins Using Ensemble Deep Learning 3263--3271
Jingshu Bi and
Yuanjie Zheng and
Chongjing Wang and
Yanhui Ding An Attention Based Bidirectional LSTM
Method to Predict the Binding of TCR and
Epitope . . . . . . . . . . . . . . . . 3272--3280
Sepideh Mazrouee ARHap: Association Rule Haplotype
Phasing . . . . . . . . . . . . . . . . 3281--3294
Jiani Ma and
Lin Zhang and
Shaojie Li and
Hui Liu BRPCA: Bounded Robust Principal
Component Analysis to Incorporate
Similarity Network for
N7-Methylguanosine(mo$^7$G) Site-Disease
Association Prediction . . . . . . . . . 3295--3306
Ghazaleh Parvini and
Katherine Braught and
David Fernández-Baca Checking Phylogenetics Decisiveness in
Theory and in Practice . . . . . . . . . 3307--3316
Enzo Battistella and
Maria Vakalopoulou and
Roger Sun and
Théo Estienne and
Marvin Lerousseau and
Sergey Nikolaev and
Émilie Alvarez Andres and
Alexandre Carré and
Stéphane Niyoteka and
Charlotte Robert and
Nikos Paragios and
Éric Deutsch COMBING: Clustering in Oncology for
Mathematical and Biological
Identification of Novel Gene Signatures 3317--3331
Aanchal Mongia and
Emilie Chouzenoux and
Angshul Majumdar Computational Prediction of Drug-Disease
Association Based on Graph-Regularized
One Bit Matrix Completion . . . . . . . 3332--3339
Omar Shetta and
Mahesan Niranjan and
Srinandan Dasmahapatra Convex Multi-View Clustering Via Robust
Low Rank Approximation With Application
to Multi-Omic Data . . . . . . . . . . . 3340--3352
Mattias Åkesson and
Prashant Singh and
Fredrik Wrede and
Andreas Hellander Convolutional Neural Networks as Summary
Statistics for Approximate Bayesian
Computation . . . . . . . . . . . . . . 3353--3365
Qiaoming Liu and
Xudong Zhao and
Guohua Wang A Clustering Ensemble Method for Cell
Type Detection by Multiobjective
Particle Optimization . . . . . . . . . 1--14
Kun Liu and
Hong-Dong Li and
Yaohang Li and
Jun Wang and
Jianxin Wang A Comparison of Topologically
Associating Domain Callers Based on Hi-C
Data . . . . . . . . . . . . . . . . . . 15--29
Jan Klosa and
Noah Simon and
Volkmar Liebscher and
Dörte Wittenburg A Fitted Sparse-Group Lasso for
Genome-Based Evaluations . . . . . . . . 30--38
Chengzhuan Yang and
Lincong Fang and
Qian Yu and
Hui Wei A Learning Robust and Discriminative
Shape Descriptor for Plant Species
Identification . . . . . . . . . . . . . 39--51
Feng Zhou and
Meng-Meng Yin and
Jing-Xiu Zhao and
Junliang Shang and
Jin-Xing Liu A Method Based On Dual-Network
Information Fusion to Predict
MiRNA--Disease Associations . . . . . . 52--60
Qiang Yu and
Xiao Zhang and
Yana Hu and
Shengpin Chen and
Liying Yang A Method for Predicting DNA Motif Length
Based On Deep Learning . . . . . . . . . 61--73
Weixian Huang and
Kaiwen Tan and
Ziye Zhang and
Jinlong Hu and
Shoubin Dong A Review of Fusion Methods for Omics and
Imaging Data . . . . . . . . . . . . . . 74--93
Ashish Ranjan and
Archana Tiwari and
Akshay Deepak A Sub-Sequence Based Approach to Protein
Function Prediction via Multi-Attention
Based Multi-Aspect Network . . . . . . . 94--105
Jun Bai and
Chuantao Yin and
Jianfei Zhang and
Yanmeng Wang and
Yi Dong and
Wenge Rong and
Zhang Xiong Adversarial Knowledge Distillation Based
Biomedical Factoid Question Answering 106--118
Katrin Sophie Bohnsack and
Marika Kaden and
Julia Abel and
Thomas Villmann Alignment-Free Sequence Comparison: a
Systematic Survey From a Machine
Learning Perspective . . . . . . . . . . 119--135
Steffy Maria Joseph and
P. S. Sathidevi An Automated cDNA Microarray Image
Analysis for the Determination of Gene
Expression Ratios . . . . . . . . . . . 136--150
Sahar Iravani and
Tim O. F. Conrad An Interpretable Deep Learning Approach
for Biomarker Detection in LC-MS
Proteomics Data . . . . . . . . . . . . 151--161
Kanchan Jha and
Sriparna Saha Analyzing Effect of Multi-Modality in
Predicting Protein-Protein Interactions 162--173
Shankarachary Ragi and
Md Hafizur Rahman and
Jamison Duckworth and
Kalimuthu Jawaharraj and
Parvathi Chundi and
Venkataramana Gadhamshetty Artificial Intelligence-Driven Image
Analysis of Bacterial Cells and Biofilms 174--184
Hao Zhang and
Chuanxu Yan and
Yewei Xia and
Jihong Guan and
Shuigeng Zhou Causal Gene Identification Using
Non-Linear Regression-Based Independence
Tests . . . . . . . . . . . . . . . . . 185--195
Naser Anjum and
Raian Latif Nabil and
Rakibul Islam Rafi and
Md. Shamsuzzoha Bayzid and
M. Saifur Rahman CD-MAWS: an Alignment-Free Phylogeny
Estimation Method Using Cosine Distance
on Minimal Absent Word Sets . . . . . . 196--205
