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Volume 1, Number 1, January, 2004Michael 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
Yamane El Zein and Mathieu Lemay and Kévin Huguenin PrivaTree: Collaborative Privacy-Preserving Training of Decision Trees on Biomedical Data . . . . . . . . 1--13 Chao Tu and Denghui Du and Tieyong Zeng and Yu Zhang Deep Multi-Dictionary Learning for Survival Prediction With Multi-Zoom Histopathological Whole Slide Images . . 14--25 Jordan Morris and Ashur Rafiev and Graeme M. Bragg and Mark L. Vousden and David B. Thomas and Alex Yakovlev and Andrew D. Brown An Event-Driven Approach to Genotype Imputation on a Custom RISC-V Cluster 26--35 Souradipto Choudhuri and Keya Sau CodonU: a Python Package for Codon Usage Analysis . . . . . . . . . . . . . . . . 36--44 Shengpeng Yu and Hong Wang and Jing Li and Jun Zhao and Cheng Liang and Yanshen Sun A Multi-Relational Graph Encoder Network for Fine-Grained Prediction of MiRNA-Disease Associations . . . . . . . 45--56 Rui Guo and Xu Tian and Hanhe Lin and Stephen McKenna and Hong-Dong Li and Fei Guo and Jin Liu Graph-Based Fusion of Imaging, Genetic and Clinical Data for Degenerative Disease Diagnosis . . . . . . . . . . . 57--68 Jonas Kristiansen Nòland and Steinar Thorvaldsen The Exact Stochastic Process of the Haploid Multi-Allelic Wright--Fisher Mutation Model . . . . . . . . . . . . . 69--83 Wenliang Tang and Zhaohong Deng and Hanwen Zhou and Wei Zhang and Fuping Hu and Kup-Sze Choi and Shitong Wang MVDINET: a Novel Multi-Level Enzyme Function Predictor With Multi-View Deep Interactive Learning . . . . . . . . . . 84--94 Shujie Dong and Yuansheng Liu and Yongshun Gong and Xiangjun Dong and Xiangxiang Zeng scCAN: Clustering With Adaptive Neighbor-Based Imputation Method for Single-Cell RNA-Seq Data . . . . . . . . 95--105 Nicol\`o Rossi and Nicola Gigante and Nicola Vitacolonna and Carla Piazza Inferring Markov Chains to Describe Convergent Tumor Evolution With CIMICE 106--119 Dandan Li and Zhen Xiao and Han Sun and Xingpeng Jiang and Weizhong Zhao and Xianjun Shen Prediction of Drug--Disease Associations Based on Multi-Kernel Deep Learning Method in Heterogeneous Graph Embedding 120--128 Changyong Yu and Yuhai Zhao and Chu Zhao and Jianyu Jin and Keming Mao and Guoren Wang MiniDBG: a Novel and Minimal de Bruijn Graph for Read Mapping . . . . . . . . . 129--142 Wei Wang and Mengxue Yu and Bin Sun and Juntao Li and Dong Liu and Hongjun Zhang and Xianfang Wang and Yun Zhou SMGCN: Multiple Similarity and Multiple Kernel Fusion Based Graph Convolutional Neural Network for Drug-Target Interactions Prediction . . . . . . . . 143--154 Rituparna Sinha and Rajat Kumar Pal and Rajat K. De ENLIGHTENMENT: a Scalable Annotated Database of Genomics and NGS-Based Nucleotide Level Profiles . . . . . . . 155--168 Eric J. Barnett and Daniel G. Onete and Asif Salekin and Stephen V. Faraone Genomic Machine Learning Meta-regression: Insights on Associations of Study Features With Reported Model Performance . . . . . . . 169--177 Yuerui Liu and Yongquan Jiang and Fan Zhang and Yan Yang A Novel Multi-Scale Graph Neural Network for Metabolic Pathway Prediction . . . . 178--187 Junchang Xin and Mingcan Wang and Luxuan Qu and Qi Chen and Weiyiqi Wang and Zhiqiong Wang BIC-LP: a Hybrid Higher-Order Dynamic Bayesian Network Score Function for Gene Regulatory Network Reconstruction . . . 188--199 Pengcheng Zeng and Zhixiang Lin scICML: Information-Theoretic Co-Clustering-Based Multi-View Learning for the Integrative Analysis of Single-Cell Multi-Omics Data . . . . . . 200--207 Bindi M. Nagda and Van Minh Nguyen and Ryan T. White promSEMBLE: Hard Pattern Mining and Ensemble Learning for Detecting DNA Promoter Sequences . . . . . . . . . . . 208--214
Fernando Cruz and João Capela and Eugénio C. Ferreira and Miguel Rocha and Oscar Dias BioISO: an Objective-Oriented Application for Assisting the Curation of Genome-Scale Metabolic Models . . . . 215--226 Hao Zhang and Jiao Jiao and Tianheng Zhao and Enshuang Zhao and Lanhui Li and Guihua Li and Borui Zhang and Qing-Ming Qin GERWR: Identifying the Key Pathogenicity-Associated sRNAs of \bionameMagnaporthe oryzae Infection in Rice Based on Graph Embedding and Random Walk With Restart . . . . . . . . . . . 227--239 Daniel Manu and Jingjing Yao and Wuji Liu and Xiang Sun GraphGANFed: a Federated Generative Framework for Graph-Structured Molecules Towards Efficient Drug Discovery . . . . 