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Volume 1, Number 1, January, 1994Anonymous Editorial: Whither Computational Biology 1--2 G. Christian Overton and Jeffrey S. Aaronson and Juergen Haas and Julie Adams QGB: a System for Querying Sequence Database Fields and Features . . . . . . 3--14 Kimberly E. Forsten and Douglas A. Lauffenburger Probability of Autocrine Ligand Capture by Cell-Surface Receptors: Implications for Ligand Secretion Measurements . . . 15--23 Bing Leng and Bruce G. Buchanan and Hugh B. Nicholas Protein Secondary Structure Prediction Using Two-Level Case-Based Reasoning . . 25--38 David J. States and Warren Gish QGB: Combined Use of Sequence Similarity and Codon Bias for Coding Region Identification . . . . . . . . . . . . . 39--50 Webb Miller and Mark Boguski and Balaji Raghavachari and Zheng Zhang and Ross C. Hardison Constructing Aligned Sequence Blocks . . 51--64 J. W. Keele and J. E. Wray and D. W. Behrens and G. A. Rohrer and S. L. F. Sunden and S. M. Kappes and M. D. Bishop and R. T. Stone and L. J. Alexander and C. W. Beattie A Conceptual Database Model for Genomic Research . . . . . . . . . . . . . . . . 65--76 V. Ferretti and B. F. Lang and D. Sankoff Skewed Base Compositions, Asymmetric Transition Matrices, and Phylogenetic Invariants . . . . . . . . . . . . . . . 77--92
Larry Goldstein and Michael S. Waterman Approximations to Profile Score Distributions . . . . . . . . . . . . . 93--104 Martin Dyer and Alan Frieze and Stephen Suen The Probability of Unique Solutions of Sequencing by Hybridization . . . . . . 105--110 G. A. Rohrer and D. W. Behrens and J. W. Keele A Simplified Procedure for Entry of Raw Genotypic Data . . . . . . . . . . . . . 111--119 Mauro Rustici and Arthur M. Lesk Three-Dimensional Searching for Recurrent Structural Motifs in Data Bases of Protein Structures . . . . . . 121--132 Michael A. Charleston and Michael D. Hendy and David Penny The Effects of Sequence Length, Tree Topology, and Number of Taxa on the Performance of Phylogenetic Methods . . 133--151 M. A. Steel and L. A. Székely and M. D. Hendy Reconstructing Trees When Sequence Sites Evolve at Variable Rates . . . . . . . . 153--163 Kenneth H. Fasman Restructuring the Genome Data Base: a Model for a Federation of Biological Databases . . . . . . . . . . . . . . . 165--171
Robert J. Robbins Genome Informatics I: Community Databases . . . . . . . . . . . . . . . 173--190 R. Knüppel and P. Dietze and W. Lehnberg and K. Frech and E. Wingender TRANSFAC Retrieval Program: a Network Model Database of Eukaryotic Transcription Regulating Sequences and Proteins . . . . . . . . . . . . . . . . 191--198 Winston Hide and John Burke and Daniel B. Da Vison Biological Evaluation of d$^2$, an Algorithm for High-Performance Sequence Comparison . . . . . . . . . . . . . . . 199--215 Zheng Zhang and Balaji Raghavachari and Ross C. Hardison and Webb Miller Chaining Multiple-Alignment Blocks . . . 217--226 Chi Wang A Subgraph Problem from Restriction Maps of DNA . . . . . . . . . . . . . . . . . 227--234 Zheng Zhang An Exponential Example for a Partial Digest Mapping Algorithm . . . . . . . . 235--239 Daniela R. Martin Equivalence Classes for the Double-Digest Problem with Coincident Cut Sites . . . . . . . . . . . . . . . 241--253
Dan Gustfield and David Shmoys and Jan Karel Lenstra and Tandy Warnow In Memoriam Eugene L. Lawler . . . . . . 255--256 Mark J. Miller and John I. Powell A Quantitative Comparison of DNA Sequence Assembly Programs . . . . . . . 257--269 Kun-Mao Chao and Ross C. Hardison and Webb Miller Recent Developments in Linear-Space Alignment Methods: a Survey . . . . . . 271--291 Pierre A. Rioux and William A. Gilbert and Timothy G. Littlejohn A Portable Search Engine and Browser for the Entrez Database . . . . . . . . . . 293--295 William R. Taylor Motif-Biased Protein Sequence Alignment 297--310 Pierre Baldi and Yves Chauvin Hidden Markov Models of the G-Protein-Coupled Receptor Family . . . 311--336 Lusheng Wang and Tao Jiang On the Complexity of Multiple Sequence Alignment . . . . . . . . . . . . . . . 337--348 Dalit Naor and Douglas L. Brutlag On Near-Optimal Alignments of Biological Sequences . . . . . . . . . . . . . . . 349--366
Donald Beaver Computing with DNA . . . . . . . . . . . 1--7 Sean R. Eddy and Graeme Mitchison and Richard Durbin Maximum Discrimination Hidden Markov Models of Sequence Consensus . . . . . . 9--23 Roger F. Sewell and Richard Durbin Method for Calculation of Probability of Matching a Bounded Regular Expression in a Random Data String . . . . . . . . . . 25--31 Mudita Jain and Eugene W. Myers A Note on Scoring Clones Given a Probe Ordering . . . . . . . . . . . . . . . . 33--37 M. A. Steel and Y. X. Fu Classifying and Counting Linear Phylogenetic Invariants for the Jukes--Cantor Model . . . . . . . . . . 39--47 Gunter Weiss and Arndt Von Haeseler Modeling the Polymerase Chain Reaction 49--61 Fengzhu Sun The Polymerase Chain Reaction and Branching Processes . . . . . . . . . . 63--86 M. S. Gelfand Prediction of Function in DNA Sequence Analysis . . . . . . . . . . . . . . . . 87--115 James W. Fickett ORFs and Genes: How Strong a Connection? 117--123 Bonnie Berger Algorithms for Protein Structural Motif Recognition . . . . . . . . . . . . . . 125--138 Paul W. Goldberg and Martin C. Golumbic and Haim Kaplan and Ron Shamir Four Strikes Against Physical Mapping of DNA . . . . . . . . . . . . . . . . . . 139--152