Tuan D. Pham Classification of \bionameCaenorhabditis
elegans Locomotion Behaviors With
Eigenfeature-Enhanced Long Short-Term
Memory Networks . . . . . . . . . . . . 206--216
Ichcha Manipur and
Maurizio Giordano and
Marina Piccirillo and
Seetharaman Parashuraman and
Lucia Maddalena Community Detection in Protein--Protein
Interaction Networks and Applications 217--237
Rizwan Qureshi and
Bin Zou and
Tanvir Alam and
Jia Wu and
Victor H. F. Lee and
Hong Yan Computational Methods for the Analysis
and Prediction of EGFR-Mutated Lung
Cancer Drug Resistance: Recent Advances
in Drug Design, Challenges and Future
Prospects . . . . . . . . . . . . . . . 238--255
Jingbo Yang and
Denan Zhang and
Yiyang Cai and
Kexin Yu and
Mingming Li and
Lei Liu and
Xiujie Chen Computational Prediction of Drug
Phenotypic Effects Based on
Substructure-Phenotype Associations . . 256--265
Wook Lee and
Seokwoo Lee and
Kyungsook Han Constructing a Cancer Patient-Specific
Network Based on Second-Order Partial
Correlations of Gene Expression and DNA
Methylation . . . . . . . . . . . . . . 266--276
Zhi-Hao Liu and
Cun-Mei Ji and
Jian-Cheng Ni and
Yu-Tian Wang and
Li-Juan Qiao and
Chun-Hou Zheng Convolution Neural Networks Using Deep
Matrix Factorization for Predicting
Circrna-Disease Association . . . . . . 277--284
Yang Hua and
Xiaoning Song and
Zhenhua Feng and
Xiao-Jun Wu and
Josef Kittler and
Dong-Jun Yu CPInformer for Efficient and Robust
Compound-Protein Interaction Prediction 285--296
Kailong Li and
Lijun Quan and
Yelu Jiang and
Yan Li and
Yiting Zhou and
Tingfang Wu and
Qiang Lyu ctP$^2$ISP: Protein--Protein Interaction
Sites Prediction Using Convolution and
Transformer With Data Augmentation . . . 297--306
Xiuquan Du and
Jiajia Hu Deep Multi-Label Joint Learning for RNA
and DNA-Binding Proteins Prediction . . 307--320
Xiao-Hui Yang and
Zi-Jun Xi and
Jie-Ping Li and
Xin-Lei Feng and
Xiao-Hong Zhu and
Si-Yi Guo and
Chun-Peng Song Deep Transfer Learning-Based
Multi-Object Detection for Plant Stomata
Phenotypic Traits Intelligent
Recognition . . . . . . . . . . . . . . 321--329
Onur Can Uner and
Halil Ibrahim Kuru and
R. Gokberk Cinbis and
Oznur Tastan and
A. Ercument Cicek DeepSide: a Deep Learning Approach for
Drug Side Effect Prediction . . . . . . 330--339
Zimo Huang and
Jun Wang and
Zhongmin Yan and
Lin Wan and
Maozu Guo Differential Gene Expression Prediction
by Ensemble Deep Networks on Histone
Modification Data . . . . . . . . . . . 340--351
Jinghang Lin and
Xiaoran Tong and
Chenxi Li and
Qing Lu Expectile Neural Networks for Genetic
Data Analysis of Complex Diseases . . . 352--359
Lucia Williams and
Alexandru I. Tomescu and
Brendan Mumey Flow Decomposition With Subpath
Constraints . . . . . . . . . . . . . . 360--370
Isabel González-Crespo and
Antonio Gómez-Caamaño and
Óscar López Pouso and
John D. Fenwick and
Juan Pardo-Montero A Biomathematical Model of Tumor
Response to Radioimmunotherapy With $
\alpha $PDL1 and $ \alpha $CTLA4 . . . . 808--821
Xiong Li and
Yangkai Lin and
Chengwang Xie and
Zejun Li and
Min Chen and
Peng Wang and
Juan Zhou A Clustering Method Unifying Cell-Type
Recognition and Subtype Identification
for Tumor Heterogeneity Analysis . . . . 822--832
Min Li and
Wenbo Shi and
Fuhao Zhang and
Min Zeng and
Yaohang Li A Deep Learning Framework for Predicting
Protein Functions With Co-Occurrence of
GO Terms . . . . . . . . . . . . . . . . 833--842
Xiaoqing Peng and
Wenjin Zhang and
Wanxin Cui and
Binrong Ding and
Qingtong Lyu and
Jianxin Wang ADmeth: a Manually Curated Database for
the Differential Methylation in
Alzheimer's Disease . . . . . . . . . . 843--851
Qichang Zhao and
Guihua Duan and
Mengyun Yang and
Zhongjian Cheng and
Yaohang Li and
Jianxin Wang AttentionDTA: Drug-Target Binding
Affinity Prediction by Sequence-Based
Deep Learning With Attention Mechanism 852--863
Jiasheng Si and
Liu Sun and
Deyu Zhou and
Jie Ren and
Lin Li Biomedical Argument Mining Based on
Sequential Multi-Task Learning . . . . . 864--874
Mahdieh Ghasemi and
Maseud Rahgozar and
Kaveh Kavousi Complex Disease Genes Identification
Using a Heterogeneous Network Embedding
Approach . . . . . . . . . . . . . . . . 875--882
Dong Jun Jee and
Yixin Kong and
Hyonho Chun Deep Nonnegative Matrix Factorization
Using a Variational Autoencoder With
Application to Single-Cell RNA
Sequencing Data . . . . . . . . . . . . 883--893
Volkan Altuntas Diffusion Alignment Coefficient (DAC): a
Novel Similarity Metric for
Protein-Protein Interaction Network . . 894--903