240--253 Zhao-Qi Hu and Yuan-Mao Hung and Li-Han Chen and Liang-Chuan Lai and Min-Hsiung Pan and Eric Y. Chuang and Mong-Hsun Tsai NURECON: a Novel Online System for Determining Nutrition Requirements Based on Microbial Composition . . . . . . . . 254--264 Sichen Jin and Yijia Zhang and Huimin Yu and Mingyu Lu SADR: Self-Supervised Graph Learning With Adaptive Denoising for Drug Repositioning . . . . . . . . . . . . . 265--277 Alina F. Leuchtenberger and Arndt von Haeseler Learning From an Artificial Neural Network in Phylogenetics . . . . . . . . 278--288 Wenjing Wang and Pengyong Han and Zhengwei Li and Ru Nie and Kangwei Wang and Lei Wang and Hongmei Liao LMGATCDA: Graph Neural Network With Labeling Trick for Predicting circRNA-Disease Associations . . . . . . 289--300 Tiantian Li and Haitao Jiang and Binhai Zhu and Lusheng Wang and Daming Zhu Flanked Block-Interchange Distance on Strings . . . . . . . . . . . . . . . . 301--311
João Paulo Pereira Zanetti and Lucas Peres Oliveira and João Meidanis and Leonid Chindelevitch Counting Sorting Scenarios and Intermediate Genomes for the Rank Distance . . . . . . . . . . . . . . . . 316--327 Nan Sheng and Xuping Xie and Yan Wang and Lan Huang and Shuangquan Zhang and Ling Gao and Hao Wang A Survey of Deep Learning for Detecting miRNA-Disease Associations: Databases, Computational Methods, Challenges, and Future Directions . . . . . . . . . . . 328--347 Tara Newman and Hiu Fung Kevin Chang and Hosna Jabbari DinoKnot: Duplex Interaction of Nucleic Acids With PseudoKnots . . . . . . . . . 348--359 Juan Wang and Zhenchang Wang and Shasha Yuan and Chunhou Zheng and Jinxing Liu and Junliang Shang A Clustering Method for Single-Cell RNA-Seq Data Based on Automatic Weighting Penalty and Low-Rank Representation . . . . . . . . . . . . . 360--371 Xiao-Hui Yang and Ye-Tong Wang and Ming-Hui Wu and Fan Li and Cheng-Long Zhou and Li-Jun Yang and Chen Zheng and Yong Li and Zhi Li and Si-Yi Guo and Chun-Peng Song SLPA-Net: a Real-Time Recognition Network for Intelligent Stomata Localization and Phenotypic Analysis . . 372--382 Shan Zhang and Yuan Zhou and Pei Geng and Qing Lu Functional Neural Networks for High-Dimensional Genetic Data Analysis 383--393 Cheng Yan and Guihua Duan PMDAGS: Predicting miRNA-Disease Associations With Graph Nonlinear Diffusion Convolution Network and Similarities . . . . . . . . . . . . . . 394--404 Sheena K. S. and Madhu S. Nair GenCoder: a Novel Convolutional Neural Network Based Autoencoder for Genomic Sequence Data Compression . . . . . . . 405--415 Wei Wang and Zhenxi Sun and Dong Liu and Hongjun Zhang and Juntao Li and Xianfang Wang and Yun Zhou MAHyNet: Parallel Hybrid Network for RNA-Protein Binding Sites Prediction Based on Multi-Head Attention and Expectation Pooling . . . . . . . . . . 416--427 Sunyong Yoo and Myeonghyeon Jeong and Subhin Seomun and Kiseong Kim and Youngmahn Han Interpretable Prediction of SARS-CoV-2 Epitope-Specific TCR Recognition Using a Pre-Trained Protein Language Model . . . 428--438 Pallavi M. Shanthappa and Neeraj Verma and Anu George and Pawan K. Dhar and Prashanth Athri Computational Prediction of Potential Vaccine Candidates From tRNA Encoded peptides (tREP) Using a Bioinformatic Workflow and Molecular Dynamics Validations . . . . . . . . . . . . . . 439--449 Arnav Solanki and James Cornette and Julia Udell and George Vasmatzis and Marc Riedel Evasive Spike Variants Elucidate the Preservation of T Cell Immune Response to the SARS-CoV-2 Omicron Variant . . . 450--460 Yuhang Jia and Siyu Li and Rui Jiang and Shengquan Chen Accurate Annotation for Differentiating and Imbalanced Cell Types in Single-Cell Chromatin Accessibility Data . . . . . . 461--471 Minglie Li and Shusen Zhou and Tong Liu and Chanjuan Liu and Mujun Zang and Qingjun Wang TSVM: Transfer Support Vector Machine for Predicting MPRA Validated Regulatory Variants . . . . . . . . . . . . . . . . 472--479 Ke Ma and Jiawei Li and Mengyuan Zhao and Ibrahim Zamit and Bin Lin and Fei Guo and Jijun Tang PPRTGI: a Personalized PageRank Graph Neural Network for TF-Target Gene Interaction Detection . . . . . . . . . 480--491 Weiling Li and Raunaq Malhotra and Steven Wu and Manjari Jha and Allen Rodrigo and Mary Poss and Raj Acharya ViPRA-Haplo: \em De Novo Reconstruction of Viral Populations Using Paired End Sequencing Data . . . . . . . . . . . . 492--500 Gabriel Cardona and Joan Carles Pons and Gerard Ribas and Tomás Martínez Coronado