Pavel A. Pevzner Combinatorial Methods for DNA Mapping and Sequencing . . . . . . . . . . . . . 153--158 Farid Alizadeh and Richard M. Karp and Deborah K. Weisser and Geoffrey Zweig Physical Mapping of Chromosomes Using Unique Probes . . . . . . . . . . . . . 159--184 Will Gillett and Jim Daues and Liz Hanks and Rob Capra Fragment Collapsing and Splitting While Assembling High-Resolution Restriction Maps . . . . . . . . . . . . . . . . . . 185--205 Martin Dyer and Alan Frieze and Stephen Suen Ordering Clone Libraries in Computational Biology . . . . . . . . . 207--218 David S. Greenberg and Sorin Istrail Physical Mapping by STS Hybridization: Algorithmic Strategies and the Challenge of Software Evaluation . . . . . . . . . 219--273 Eugene W. Myers Toward Simplifying and Accurately Formulating Fragment Assembly . . . . . 275--290 Ramana M. Idury and Michael S. Waterman A New Algorithm for DNA Sequence Assembly . . . . . . . . . . . . . . . . 291--306 Chris Armen and Clifford Stein Short Superstrings and the Structure of Overlapping Strings . . . . . . . . . . 307--332 Steven S. Skiena and Gopalakrishnan Sundaram Reconstructing Strings from Substrings 333--353 Aleksandar Milosavljevi\'c DNA Sequence Recognition by Hybridization to Short Oligomers . . . . 355--370 A. R. Rubinov and M. S. Gelfand Reconstruction of a String from Substring Precedence Data . . . . . . . 371--381 Oleg Razgulyaev and Anatoly Rubinov and Mikhail Gelfand and Alexander Chetverin Sequencing Potential of Nested Strand Hybridization . . . . . . . . . . . . . 383--395
Richa Agarwala and David Fernández-Baca and Giora Slutzki Fast Algorithms for Inferring Evolutionary Trees . . . . . . . . . . . 397--407 Jian Sun and Wen-Yuan Song and Li-Huang Zhu and Run-Sheng Chen Analysis of tRNA Gene Sequences by Neural Network . . . . . . . . . . . . . 409--416 Sophie Schbath and Bernard Prum and Elisabeth De Turckheim Exceptional Motifs in Different Markov Chain Models for a Statistical Analysis of DNA Sequences . . . . . . . . . . . . 417--437 M. A. Charleston Toward a Characterization of Landscapes of Combinatorial Optimization Problems, with Special Attention to the Phylogeny Problem . . . . . . . . . . . . . . . . 439--450 K. C. Worley and K. Y. King and S. Chua and E. R. B. Mccabe and R. F. Smith Identification of New Members of a Carbohydrate Kinase-Encoding Gene Family 451--458 Sandeep K. Gupta and John D. Kececioglu and Alejandro A. Schäffer Improving the Practical Space and Time Efficiency of the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment . . . . . . . . . . . 459--472 Steven Salzberg Locating Protein Coding Regions in Human DNA Using a Decision Tree Algorithm . . 473--485 Pierre Baldi Substitution Matrices and Hidden Markov Models . . . . . . . . . . . . . . . . . 487--491
Boris Mirkin and Ilya Muchnik and Temple F. Smith A Biologically Consistent Model for Comparing Molecular Phylogenies . . . . 493--507 H. Todd Wareham A Simplified Proof of the NP- and MAX SNP-Hardness of Multiple Sequence Tree Alignment . . . . . . . . . . . . . . . 509--514 Craig Benham and Sampath Kannan and Michael Paterson and Tandy Warnow Hen's Teeth and Whale's Feet: Generalized Characters and Their Compatibility . . . . . . . . . . . . . 515--525 Boris A. Reva and Dmitrii S. Rykunov and Arthur J. Olson and Alexei V. Finkelstein Constructing Lattice Models of Protein Chains with Side Groups . . . . . . . . 527--535 Victor M. Markowitz Heterogeneous Molecular Biology Databases . . . . . . . . . . . . . . . 537--538 Stanley Letovsky Beyond the Information Maze . . . . . . 539--546 Victor M. Markowitz and Otto Ritter Characterizing Heterogeneous Molecular Biology Database Systems . . . . . . . . 547--556 S. B. Davidson and C. Overton and P. Buneman Challenges in Integrating Biological Data Sources . . . . . . . . . . . . . . 557--572 Peter D. Karp A Strategy for Database Interoperation 573--586
Pankaj Agarwal and David J. States A Bayesian Evolutionary Distance for Parametrically Aligned Sequences . . . . 1--17 Michael D. Hendy and David Penny Complete Families of Linear Invariants for Some Stochastic Models of Sequence Evolution, with and without the Molecular Clock Assumption . . . . . . . 19--31 Eugene W. Myers Approximate Matching of Network Expressions with Spacers . . . . . . . . 33--51 William E. Hart and Sorin C. Istrail Fast Protein Folding in the Hydrophobic--Hydrophilic Model within Three-Eighths of Optimal . . . . . . . . 53--96 Yoshikane Takahashi A Mathematical Solution to a Network Designing Problem . . . . . . . . . . . 97--141 Rajani R. Joshi and K. Krishnanand Probabilistic Learning in Immune Network: Weighted Tree Matching Model 143--162 Sòren Kamaric Riis and Anders Krogh Improving Prediction of Protein Secondary Structure Using Structured Neural Networks and Multiple Sequence Alignments . . . . . . . . . . . . . . . 163--183 Simon Tsang and Milton H. Saier, Jr. A Simple Flexible Program for the Computational Analysis of Amino Acyl Residue Distribution in Proteins: Application to the Distribution of Aromatic versus Aliphatic Hydrophobic Amino Acids in Transmembrane $ \alpha $-Helical Spanners of Integral Membrane Transport Proteins . . . . . . . . . . . 185--190 Peter D. Karp and Suzanne Paley Integrated Access to Metabolic and Genomic Data . . . . . . . . . . . . . . 191--212