Mobeen Ur Rehman and
Hilal Tayara and
Kil To Chong DL-m6A: Identification of
N6-Methyladenosine Sites in Mammals
Using Deep Learning Based on Different
Encoding Schemes . . . . . . . . . . . . 904--911
Zhong-Ze Yu and
Chun-Xiang Peng and
Jun Liu and
Biao Zhang and
Xiao-Gen Zhou and
Gui-Jun Zhang DomBpred: Protein Domain Boundary
Prediction Based on Domain-Residue
Clustering Using Inter-Residue Distance 912--922
Xin Huang and
Benzhe Su and
Chenbo Zhu and
Xinyu He and
Xiaohui Lin Dynamic Network Construction for
Identifying Early Warning Signals Based
On a Data-Driven Approach: Early
Diagnosis Biomarker Discovery for
Gastric Cancer . . . . . . . . . . . . . 923--931
Xuan Lin and
Zhe Quan and
Zhi-Jie Wang and
Yan Guo and
Xiangxiang Zeng and
Philip S. Yu Effectively Identifying Compound-Protein
Interaction Using Graph Neural
Representation . . . . . . . . . . . . . 932--943
Yongxian Fan and
Guicong Sun and
Xiaoyong Pan ELMo4m6A: a Contextual Language
Embedding-Based Predictor for Detecting
RNA N6-Methyladenosine Sites . . . . . . 944--954
Shamima Rashid and
Suresh Sundaram and
Chee Keong Kwoh Empirical Study of Protein Feature
Representation on Deep Belief Networks
Trained With Small Data for Secondary
Structure Prediction . . . . . . . . . . 955--966
Chao Wang and
Quan Zou and
Ying Ju and
Hua Shi Enhancer-FRL: Improved and Robust
Identification of Enhancers and Their
Activities Using Feature Representation
Learning . . . . . . . . . . . . . . . . 967--975
Shichao Liu and
Yang Zhang and
Yuxin Cui and
Yang Qiu and
Yifan Deng and
Zhongfei Zhang and
Wen Zhang Enhancing Drug-Drug Interaction
Prediction Using Deep Attention Neural
Networks . . . . . . . . . . . . . . . . 976--985
Yang Shen and
Jinlin Zhu and
Zhaohong Deng and
Wenwei Lu and
Hongchao Wang EnsDeepDP: an Ensemble Deep Learning
Approach for Disease Prediction Through
Metagenomics . . . . . . . . . . . . . . 986--998
Leandro Di Persia and
Tiago Lopez and
Agustin Arce and
Diego H. Milone and
Georgina Stegmayer exp2GO: Improving Prediction of
Functions in the Gene Ontology With
Expression Data . . . . . . . . . . . . 999--1008
Filippo Castiglione and
Christine Nardini and
Elia Onofri and
Marco Pedicini and
Paolo Tieri Explainable Drug Repurposing Approach
From Biased Random Walks . . . . . . . . 1009--1019
Tri Minh Nguyen and
Thomas P. Quinn and
Thin Nguyen and
Truyen Tran Explaining Black Box Drug Target
Prediction Through Model Agnostic
Counterfactual Samples . . . . . . . . . 1020--1029
Chunyan Tang and
Cheng Zhong and
Mian Wang and
Fengfeng Zhou FMGNN: a Method to Predict
Compound-Protein Interaction With
Pharmacophore Features and
Physicochemical Properties of Amino
Acids . . . . . . . . . . . . . . . . . 1030--1040
Jiwen Liu and
Zhufang Kuang and
Lei Deng GCNPCA: miRNA-Disease Associations
Prediction Algorithm Based on Graph
Convolutional Neural Networks . . . . . 1041--1052
Zhen Tian and
Haichuan Fang and
Zhixia Teng and
Yangdong Ye GOGCN: Graph Convolutional Network on
Gene Ontology for Functional Similarity
Analysis of Genes . . . . . . . . . . . 1053--1064
Thang Chu and
Thuy Trang Nguyen and
Bui Duong Hai and
Quang Huy Nguyen and
Tuan Nguyen Graph Transformer for Drug Response
Prediction . . . . . . . . . . . . . . . 1065--1072
Bryan Herrera-Romero and
Diego Almeida-Galárraga and
Graciela M. Salum and
Fernando Villalba-Meneses and
Marco Esteban Gudiño-Gomezjurado GUSignal: an Informatics Tool to Analyze
Glucuronidase Gene Expression in
\bionameArabidopsis thaliana Roots . . . 1073--1080
Junwei Sun and
Haoping Ji and
Yingcong Wang and
Yanfeng Wang Hybrid Projective Synchronization via PI
Controller Based on DNA Strand
Displacement . . . . . . . . . . . . . . 1081--1091
Vicky Zheng and
Ahmet Erdem Sariyuce and
Jaroslaw Zola Identifying Taxonomic Units in
Metagenomic DNA Streams on Mobile
Devices . . . . . . . . . . . . . . . . 1092--1103
Yasin Görmez and
Zafer Aydin IGPRED-MultiTask: a Deep Learning Model
to Predict Protein Secondary Structure,
Torsion Angles and Solvent Accessibility 1104--1113
Yongping Du and
Jingya Yan and
Yuxuan Lu and
Yiliang Zhao and
Xingnan Jin Improving Biomedical Question Answering
by Data Augmentation and Model Weighting 1114--1124
Carlos Martín-Vide and
Miguel A. Vega-Rodríguez Algorithms for Computational Biology:
Eighth Edition . . . . . . . . . . . . . 1626--1627
Alexsandro Oliveira Alexandrino and
Klairton Lima Brito and
Andre Rodrigues Oliveira and
Ulisses Dias and
Zanoni Dias Reversal and Indel Distance With