Raj K. Singh and Alexander Tropsha and Iosif I. Vaisman Delaunay Tessellation of Proteins: Four Body Nearest-Neighbor Propensities of Amino Acid Residues . . . . . . . . . . 213--221 M. S. Gelfand and L. I. Podolsky and T. V. Astakhova and M. A. Roytberg Recognition of Genes in Human DNA Sequences . . . . . . . . . . . . . . . 223--234 Bernd Schierwater and Dirk Metzler and Katja Krüger and Bruno Streit The Effects of Nested Primer Binding Sites on the Reproducibility of PCR: Mathematical Modeling and Computer Simulation Studies . . . . . . . . . . . 235--251 Martijn A. Huynen and Alan Perelson and Wayne A. Vieira and Peter F. Stadler Base Pairing Probabilities in a Complete HIV-1 RNA . . . . . . . . . . . . . . . 253--274 David Bryant Hunting for Trees in Binary Character Sets: Efficient Algorithms for Extraction, Enumeration, and Optimization . . . . . . . . . . . . . . 275--288 Ina Koch and Thomas Lengauer and Egon Wanke An Algorithm for Finding Maximal Common Subtopologies in a Set of Protein Structures . . . . . . . . . . . . . . . 289--306 Colleen Kelly and Gary A. Churchill Biases in Amino Acid Replacement Matrices and Alignment Scores Due to Rate Heterogeneity . . . . . . . . . . . 307--318 Prakash Nadkarni and Kei-Hoi Cheung and Carmela Castiglione and Perry Miller and Kenneth Kidd DNA Workbench: a Database Package to Manage Regional Physical Mapping . . . . 319--329 Martin Dyer and Alan Frieze and Stephen Suen Corrigendum to \booktitleProbability of Unique Solutions of Sequencing by Hybridization . . . . . . . . . . . . . 331--331
Ying Xu and Richard J. Mural and Edward C. Uberbacher An Iterative Algorithm for Correcting Sequencing Errors in DNA Coding Regions 333--344 Ming-Ying Leung and Genevieve M. Marsh and Terence P. Speed Over- and Underrepresentation of Short DNA Words in Herpesvirus Genomes . . . . 345--360 Hiroshi Mamitsuka A Learning Method of Hidden Markov Models for Sequence Discrimination . . . 361--373 Thomas D. Wu A Segment-Based Dynamic Programming Algorithm for Predicting Gene Structure 375--394 E. Knill and A. Schliep and D. C. Torney Interpretation of Pooling Experiments Using the Markov Chain Monte Carlo Method . . . . . . . . . . . . . . . . . 395--406 Hugh Salamon and Jorma Tarhio and Kjersti Rònningen and Glenys Thomson On Distinguishing Unique Combinations in Biological Sequences . . . . . . . . . . 407--423 Richard Arratia and Daniela Martin and Gesine Reinert and Michael S. Waterman Poisson Process Approximation for Sequence Repeats, and Sequencing by Hybridization . . . . . . . . . . . . . 425--463 Robert J. Robbins Bioinformatics: Essential Infrastructure for Global Biology$^1$ . . . . . . . . . 465--478
R. C. Griffiths and P. Marjoram Ancestral Inference from Samples of DNA Sequences with Recombination . . . . . . 479--502 Suchendra M. Bhandarkar and Sridhar Chirravuri and Jonathan Arnold Parallel Computing of Physical Maps --- a Comparative Study in SIMD and MIMD Parallelism . . . . . . . . . . . . . . 503--528 Rajani R. Joshi A Self-Organizing Cognitive Network of Antibody Repertoire Development . . . . 529--545 Cathy H. Wu and Sheng Zhao and Hsi-Lien Chen A Protein Class Database Organized with ProSite Protein Groups and PIR Superfamilies . . . . . . . . . . . . . 547--561 Gene Myers and Sanford Selznick and Zheng Zhang and Webb Miller Progressive Multiple Alignment with Constraints . . . . . . . . . . . . . . 563--572 Michael Teitelman and Frank H. Eeckman Principal Component Analysis and Large-Scale Correlations in Non-Coding Sequences of Human DNA . . . . . . . . . 573--576
William E. Hart and Sorin Istrail Robust Proofs of NP-Hardness for Protein Folding: General Lattices and Energy Potentials . . . . . . . . . . . . . . . 1--22 Martin Vingron and Arndt Von Haeseler Towards Integration of Multiple Alignment and Phylogenetic Tree Construction . . . . . . . . . . . . . . 23--34 Miroslav S. Tanushev and Richard Arratia Central Limit Theorem for Renewal Theory for Several Patterns . . . . . . . . . . 35--44 Timothy L. Bailey and Michael Gribskov Score Distributions for Simultaneous Matching to Multiple Motifs . . . . . . 45--59 Sophie Schbath Coverage Processes in Physical Mapping by Anchoring Random Clones . . . . . . . 61--82 Michael P. Ponomarenko and Anna N. Kolchanova and Nikolay A. Kolchanov Generating Programs for Predicting the Activity of Functional Sites . . . . . . 83--90
Thomas S. Anantharaman and Bud Mishra and David C. Schwartz Genomics via Optical Mapping II: Ordered Restriction Maps . . . . . . . . . . . . 91--118 Vlado Dan\vcík and Sridhar Hannenhalli and S. Muthukrishnan Hardness of Flip-Cut Problems from Optical Mapping . . . . . . . . . . . . 119--125 John Henderson and Steven Salzberg and Kenneth H. Fasman Finding Genes in DNA with a Hidden Markov Model . . . . . . . . . . . . . . 127--141 Paul E. Kearney A Six-Point Condition for Ordinal Matrices . . . . . . . . . . . . . . . . 143--156 Martin Farach Recognizing Circular Decomposable Metrics . . . . . . . . . . . . . . . . 157--162 Dorit S. Hochbaum and Anu Pathria Path Costs in Evolutionary Tree Reconstruction . . . . . . . . . . . . . 163--175 Louxin Zhang On a Mirkin--Muchnik--Smith Conjecture for Comparing Molecular Phylogenies . . 177--187 Sophie Schbath An Efficient Statistic to Detect Over- and Under-represented Words in DNA Sequences . . . . . . . . . . . . . . . 189--192 Jacob Z. Dalgaard and Michael J. Moser and Richard Hughey and I. Saira Mian Statistical Modeling, Phylogenetic Analysis and Structure Prediction of a Protein Splicing Domain Common to Inteins and Hedgehog Proteins . . . . . 193--214
Michael S. Waterman and Sorin Istrail and Pavel A. Pevzner Preface: Special RECOMB'97 Issues . . . 215--215 Temple F. Smith and Loredana Lo Conte and Jadwiga Bienkowska and Chrysanthe Gaitatzes and Robert G. Rogers, Jr. and Richard Lathrop Current Limitations to Protein Threading Approaches . . . . . . . . . . . . . . . 217--225 K. A. Dill and A. T. Phillips and J. B. Rosen Protein Structure and Energy Landscape Dependence on Sequence Using a Continuous Energy Function . . . . . . . 227--239 William E. Hart and Sorin Istrail Lattice and Off-Lattice Side Chain Models of Protein Folding: Linear Time Structure Prediction Better than 86% of Optimal . . . . . . . . . . . . . . . . 241--259 Bonnie Berger and Mona Singh An Iterative Method for Improved Protein Structural Motif Recognition . . . . . . 261--273 Richa Agarwala and Serafim Batzoglou and Vlado Dan\vcík and Scott E. Decatur and Sridhar Hannenhalli and Martin Farach and S. Muthukrishnan and Steven Skiena Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model . . . . . 275--296 Sing-Hoi Sze and Pavel A. Pevzner Las Vegas Algorithms for Gene Recognition: Suboptimal and Error-Tolerant Spliced Alignment . . . . 297--309 Martin G. Reese and Frank H. Eeckman and David Kulp and David Haussler Improved Splice Site Detection in Genie 311--323 Ying Xu and Edward C. Uberbacher Automated Gene Identification in Large-Scale Genomic Sequences$^1$ . . . 325--338 Zheng Zhang and William R. Pearson and Webb Miller Aligning a DNA Sequence with a Protein Sequence . . . . . . . . . . . . . . . . 339--349 Gary Benson Sequence Alignment with Tandem Duplication . . . . . . . . . . . . . . 351--367 Eric L. Anson and Eugene W. Myers ReAligner: a Program for Refining DNA Sequence Multi-Alignments . . . . . . . 369--383 Tetsuo Shibuya and Hiroshi Imai New Flexible Approaches for Multiple Sequence Alignment . . . . . . . . . . . 385--413 Benno Schwikowski and Martin Vingron The Deferred Path Heuristic for the Generalized Tree Alignment Problem . . . 415--431
Thomas Christof and Michael Jünger and John Kececioglu and Petra Mutzel and Gerhard Reinelt A Branch-and-Cut Approach to Physical Mapping of Chromosomes by Unique End-Probes . . . . . . . . . . . . . . . 433--447 Mudita Jain and Eugene W. Myers Algorithms for Computing and Integrating Physical Maps Using Unique Probes . . . 449--466 Fengzhu Sun and Gary Benson and Norm Arnheim and Michael Waterman Pooling Strategies for Establishing Physical Genome Maps Using FISH . . . . 467--486 Donna Slonim and Leonid Kruglyak and Lincoln Stein and Eric Lander Building Human Genome Maps with Radiation Hybrids . . . . . . . . . . . 487--504 S. C. Heath Markov Chain Monte Carlo Methods for Radiation Hybrid Mapping . . . . . . . . 505--515 Amir Ben-Dor and Benny Chor On Constructing Radiation Hybrid Maps 517--533 Shili Lin and Terence P. Speed An Algorithm for Haplotype Analysis . . 535--546 Jaime Cohen and Martin Farach Numerical Taxonomy on Data: Experimental Results . . . . . . . . . . . . . . . . 547--558 David Sankoff and Vincent Ferretti and Joseph H. Nadeau Conserved Segment Identification . . . . 559--565
Leonid Kruglyak and Eric S. Lander Faster Multipoint Linkage Analysis Using Fourier Transforms . . . . . . . . . . . 1--7 S. Rao Kosaraju and Alejandro A. Schäffer and Leslie G. Biesecker Approximation Algorithms for a Genetic Diagnostics Problem . . . . . . . . . . 9--26 Bonnie Berger and Tom Leighton Protein Folding in the Hydrophobic--Hydrophilic (\em HP) Model is NP-Complete . . . . . . . . . . . . . 27--40 Vincent Escalier and Joél Pothier and Henri Soldano and Alain Viari Pairwise and Multiple Identification of Three-Dimensional Common Substructures in Proteins . . . . . . . . . . . . . . 41--56 I. Saira Mian and Michael J. Moser and William R. Holley and Aloke Chatterjee Statistical Modelling and Phylogenetic Analysis of a Deaminase Domain . . . . . 57--72 Daniel E. Bentil Modelling and Simulation of Motility in Actomyosin Systems . . . . . . . . . . . 73--86 Gary Benson and Xiaoping Su On the Distribution of $K$-tuple Matches for Sequence Homology: a Constant Time Exact Calculation of the Variance . . . 87--100 Andrew F. Siegel and Jared C. Roach and Ger Van Den Engh Expectation and Variance of True and False Fragment Matches in DNA Restriction Mapping . . . . . . . . . . 101--111 Andrew F. Siegel and Jared C. Roach and Charles Magness and Ed Thayer and Ger Van Den Engh Optimization of Restriction Fragment DNA Mapping . . . . . . . . . . . . . . . . 113--126 Lusheng Wang and Dan Gusfield Constructing Additive Trees When the Error Is Small . . . . . . . . . . . . . 127--133 O. Eulenstein and B. Mirkin and M. Vingron Duplication-Based Measures of Difference Between Gene and Species Trees . . . . . 135--148 Arndt Von Haeseler and Michael Schöniger Evolution of DNA or Amino Acid Sequences with Dependent Sites . . . . . . . . . . 149--163 Semyon Kruglyak Multistage Sequencing by Hybridization 165--171