Intergenic Region Information . . . . . 1628--1640
Klairton Lima Brito and
Alexsandro Oliveira Alexandrino and
Andre Rodrigues Oliveira and
Ulisses Dias and
Zanoni Dias Genome Rearrangement Distance With a
Flexible Intergenic Regions Aspect . . . 1641--1653
Kaari Landry and
Aivee Teodocio and
Manuel Lafond and
Olivier Tremblay-Savard Defining Phylogenetic Network Distances
Using Cherry Operations . . . . . . . . 1654--1666
Chenqi Mou and
Wenwen Ju Sparse Triangular Decomposition for
Computing Equilibria of Biological
Dynamic Systems Based on Chordal Graphs 1667--1678
David Schaller and
Manuela Geiß and
Marc Hellmuth and
Peter F. Stadler Best Match Graphs With Binary Trees . . 1679--1690
Yin Yao and
Martin C. Frith Improved DNA-Versus-Protein Homology
Search for Protein Fossils . . . . . . . 1691--1699
Paul Zaharias and
Vladimir Smirnov and
Tandy Warnow Large-Scale Multiple Sequence Alignment
and the Maximum Weight Trace Alignment
Merging Problem . . . . . . . . . . . . 1700--1712
Kaitao Wu and
Lexiang Wang and
Bo Liu and
Yang Liu and
Yadong Wang and
Junyi Li PSPGO: Cross-Species Heterogeneous
Network Propagation for Protein Function
Prediction . . . . . . . . . . . . . . . 1713--1724
Alejandro F. Villaverde and
Elba Raimúndez and
Jan Hasenauer and
Julio R. Banga Assessment of Prediction Uncertainty
Quantification Methods in Systems
Biology . . . . . . . . . . . . . . . . 1725--1736
Jinmiao Song and
Shengwei Tian and
Long Yu and
Qimeng Yang and
Yuanxu Wang and
Qiguo Dai and
Xiaodong Duan ISLMI: Predicting lncRNA--miRNA
Interactions Based on Information
Injection and Second-Order Graph
Convolution Network . . . . . . . . . . 1737--1745
Yan Kang and
Haining Wang and
Bin Pu and
Liu Tao and
Jianguo Chen and
Philip S. Yu A Hybrid Two-Stage
Teaching-Learning-Based Optimization
Algorithm for Feature Selection in
Bioinformatics . . . . . . . . . . . . . 1746--1760
Pranab Das and
Yogita Thakran and
S. R. Ngamwal Anal and
Vipin Pal and
Anju Yadav BRMCF: Binary Relevance and MLSMOTE
Based Computational Framework to Predict
Drug Functions From Chemical and
Biological Properties of Drugs . . . . . 1761--1773
Wen-Yu Xi and
Feng Zhou and
Ying-Lian Gao and
Jin-Xing Liu and
Chun-Hou Zheng LDCMFC: Predicting Long Non-Coding RNA
and Disease Association Using
Collaborative Matrix Factorization Based
on Correntropy . . . . . . . . . . . . . 1774--1782
Ramkishore Bhattacharyya Bidirectional Association Discovery
Leads to Precise Identification of Lung
Cancer Biomarkers and Genome Taxa Class 1783--1794
Vianney Kengne Tchendji and
Franklin Ingrid Kamga Youmbi and
Clémentin Tayou Djamegni and
Jerry Lacmou Zeutouo A Parallel Tiled and Sparsified
Four-Russians Algorithm for Nussinov's
RNA Folding . . . . . . . . . . . . . . 1795--1806
Jie Xu and
Guanxue Yang and
Guohai Liu and
Hui Liu Inferring Gene Regulatory Networks via
Ensemble Path Consistency Algorithm
Based on Conditional Mutual Information 1807--1816
Pradeep Kumar Das and
Biswajeet Sahoo and
Sukadev Meher An Efficient Detection and
Classification of Acute Leukemia Using
Transfer Learning and Orthogonal Softmax
Layer-Based Model . . . . . . . . . . . 1817--1828
Marcelo Rodrigues de Holanda Maia and
Alexandre Plastino and
Alex Freitas and
João Pedro de Magalhães Interpretable Ensembles of Classifiers
for Uncertain Data With Bioinformatics
Applications . . . . . . . . . . . . . . 1829--1841
Shutao Chen and
Lin Zhang and
Xiangzhi Chen and
Hui Liu FGFICA: Independent Component Analysis
of Fusion Genomic Features for Mining
Epi-Transcriptome Profiling Data . . . . 1842--1853
Hui Yu and
KangKang Li and
JianYu Shi DGANDDI: Double Generative Adversarial
Networks for Drug-Drug Interaction
Prediction . . . . . . . . . . . . . . . 1854--1863
Jun Bai and
Chuantao Yin and
Zimeng Wu and
Jianfei Zhang and
Yanmeng Wang and
Guanyi Jia and
Wenge Rong and
Zhang Xiong Improving Biomedical ReQA With
Consistent NLI-Transfer and
Post-Whitening . . . . . . . . . . . . . 1864--1875
Xiangbin Lin and
Weizhuang Kong and
Jianxiu Li and
Xuexiao Shao and
Changting Jiang and
Ruilan Yu and
Xiaowei Li and
Bin Hu Aberrant Static and Dynamic Functional
Brain Network in Depression Based on EEG
Source Localization . . . . . . . . . . 1876--1889
Prasun Chandra Tripathi and
Soumen Bag An Attention-Guided CNN Framework for
Segmentation and Grading of Glioma Using
$3$D MRI Scans . . . . . . . . . . . . . 1890--1904
Shuhui Liu and
Yupei Zhang and
Xuequn Shang GLassonet: Identifying Discriminative
Gene Sets Among Molecular Subtypes of
Breast Cancer . . . . . . . . . . . . . 1905--1916
Hegang Chen and
Yuyin Lu and
Yuedong Yang and
Yanghui Rao A Drug Combination Prediction Framework
Based on Graph Convolutional Network and
Heterogeneous Information . . . . . . . 1917--1925
Shengli Zhang and
Yuanyuan Jing PreVFs-RG: a Deep Hybrid Model for
Identifying Virulence Factors Based on
Residual Block and Gated Recurrent Unit 1926--1934
Minghua Zhao and
Min Yuan and
Yaning Yang and
Steven X. Xu CPGL: Prediction of Compound-Protein
Interaction by Integrating Graph
Attention Network With Long Short-Term
Memory Neural Network . . . . . . . . . 1935--1942
Qichang Zhao and
Guihua Duan and
Haochen Zhao and
Kai Zheng and
Yaohang Li and
Jianxin Wang GIFDTI: Prediction of Drug-Target
Interactions Based on Global Molecular
and Intermolecular Interaction
Representation Learning . . . . . . . . 1943--1952
Qi Dang and
Yong Liang and
Dong Ouyang and
Rui Miao and
Caijin Ling and
Xiaoying Liu and
Shengli Xie Improved Computational
Drug-Repositioning by Self-Paced
Non-Negative Matrix Tri-Factorization 1953--1962
Honghao Gao and
Zijian Zhang and
Ramón J. Durán Barroso Guest Editorial Special Issue on
Multi-Modal Biomedical Computing-Deep
Transfer Learning . . . . . . . . . . . 2363--2366
Wei Wang and
Xinhua Yu and
Bo Fang and
Yue Zhao and
Yongyong Chen and
Wei Wei and
Junxin Chen Cross-Modality LGE-CMR Segmentation
Using Image-to-Image Translation Based
Data Augmentation . . . . . . . . . . . 2367--2375
Zhichen Ni and
Honglong Chen and
Zhe Li and
Xiaomeng Wang and
Na Yan and
Weifeng Liu and
Feng Xia MSCET: a Multi-Scenario Offloading
Schedule for Biomedical Data Processing
and Analysis in Cloud-Edge-Terminal
Collaborative Vehicular Networks . . . . 2376--2386
Yuanpeng Zhang and
Kaijian Xia and
Yizhang Jiang and
Pengjiang Qian and
Weiwei Cai and
Chengyu Qiu and
Khin Wee Lai and
Dongrui Wu Multi-Modality Fusion & Inductive
Knowledge Transfer Underlying Non-Sparse
Multi-Kernel Learning and Distribution
Adaption . . . . . . . . . . . . . . . . 2387--2397
Nan Chen and
Man Guo and
Yongchao Li and
Xiping Hu and
Zhijun Yao and
Bin Hu Estimation of Discriminative Multimodal
Brain Network Connectivity Using
Message-Passing-Based Nonlinear Network
Fusion . . . . . . . . . . . . . . . . . 2398--2406
Jinxia Wang and
Liang Qiao and
Haibin Lv and
Zhihan Lv Deep Transfer Learning-Based Multi-Modal
Digital Twins for Enhancement and
Diagnostic Analysis of Brain MRI Image 2407--2419
Fayaz Ali Dharejo and
Muhammad Zawish and
Farah Deeba and
Yuanchun Zhou and
Kapal Dev and
Sunder Ali Khowaja and
Nawab Muhammad Faseeh Qureshi Multimodal-Boost: Multimodal Medical
Image Super-Resolution Using
Multi-Attention Network With Wavelet
Transform . . . . . . . . . . . . . . . 2420--2433
Yuexin Bian and
Jintai Chen and
Xiaojun Chen and
Xiaoxian Yang and
Danny Z. Chen and
Jian Wu Identifying Electrocardiogram
Abnormalities Using a
Handcrafted-Rule-Enhanced Neural Network 2434--2444
Imran Ahmed and
Abdellah Chehri and
Gwanggil Jeon and
Francesco Piccialli Automated Pulmonary Nodule
Classification and Detection Using Deep
Learning Architectures . . . . . . . . . 2445--2456
Qi-Qi Chen and
Zhao-Hui Sun and
Chuan-Feng Wei and
Edmond Q. Wu and
Dong Ming Semi-Supervised $3$D Medical Image
Segmentation Based on Dual-Task
Consistent Joint Learning and Task-Level
Regularization . . . . . . . . . . . . . 2457--2467
Mainak Adhikari and
Abhishek Hazra and
Sudarshan Nandy Deep Transfer Learning for Communicable
Disease Detection and Recommendation in
Edge Networks . . . . . . . . . . . . . 2468--2479
Xiaolong Xu and
Haoyan Xu and
Liying Wang and
Yuanyuan Zhang and
Fu Xaio Hygeia: a Multilabel Deep Learning-Based
Classification Method for Imbalanced
Electrocardiogram Data . . . . . . . . . 2480--2493
Yuxin Ma and
Shuo Wang and
Yang Hua and
Ruhui Ma and
Tao Song and
Zhengui Xue and
Heng Cao and
Haibing Guan Perceptual Data Augmentation for
Biomedical Coronary Vessel Segmentation 2494--2505
Jianyuan Li and
Xiong Luo and
Huimin Ma and
Wenbing Zhao A Hybrid Deep Transfer Learning Model
With Kernel Metric for COVID-19
Pneumonia Classification Using Chest CT
Images . . . . . . . . . . . . . . . . . 2506--2517
Ilias Siniosoglou and
Vasileios Argyriou and
Panagiotis Sarigiannidis and
Thomas Lagkas and
Antonios Sarigiannidis and
Sotirios K. Goudos and
Shaohua Wan Post-Processing Fairness Evaluation of
Federated Models: an Unsupervised
Approach in Healthcare . . . . . . . . . 2518--2529
Wentian Cai and
Linsen Xie and
Weixian Yang and
Yijiang Li and