Alberto Apostolico and Raffaele Giancarlo Sequence Alignment in Molecular Biology 173--196 Zheng Zhang and Piotr Berman and Webb Miller Alignments Without Low-Scoring Regions 197--210 Timothy L. Bailey and Michael Gribskov Methods and Statistics for Combining Motif Match Scores . . . . . . . . . . . 211--221 Gesine Reinert and Sophie Schbath Compound Poisson and Poisson Process Approximations for Occurrences of Multiple Words in Markov Chains . . . . 223--253 Lloyd M. Smith and Robert M. Corn and Anne E. Condon and Max G. Lagally and Anthony G. Frutos and Qinghua Liu and Andrew J. Thiel A Surface-Based Approach to DNA Computation . . . . . . . . . . . . . . 255--267 Qinghua Liu and Anthony G. Frutos and Andrew J. Thiel and Robert M. Corn and Lloyd M. Smith DNA Computing on Surfaces: Encoding Information at the Single Base Level . . 269--278 Alvis Brazma and Inge Jonassen and Ingvar Eidhammer and David Gilbert Approaches to the Automatic Discovery of Patterns in Biosequences . . . . . . . . 279--305 Michael T. Laub and Douglas W. Smith Finding Intron/Exon Splice Junctions Using INFO, INterruption Finder and Organizer . . . . . . . . . . . . . . . 307--321 Sharon Browning Relationship Information Contained in Gamete Identity by Descent Data . . . . 323--334 Teresa M. Przytycka Transforming Rooted Agreement into Unrooted Agreement . . . . . . . . . . . 335--349 Nora Benhabil\`es and Xavier Gallet and Annick Thomas-Soumarmon and Robert Brasseur A Descriptive Analysis of Populations of Three-Dimensional Structures Calculated from Primary Sequences of Proteins by OSIRIS . . . . . . . . . . . . . . . . . 351--366
Pavel A. Pevzner Preface . . . . . . . . . . . . . . . . 367--367 Azat Ya Badretdinov and Alexei V. Finkelstein How Homologs Can Help to Predict Protein Folds Even Though They Cannot Be Predicted for Individual Sequences . . . 369--376 Amir Ben-Dor and Benny Chor and Dan Graur and Ron Ophir and Dan Pelleg Constructing Phylogenies from Quartets: Elucidation of Eutherian Superordinal Relationships . . . . . . . . . . . . . 377--390 Maria Bonet and Mike Steel and Tandy Warnow and Shibu Yooseph Better Methods for Solving Parsimony and Compatibility . . . . . . . . . . . . . 391--407 Cheng Che Chen and Jas Winder Pal Singh and Russ B. Altman Hierarchical Organization of Molecular Structure Computations . . . . . . . . . 409--422 Pierluigi Crescenzi and Deborah Goldman and Christos Papadimitriou and Antonio Piccolboni and Mihalis Yannakakis On the Complexity of Protein Folding . . 423--465 Israel Gelfand and Alexander Kister and Casimir Kulikowski and Ognyan Stoyanov Algorithmic Determination of Core Positions in the $ V_L $ and $ V_H $ Domains of Immunoglobulin Molecules . . 467--477 William Noble Grundy Homology Detection via Family Pairwise Search . . . . . . . . . . . . . . . . . 479--491 Ian Holmes and Richard Durbin Dynamic Programming Alignment Accuracy 493--504 Jae K. Lee and Vlado Dan\vcík and Michael S. Waterman Estimation for Restriction Sites Observed by Optical Mapping Using Reversible-Jump Markov Chain Monte Carlo 505--515 Hans-Peter Lenhof and Knut Reinert and Martin Vingron A Polyhedral Approach to RNA Sequence Structure Alignment . . . . . . . . . . 517--530 Boris A. Reva and D. S. Rykunov and Alexei V. Finkelstein and Jeffrey Skolnick Optimization of Protein Structure on Lattices Using a Self-Consistent Field Approach . . . . . . . . . . . . . . . . 531--538 Marie-France Sagot and Eugene W. Myers Identifying Satellites and Periodic Repetitions in Biological Sequences . . 539--553 David Sankoff and Mathieu Blanchette Multiple Genome Rearrangement and Breakpoint Phylogeny . . . . . . . . . . 555--570 Wynn L. Walker and David S. Goodsell and Elliot M. Landaw An Analysis of a Class of DNA Sequence Reading Molecules . . . . . . . . . . . 571--583 Thomas D. Wu and Scott C. Schmidler and Trevor Hastie and Douglas L. Brutlag Regression Analysis of Multiple Protein Structures . . . . . . . . . . . . . . . 585--595 Ying Xu and Dong Xu and Edward C. Uberbacher An Efficient Computational Method for Globally Optimal Threading1 . . . . . . 597--614
Sam Roweis and Erik Winfree and Richard Burgoyne and Nickolas V. Chelyapov and Myron F. Goodman and Paul W. K. Rothemund and Leonard M. Adleman A Sticker-Based Model for DNA Computation . . . . . . . . . . . . . . 615--629 Bilha Sandak and Ruth Nussinov and Haim J. Wolfson A Method for Biomolecular Structural Recognition and Docking Allowing Conformational Flexibility . . . . . . . 631--654 Wing Hung Wong and Yan Cui and Run Sheng Chen Torsional Relaxation for Biopolymers . . 655--665 Steven Salzberg and Arthur L. Delcher and Kenneth H. Fasman and John Henderson A Decision Tree System for Finding Genes in DNA . . . . . . . . . . . . . . . . . 667--680 Roderic Guigó Assembling Genes from Predicted Exons in Linear Time with Dynamic Programming . . 681--702 Ronna R. Mallios Iterative Stepwise Discriminant Analysis: a Meta-Algorithm for Detecting Quantitative Sequence Motifs . . . . . . 703--711 Steven N. Evans and Xiaowen Zhou Constructing and Counting Phylogenetic Invariants . . . . . . . . . . . . . . . 713--724 Laxmi Parida A Uniform Framework for Ordered Restriction Map Problems . . . . . . . . 725--739 Nicholas Tran An Easy Case of Sorting by Reversals . . 741--746 Takako Takai-Igarashi and Yoko Nadaoka and Tsuguchika Kaminuma A Database for Cell Signaling Networks 747--754