Ying Gao and
Tingting Wang DFTNet: Dual-Path Feature Transfer
Network for Weakly Supervised Medical
Image Segmentation . . . . . . . . . . . 2530--2540
Qingbin Wang and
Kaiyi Chen and
Wanrong Dou and
Yutao Ma Cross-Attention Based Multi-Resolution
Feature Fusion Model for Self-Supervised
Cervical OCT Image Classification . . . 2541--2554
Ke Yan and
Xinlu Guo and
Zhiwei Ji and
Xiaokang Zhou Deep Transfer Learning for Cross-Species
Plant Disease Diagnosis Adapting Mixed
Subdomains . . . . . . . . . . . . . . . 2555--2564
Yi Ding and
Xue Qin and
Mingfeng Zhang and
Ji Geng and
Dajiang Chen and
Fuhu Deng and
Chunhe Song RLSegNet: an Medical Image Segmentation
Network Based on Reinforcement Learning 2565--2576
Tingting Liang and
Congying Xia and
Ziqiang Zhao and
Yixuan Jiang and
Yuyu Yin and
Philip S. Yu Transferring From Textual Entailment to
Biomedical Named Entity Recognition . . 2577--2586
Abdul Qayyum and
Imran Razzak and
M. Tanveer and
Moona Mazher and
Bandar Alhaqbani High-Density Electroencephalography and
Speech Signal Based Deep Framework for
Clinical Depression Diagnosis . . . . . 2587--2597
Sheng Ren and
Kehua Guo and
Xiaokang Zhou and
Bin Hu and
Feihong Zhu and
Entao Luo Medical Image Super-Resolution Based on
Semantic Perception Transfer Learning 2598--2609
Mei-Neng Wang and
Xue-Jun Xie and
Zhu-Hong You and
Leon Wong and
Li-Ping Li and
Zhan-Heng Chen Combining $K$ Nearest Neighbor With
Nonnegative Matrix Factorization for
Predicting CircRNA-Disease Associations 2610--2618
Shixuan Guan and
Quan Zou and
Hongjie Wu and
Yijie Ding Protein-DNA Binding Residues Prediction
Using a Deep Learning Model With
Hierarchical Feature Extraction . . . . 2619--2628
Zheng-Wei Li and
Qian-Kun Wang and
Chang-An Yuan and
Peng-Yong Han and
Zhu-Hong You and
Lei Wang Predicting MiRNA-Disease Associations by
Graph Representation Learning Based on
Jumping Knowledge Networks . . . . . . . 2629--2638
Chengxi Huang and
Wei Wang and
Xin Zhang and
Shui-Hua Wang and
Yu-Dong Zhang Tuberculosis Diagnosis Using Deep
Transferred EfficientNet . . . . . . . . 2639--2646
Qing Ye and
Xiaolong Zhang and
Xiaoli Lin Drug-Target Interaction Prediction via
Graph Auto-Encoder and Multi-Subspace
Deep Neural Networks . . . . . . . . . . 2647--2658
Shanshan Wang and
Ruoyou Wu and
Cheng Li and
Juan Zou and
Ziyao Zhang and
Qiegen Liu and
Yan Xi and
Hairong Zheng PARCEL: Physics-Based Unsupervised
Contrastive Representation Learning for
Multi-Coil MR Imaging . . . . . . . . . 2659--2670
Seokwoo Lee and
Wook Lee and
Shulei Ren and
Byungkyu Park and
Kyungsook Han Constructing Integrative ceRNA Networks
and Finding Prognostic Biomarkers in
Renal Cell Carcinoma . . . . . . . . . . 2671--2680
Xinguo Lu and
Guanyuan Chen and
Jinxin Li and
Xiangjin Hu and
Fengxu Sun MAGCN: a Multiple Attention Graph
Convolution Networks for Predicting
Synthetic Lethality . . . . . . . . . . 2681--2689
Qinhu Zhang and
Youhong Xu and
Siguo Wang and
Yong Wu and
Yuannong Ye and
Chang-An Yuan and
Valeriya Gribova and
Vladimir Fedorovich Filaretov and
De-Shuang Huang Using Fully Convolutional Network to
Locate Transcription Factor Binding
Sites Based on DNA Sequence and
Conservation Information . . . . . . . . 2690--2699
Abbas Saad Alatrany and
Wasiq Khan and
Abir J. Hussain and
Jamila Mustafina and
Dhiya Al-Jumeily Transfer Learning for Classification of
Alzheimer's Disease Based on Genome Wide
Data . . . . . . . . . . . . . . . . . . 2700--2711
Haochen Zhao and
Guihua Duan and
Peng Ni and
Cheng Yan and
Yaohang Li and
Jianxin Wang RNPredATC: a Deep Residual
Learning-Based Model With Applications
to the Prediction of Drug-ATC Code
Association . . . . . . . . . . . . . . 2712--2723
Wuli Xu and
Lei Duan and
Huiru Zheng and
Jesse Li-Ling and
Weipeng Jiang and
Yidan Zhang and
Tingting Wang and
Ruiqi Qin An Integrative Disease Information
Network Approach to Similar Disease
Detection . . . . . . . . . . . . . . . 2724--2735
Kevin Sutanto and
Marcel Turcotte Assessing Global-Local Secondary
Structure Fingerprints to Classify RNA
Sequences With Deep Learning . . . . . . 2736--2747
Wei Peng and
Ming Liu and
Wei Dai and
Tielin Chen and
Yu Fu and
Yi Pan Multi-View Feature Aggregation for
Predicting Microbe-Disease Association 2748--2758
Ahmed Bin Zaman and
Toki Tahmid Inan and
Kenneth De Jong and
Amarda Shehu Adaptive Stochastic Optimization to
Improve Protein Conformation Sampling 2759--2771
Xiaoshuai Zhang and
Lixin Wang and
Hucheng Liu and
Xiaofeng Zhang and
Bo Liu and
Yadong Wang and