Bonnie Berger and Gunnar W. Hoest and James R. Paulson and Peter W. Shor On the Structure of the Scaffolding Core of Bacteriophage T4 . . . . . . . . . . 1--12 Ashwin Nayak and Alistair Sinclair and Uri Zwick Spatial Codes and the Hardness of String Folding Problems . . . . . . . . . . . . 13--36 Richard Desper and Feng Jiang and Olli-P. Kallioniemi and Holger Moch and Christos H. Papadimitriou and Alejandro A. Schäffer Inferring Tree Models for Oncogenesis from Comparative Genome Hybridization Data . . . . . . . . . . . . . . . . . . 37--51 Leonard M. Adleman and Paul W. K. Rothemund and Sam Roweis and Erik Winfree On Applying Molecular Computation to the Data Encryption Standard . . . . . . . . 53--63 Sam Roweis and Erik Winfree On the Reduction of Errors in DNA Computation . . . . . . . . . . . . . . 65--75 Fengzhu Sun Modeling DNA Shuffling . . . . . . . . . 77--90 Richard Mott and Roger Tribe Approximate Statistics of Gapped Alignments . . . . . . . . . . . . . . . 91--112 J. B\la\.zewicz and P. Formanowicz and M. Kasprzak and W. T. Markiewicz and J. W\ceglarz DNA Sequencing With Positive and Negative Errors . . . . . . . . . . . . 113--123 David Loewenstern and Peter N. Yianilos Significantly Lower Entropy Estimates for Natural DNA Sequences . . . . . . . 125--142
S. Istrail and R. Schwartz and J. King Lattice Simulations of Aggregation Funnels for Protein Folding . . . . . . 143--162 Sun Kim and Alberto Maria Segre AMASS: a Structured Pattern Matching Approach to Shotgun Sequence Assembly 163--186 Dan Fasulo and Tao Jiang and Richard M. Karp and Reuben J. Settergren and Ed Thayer An Algorithmic Approach to Multiple Complete Digest Mapping . . . . . . . . 187--207 Jason T. L. Wang and Steve Rozen and Bruce A. Shapiro and Dennis Shasha and Zhiyuan Wang and Maisheng Yin New Techniques for DNA Sequence Classification . . . . . . . . . . . . . 209--218 Thomas D. Wu and Craig G. Nevill-Manning and Douglas L. Brutlag Minimal-Risk Scoring Matrices for Sequence Analysis . . . . . . . . . . . 219--235 Guy Mayraz and Ron Shamir Construction of Physical Maps from Oligonucleotide Fingerprints Data . . . 237--252 Lihua Yu and Temple F. Smith Positional Statistical Significance in Sequence Alignment . . . . . . . . . . . 253--259 Gary A. Churchill and Betty Lazareva Bayesian Restoration of a Hidden Markov Chain with Applications to DNA Sequencing . . . . . . . . . . . . . . . 261--277
Sorin Istrail Special RECOMB'99 Issue . . . . . . . . 279--279 Amir Ben-Dor and Ron Shamir and Zohar Yakhini Clustering Gene Expression Patterns . . 281--297 Jadwiga R. Bie\'nkowska and Robert G. Rogers, Jr. and Temple F. Smith Performance of Threading Scoring Functions Designed Using New Optimization Method . . . . . . . . . . 299--311 L. Paul Chew and Dan Huttenlocher and Klara Kedem and Jon Kleinberg Fast Detection of Common Geometric Substructure in Proteins . . . . . . . . 313--325 Vlado Dan\vcík and Theresa A. Addona and Karl R. Clauser and James E. Vath and Pavel A. Pevzner \em De Novo Peptide Sequencing via Tandem Mass Spectrometry . . . . . . . . 327--342 Christian V. Forst and Klaus Schulten Evolution of Metabolisms: a New Method for the Comparison of Metabolic Pathways Using Genomics Information . . . . . . . 343--360 Alan M. Frieze and Franco P. Preparata and Eli Upfal Optimal Reconstruction of a Sequence from its Probes . . . . . . . . . . . . 361--368 Daniel H. Huson and Scott M. Nettles and Tandy J. Warnow Disk-Covering, a Fast-Converging Method for Phylogenetic Tree Reconstruction . . 369--386 Jon M. Kleinberg Efficient Algorithms for Protein Sequence Design and the Analysis of Certain Evolutionary Fitness Landscapes 387--404 Richard H. Lathrop An Anytime Local-to-Global Optimization Algorithm for Protein Threading in O(m$^2$ ñ$^2$ ) Space . . . . . . . . . . 405--418 Lior Pachter and Serafim Batzoglou and Valentin I. Spitkovsky and Eric Banks and Eric S. Lander and Daniel J. Kleitman and Bonnie Berger A Dictionary-Based Approach for Gene Annotation . . . . . . . . . . . . . . . 419--430 David Sankoff and Mathieu Blanchette Phylogenetic Invariants for Genome Rearrangements . . . . . . . . . . . . . 431--445 Peter Willett Dissimilarity-Based Algorithms for Selecting Structurally Diverse Sets of Compounds . . . . . . . . . . . . . . . 447--457 John C. Wooley Trends in Computational Biology: a Summary Based on a RECOMB Plenary Lecture, 1999 . . . . . . . . . . . . . 459--474
Gesine Reinert and Sophie Schbath and Michael S. Waterman Probabilistic and Statistical Properties of Words: An Overview . . . . . . . . . 1--46 Sophie Schbath and Nathalie Bossard and Simon Tavaré The Effect of Nonhomogeneous Clone Length Distribution on the Progress of an STS Mapping Project . . . . . . . . . 47--57 Vineet Bafna and Sridhar Hannenhalli and Ken Rice and Lisa Vawter Ligand-Receptor Pairing Via Tree Comparison . . . . . . . . . . . . . . . 59--70 Alberto Apostolico and Mary Ellen Bock and Stefano Lonardi and Xuyan Xu Efficient Detection of Unusual Words . . 71--94 Tommi Jaakkola and Mark Diekhans and David Haussler A Discriminative Framework for Detecting Remote Protein Homologies . . . . . . . 95--114 Dirk Drasdo and Terence Hwa and Michael Lässig Scaling Laws and Similarity Detection in Sequence Alignment with Gaps . . . . . . 115--141 Dai Wang and Cheng Zhao and Rong Cheng and Fengzhu Sun Estimation of the Mutation Rate During Error-prone Polymerase Chain Reaction 143--158 Gráinne McGuire and Frank Wright and Michael J. Prentice A Bayesian Model for Detecting Past Recombination Events in DNA Multiple Alignments . . . . . . . . . . . . . . . 159--170 Martin Fekete and Ivo L. Hofacker and Peter F. Stadler Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers . . . . . . . . . . . . . . . 171--182 Igor N. Berezovsky and Natalia G. Esipova and Vladimir G. Tumanyan Hierarchy of Regions of Amino Acid Sequence with Respect to Their Role in the Protein Spatial Structure . . . . . 183--192 Sophie Schbath An Overview on the Distribution of Word Counts in Markov Chains . . . . . . . . 193--201 Zheng Zhang and Scott Schwartz and Lukas Wagner and Webb Miller A Greedy Algorithm for Aligning DNA Sequences . . . . . . . . . . . . . . . 203--214 V. E. Ramensky and V. Ju. Makeev and M. A. Roytberg and V. G. Tumanyan DNA Segmentation Through the Bayesian Approach . . . . . . . . . . . . . . . . 215--231 Scott C. Schmidler and Jun S. Liu and Douglas L. Brutlag Bayesian Segmentation of Protein Secondary Structure . . . . . . . . . . 233--248 François Rodolphe and Catherine Mathé Translation Conditional Models for Protein Coding Sequences . . . . . . . . 249--260 Gaston H. Gonnet and Chantal Korostensky and Steve Benner Evaluation Measures of Multiple Sequence Alignments . . . . . . . . . . . . . . . 261--276 Vincent Moulton and Michael Zuker and Michael Steel and Robin Pointon and David Penny Metrics on RNA Secondary Structures . . 277--292 Piotr Berman and Zheng Zhang and Yuri I. Wolf and Eugene V. Koonin and Webb Miller Winnowing Sequences from a Database Search . . . . . . . . . . . . . . . . . 293--302 Richard M. Karp and Ron Shamir Algorithms for Optical Mapping . . . . . 303--316 Edward C. Thayer and Chris Bystroff and David Baker Detection of Protein Coding Sequences Using a Mixture Model for Local Protein Amino Acid Sequence . . . . . . . . . . 317--327
Ron Shamir Preface: Special RECOMB 2000 Issue . . . 329--330 Tatsuya Akutsu and Satoru Miyano and Satoru Kuhara Algorithms for Identifying Boolean Networks and Related Biological Networks Based on Matrix Multiplication and Fingerprint Function . . . . . . . . . . 331--343 Laurent Marsan and Marie-France Sagot Algorithms for Extracting Structured Motifs Using a Suffix Tree with an Application to Promoter and Regulatory Site Consensus Identification . . . . . 345--362 Y. Zenmei Ohkubo and Gordon M. Crippen Potential Energy Function for Continuous State Models of Globular Proteins . . . 363--379 Alberto Apostolico and Gill Bejerano Optimal Amnesic Probabilistic Automata or How to Learn and Classify Proteins in Linear Time and Space . . . . . . . . . 381--393 Steffen Heber and Jens Stoye and Marcus Frohme and Jörg Hoheisel and Martin Vingron Contig Selection in Physical Mapping . . 395--408 Rune B. Lyngsò and Christian N. S. Pedersen RNA Pseudoknot Prediction in Energy-Based Models . . . . . . . . . . 409--427 Kevin Chen and Dannie Durand and Martin Farach-Colton NOTUNG: a Program for Dating Gene Duplications and Optimizing Gene Family Trees . . . . . . . . . . . . . . . . . 429--447 Ying Xu and Dong Xu and Oakley H. Crawford and J. Ralph Einstein A Computational Method for NMR-Constrained Protein Threading . . . 449--467 Jon M. Sorenson and Teresa Head-Gordon Matching Simulation and Experiment: a New Simplified Model for Simulating Protein Folding . . . . . . . . . . . . 469--481 Alexander Zien and Ralf Zimmer and Thomas Lengauer A Simple Iterative Approach to Parameter Optimization . . . . . . . . . . . . . . 483--501 Amir Ben-Dor and Richard Karp and Benno Schwikowski and Zohar Yakhini Universal DNA Tag Systems: a Combinatorial Design Scheme . . . . . . 503--519 David Sankoff and David Bryant and Mélanie Deneault and B. Franz Lang and Gertraud Burger Early Eukaryote Evolution Based on Mitochondrial Gene Order Breakpoints . . 521--535 Chris Bailey-Kellogg and Alik Widge and John J. Kelley and Marcelo J. Berardi and John H. Bushweller and Bruce Randall Donald The NOESY Jigsaw: Automated Protein Secondary Structure and Main-Chain Assignment from Sparse, Unassigned NMR Data . . . . . . . . . . . . . . . . . . 537--558 Amir Ben-Dor and Laurakay Bruhn and Nir Friedman and Iftach Nachman and Mich\`el Schummer and Zohar Yakhini Tissue Classification with Gene Expression Profiles . . . . . . . . . . 559--583 Reece K. Hart and Ajay K. Royyuru and Gustavo Stolovitzky and Andrea Califano Systematic and Fully Automated Identification of Protein Sequence Patterns . . . . . . . . . . . . . . . . 585--600 Nir Friedman and Michal Linial and Iftach Nachman and Dana Pe'er Using Bayesian Networks to Analyze Expression Data . . . . . . . . . . . . 601--620 Franco P. Preparata and Eli Upfal Sequencing-by-Hybridization at the Information-Theory Bound: an Optimal Algorithm . . . . . . . . . . . . . . . 621--630 Anonymous Abstracts from TIGR's Fourth Annual Conference on Computational Genomics November 16--19, 2000 Baltimore, MD . . 631--651
Martin Lermen and Knut Reinert The Practical Use of the $ A* $ Algorithm for Exact Multiple Sequence Alignment . . . . . . . . . . . . . . . 655--671 Ognyan Stoyanov and Alexander Kister and Israel Gelfand and Casimir Kulikowski and Cyrus Chothia Geometric Invariant Core for the $ C_L $ and $C$$_{H 1}$ Domains of Immunoglobulin Molecules . . . . . . . . 673--684 Ingvar Eidhammer and Inge Jonassen and William R. Taylor Structure Comparison and Structure Patterns . . . . . . . . . . . . . . . . 685--716 Simon E. Cawley and Terence P. Speed DNA Sequencing with Transposons . . . . 717--729 Vladimir Makarenkov and Bruno Leclerc Comparison of Additive Trees Using Circular Orders . . . . . . . . . . . . 731--744 Richard M. Karp and Itsik Pe'er and Ron Shamir An Algorithm Combining Discrete and Continuous Methods for Optical Mapping 745--760