Junyi Li Prot2GO: Predicting GO Annotations From
Protein Sequences and Interactions . . . 2772--2780
Jiatao Chen and
Liang Zhang and
Ke Cheng and
Bo Jin and
Xinjiang Lu and
Chao Che Predicting Drug-Target Interaction Via
Self-Supervised Learning . . . . . . . . 2781--2789
Jing Sun and
Li Pan and
Bin Li and
Haoyue Wang and
Bo Yang and
Wenbin Li A Construction Method of Dynamic Protein
Interaction Networks by Using Relevant
Features of Gene Expression Data . . . . 2790--2801
He-Ming Chu and
Xiang-Zhen Kong and
Jin-Xing Liu and
Chun-Hou Zheng and
Han Zhang A New Binary Biclustering Algorithm
Based on Weight Adjacency Difference
Matrix for Analyzing Gene Expression
Data . . . . . . . . . . . . . . . . . . 2802--2809
Nan Sheng and
Lan Huang and
Ling Gao and
Yangkun Cao and
Xuping Xie and
Yan Wang A Survey of Computational Methods and
Databases for lncRNA-MiRNA Interaction
Prediction . . . . . . . . . . . . . . . 2810--2826
Ji Lv and
Guixia Liu and
Yuan Ju and
Houhou Huang and
Ying Sun AADB: a Manually Collected Database for
Combinations of Antibiotics With
Adjuvants . . . . . . . . . . . . . . . 2827--2836
Yeganeh Madadi and
Aboozar Monavarfeshani and
Hao Chen and
W. Daniel Stamer and
Robert W. Williams and
Siamak Yousefi Artificial Intelligence Models for Cell
Type and Subtype Identification Based on
Single-Cell RNA Sequencing Data in
Vision Science . . . . . . . . . . . . . 2837--2852
Zhen Gao and
Jin Tang and
Junfeng Xia and
Chun-Hou Zheng and
Pi-Jing Wei CNNGRN: a Convolutional Neural
Network-Based Method for Gene Regulatory
Network Inference From Bulk Time-Series
Expression Data . . . . . . . . . . . . 2853--2861
Yu Cao and
Wenya Pi and
Chun-Yu Lin and
Ulrike Münzner and
Masahiro Ohtomo and
Tatsuya Akutsu Common Attractors in Multiple Boolean
Networks . . . . . . . . . . . . . . . . 2862--2873
Ze-Gang Wei and
Xu Chen and
Xiao-Dan Zhang and
Hao Zhang and
Xing-Guo Fan and
Hong-Yan Gao and
Fei Liu and
Yu Qian Comparison of Methods for Biological
Sequence Clustering . . . . . . . . . . 2874--2888
Nikolai Romashchenko and
Benjamin Linard and
Eric Rivals and
Fabio Pardi Computing Phylo-$k$-Mers . . . . . . . . 2889--2897
Niannian Liu and
Zequn Zhang and
Yanan Wu and
Yinglong Wang and
Ying Liang CRBSP:Prediction of CircRNA--RBP Binding
Sites Based on Multimodal Intermediate
Fusion . . . . . . . . . . . . . . . . . 2898--2906
Fan Zhang and
Yawei Zhang and
Xiaoke Zhu and
Xiaopan Chen and
Fuhao Lu and
Xinhong Zhang DeepSG2PPI: a Protein-Protein
Interaction Prediction Method Based on
Deep Learning . . . . . . . . . . . . . 2907--2919
Visweswaran Ravikumar and
Tong Xu and
Wajd N. Al-Holou and
Salar Fattahi and
Arvind Rao Efficient Inference of Spatially-Varying
Gaussian Markov Random Fields With
Applications in Gene Regulatory Networks 2920--2932
Bo Zhao and
Jun Bai and
Chen Li and
Jianfei Zhang and
Wenge Rong and
Yuanxin Ouyang and
Zhang Xiong Enhancing Biomedical ReQA With
Adversarial Hard In-Batch Negative
Samples . . . . . . . . . . . . . . . . 2933--2944
Zhipeng Cai and
Min Li and
Pavel Skums and
Yanjie Wei Guest Editors' Introduction to the
Special Section on Bioinformatics
Research and Applications . . . . . . . 3329--3331
Hunmin Lee and
Mingon Kang and
Donghyun Kim and
Daehee Seo and
Yingshu Li Epidemic Vulnerability Index for
Effective Vaccine Distribution Against
Pandemic . . . . . . . . . . . . . . . . 3332--3342
Qing Zhao and
Jianqiang Li and
Linna Zhao and
Zhichao Zhu Knowledge Guided Feature Aggregation for
the Prediction of Chronic Obstructive
Pulmonary Disease With Chinese EMRs . . 3343--3352
Yueyue Wang and
Xiujuan Lei and
Yi Pan Microbe-Disease Association Prediction
Using RGCN Through Microbe-Drug-Disease
Network . . . . . . . . . . . . . . . . 3353--3362
Wei Peng and
Zicheng Che and
Wei Dai and
Shoulin Wei and
Wei Lan Predicting miRNA-Disease Associations
From miRNA-Gene-Disease Heterogeneous
Network With Multi-Relational Graph
Convolutional Network Model . . . . . . 3363--3375
Sarwan Ali and
Bikram Sahoo and
Muhammad Asad Khan and
Alexander Zelikovsky and
Imdad Ullah Khan and
Murray Patterson Efficient Approximate Kernel Based Spike
Sequence Classification . . . . . . . . 3376--3388
Yuxia Guan and
Ying An and
Jingrui Xu and
Ning Liu and
Jianxin Wang HA-ResNet: Residual Neural Network With
Hidden Attention for ECG Arrhythmia
Detection Using Two-Dimensional Signal 3389--3398
Qiang Li and
Hong Song and
Zenghui Wei and
Fengbo Yang and
Jingfan Fan and
Danni Ai and
Yucong Lin and
Xiaoling Yu and
Jian Yang Densely Connected U-Net With Criss-Cross
Attention for Automatic Liver Tumor
Segmentation in CT Images . . . . . . . 3399--3410
Zhilong Lv and
Yuexiao Lin and
Rui Yan and
Ying Wang and
Fa Zhang TransSurv: Transformer-Based Survival
Analysis Model Integrating
Histopathological Images and Genomic
Data for Colorectal Cancer . . . . . . . 3411--3420
Cheng Chen and
Yuguo Zha and
Daming Zhu and
Kang Ning and
Xuefeng Cui ContactLib-ATT: a Structure-Based Search
Engine for Homologous Proteins . . . . . 3421--3429
Jiamin Chen and
Jianliang Gao and
Tengfei Lyu and
Babatounde Moctard Oloulade and
Xiaohua Hu AutoMSR: Auto Molecular Structure
Representation Learning for Multi-label
Metabolic Pathway Prediction . . . . . . 3430--3439
Hong-Dong Li and
Chao Deng and
Xiao-Qi Zhang and
Cui-Xiang Lin A Gene Set-Integrated Approach for
Predicting Disease-Associated Genes . . 3440--3450
Haitao Fu and
Cecheng Zhao and
Xiaohui Niu and
Wen Zhang DRLM: a Robust Drug Representation
Learning Method and its Applications . . 3451--3460
Yurong Qian and
Jingjing Zheng and
Ying Jiang and
Shaoqiu Li and
Lei Deng Prediction of circRNA-MiRNA Association
Using Singular Value Decomposition and
Graph Neural Networks . . . . . . . . . 3461--3468
Enhao Cheng and
Jun Zhao and
Hong Wang and
Shuguang Song and
Shuxian Xiong and
Yanshen Sun Dual Network Contrastive Learning for
Predicting Microbe-Disease Associations 3469--3481
Tiansu Gong and
Fusong Ju and
Shiwei Sun and
Dongbo Bu SASA-Net: a Spatial-Aware Self-Attention
Mechanism for Building Protein $3$D
Structure Directly From Inter- Residue
Distances . . . . . . . . . . . . . . . 3482--3488
Huan Wang and
Ruigang Liu and
Baijing Wang and
Yifan Hong and
Ziwen Cui and
Qiufen Ni Multitype Perception Method for
Drug-Target Interaction Prediction . . . 3489--3498
Qingqing Cao and
Jianping Zhao and
Haiyun Wang and
Qi Guan and
Chunhou Zheng An Integrated Method Based on
Wasserstein Distance and Graph for
Cancer Subtype Discovery . . . . . . . . 3499--3510
Abhijit Mondal and
Mukul S. Bansal Generalizing the Domain-Gene-Species
Reconciliation Framework to Microbial
Genes and Domains . . . . . . . . . . . 3511--3522
Han Zhang and
Zexuan Zhu and
Hui Li and
Shan He Network Biomarker Detection From Gene
Co-Expression Network Using Gaussian
Mixture Model Clustering . . . . . . . . 3523--3534
Wenming Wu and
Wensheng Zhang and
Weimin Hou and
Xiaoke Ma Multi-View Clustering With Graph
Learning for scRNA-Seq Data . . . . . . 3535--3546
Dayun Liu and
Xianghui Li and
Liangliang Zhang and
Xiaowen Hu and
Jiaxuan Zhang and
Zhirong Liu and
Lei Deng HGNNLDA: Predicting lncRNA-Drug
Sensitivity Associations via a Dual
Channel Hypergraph Neural Network . . . 3547--3555
Jing Yang and
Zhengshu Lu and
Xu Chen and
Deling Xu and
Dewu Ding and
Yanrui Ding GCNA-Cluster: a Gene Co-Expression
Network Alignment to Cluster Cancer
Patients Algorithm for Identifying
Subtypes of Pancreatic Ductal
Adenocarcinoma . . . . . . . . . . . . . 3556--3566
Baoli Jia and
Qingfang Meng and
Yuehui Chen and
Hongri Yang Prediction of Membrane Protein
Amphiphilic Helix Based on Horizontal
Visibility Graph and Graph Convolution
Network . . . . . . . . . . . . . . . . 3567--3574
Yakub K. Saheed and
Bukola F. Balogun and
Braimah Joseph Odunayo and
Mustapha Abdulsalam Microarray Gene Expression Data
Classification via Wilcoxon Sign Rank
Sum and Novel Grey Wolf Optimized
Ensemble Learning Models . . . . . . . . 3575--3587
Yinyin Gong and
Rui Li and
Bin Fu and
Yan Liu and
Jilong Wang and
Renfa Li and
Danny Z. Chen A CNN-LSTM Ensemble Model for Predicting
Protein-Protein Interaction Binding
Sites . . . . . . . . . . . . . . . . . 3588--3599
Xin Wang and
Jie Li and
Guohua Wang MicroRNA Promoter Identification in
Human With a Three-level Prediction
Method . . . . . . . . . . . . . . . . . 3600--3608
Yahui Cao and
Tao Zhang and
Xin Zhao and
Xue Jia and
Bingzhi Li MooSeeker: a Metabolic Pathway Design
Tool Based on Multi-Objective
Optimization Algorithm . . . . . . . . . 3609--3622
Taoning Chen and
Tingfang Wu and
Deng Pan and
Jinxing Xie and
Jin Zhi and
Xuejiao Wang and
Lijun Quan and
Qiang Lyu TransRNAm: Identifying Twelve Types of
RNA Modifications by an Interpretable
Multi-Label Deep Learning Model Based on
Transformer . . . . . . . . . . . . . . 3623--3634
Weizhong Zhao and
Wenjie Yao and
Xingpeng Jiang and
Tingting He and
Chuan Shi and
Xiaohua Hu An Explainable Framework for Predicting
Drug-Side Effect Associations via
Meta-Path-Based Feature Learning in
Heterogeneous Information Network . . . 3635--3647