Tobias Müller and Martin Vingron Modeling Amino Acid Replacement . . . . 761--776 Pavel A. Pevzner and Vlado Dan\vcík and Chris L. Tang Mutation-Tolerant Protein Identification by Mass Spectrometry . . . . . . . . . . 777--787 Richard Desper and Feng Jiang and Olli-P. Kallioniemi and Holger Moch and Christos H. Papadimitriou and Alejandro A. Schäffer Distance-Based Reconstruction of Tree Models for Oncogenesis . . . . . . . . . 789--803 Trey Ideker and Vesteinn Thorsson and Andrew F. Siegel and Leroy E. Hood Testing for Differentially-Expressed Genes by Maximum-Likelihood Analysis of Microarray Data . . . . . . . . . . . . 805--817 M. Kathleen Kerr and Mitchell Martin and Gary A. Churchill Analysis of Variance for Gene Expression Microarray Data . . . . . . . . . . . . 819--837 Dirk Faulhammer and Richard J. Lipton and Laura F. Landweber Fidelity of Enzymatic Ligation for DNA Computing . . . . . . . . . . . . . . . 839--848 I. S. Mian and I. Dubchak Representing and Reasoning about Protein Families Using Generative and Discriminative Methods . . . . . . . . . 849--862
Gad M. Landau and Jeanette P. Schmidt and Dina Sokol An Algorithm for Approximate Tandem Repeats . . . . . . . . . . . . . . . . 1--18 Chris Bailey-Kellogg and John J. Kelleyiii and Cliff Stein and Bruce Randall Donald Reducing Mass Degeneracy in SAR by MS by Stable Isotopic Labeling . . . . . . . . 19--36 M. A. Newton and C. M. Kendziorski and C. S. Richmond and F. R. Blattner and K. W. Tsui On Differential Variability of Expression Ratios: Improving Statistical Inference about Gene Expression Changes from Microarray Data . . . . . . . . . . 37--52 David Liben-Nowell On the Structure of Syntenic Distance 53--67 Lusheng Wang and Kaizhong Zhang and Louxin Zhang Perfect Phylogenetic Networks with Recombination . . . . . . . . . . . . . 69--78 Michael A. Charleston Hitch-Hiking: a Parallel Heuristic Search Strategy, Applied to the Phylogeny Problem . . . . . . . . . . . 79--91
Nathaniel Leibowitz and Ruth Nussinov and Haim J. Wolfson MUSTA --- a General, Efficient, Automated Method for Multiple Structure Alignment and Detection of Common Motifs: Application to Proteins . . . . 93--121 Peter B. Gilbert and Vladimir A. Novitsky and Monty A. Montano and Max Essex An Efficient Test for Comparing Sequence Diversity between Two Populations . . . 123--139 Earl Hubbell Multiplex Sequencing by Hybridization 141--149 Jeff Elhai Determination of Bias in the Relative Abundance of Oligonucleotides in DNA Sequences . . . . . . . . . . . . . . . 151--175 T. Gregory Dewey A Sequence Alignment Algorithm with an Arbitrary Gap Penalty Function . . . . . 177--190 Hongyu Zhao and Feng Liang On Relationship Inference Using Gamete Identity by Descent Data . . . . . . . . 191--200
Amit Marathe and Anne E. Condon and Robert M. Corn On Combinatorial DNA Word Design . . . . 201--219 Xun Gu Mathematical Modeling for Functional Divergence after Gene Duplication . . . 221--234 Pierre Nicod\`eme Fast Approximate Motif Statistics . . . 235--248 Yi-Kuo Yu and Terence Hwa Statistical Significance of Probabilistic Sequence Alignment and Related Local Hidden Markov Models . . . 249--282 Paul Horton Tsukuba BB: a Branch and Bound Algorithm for Local Multiple Alignment of DNA and Protein Sequences . . . . . . . . . . . 283--303 Dan Gusfield Inference of Haplotypes from Samples of Diploid Populations: Complexity and Algorithms . . . . . . . . . . . . . . . 305--323 Ting Chen and Ming-Yang Kao and Matthew Tepel and John Rush and George M. Church A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry . . . . . . . . . . . . . . 325--337 David B. Searls From Jabberwocky to Genome: Lewis Carroll and Computational Biology . . . 339--348
Stéphane Robin and Sophie Schbath Numerical Comparison of Several Approximations of the Word Count Distribution in Random Sequences . . . . 349--359 A. Ben-Dor and I. Pe'er and R. Shamir and R. Sharan On the Complexity of Positional Sequencing by Hybridization . . . . . . 361--371 S. Mercier and J. J. Daudin Exact Distribution for the Local Score of One i.i.d. Random Sequence . . . . . 373--380 C. Devauchelle and A. Grossmann and A. Hénaut and M. Holschneider and M. Monnerot and J. L. Risler and B. Torrésani Rate Matrices for Analyzing Large Families of Protein Sequences . . . . . 381--399 Dirk Husmeier and Frank Wright Detection of Recombination in DNA Multiple Alignments with Hidden Markov Models . . . . . . . . . . . . . . . . . 401--427 Mattias Wahde and John Hertz Modeling Genetic Regulatory Dynamics in Neural Development . . . . . . . . . . . 429--442 Andrew B. Goryachev and Pascale F. Macgregor and Aled M. Edwards Unfolding of Microarray Data . . . . . . 443--461
Semyon Kruglyak and Haixu Tang A New Estimator of Significance of Correlation in Time Series Data . . . . 463--470 Kuang Lin and Alex C. W. May and William R. Taylor Amino Acid Substitution Matrices from an Artificial Neural Network Model . . . . 471--481 David A. Bader and Bernard M. E. Moret and Mi Yan A Linear-Time Algorithm for Computing Inversion Distance between Signed Permutations with an Experimental Study 483--491 S. H. Muggleton and C. H. Bryant and A. Srinivasan and A. Whittaker and S. Topp and C. Rawlings Are Grammatical Representations Useful for Learning from Biological Sequence Data? --- a Case Study . . . . . . . . . 493--521 Glenn A. Williams and Jonathan M. Dugan and Russ B. Altman Constrained Global Optimization for Estimating Molecular Structure from Atomic Distances . . . . . . . . . . . . 523--547 John D. Storey and David Siegmund Approximate $P$-Values for Local Sequence Alignments: Numerical Studies 549--556
David M. Rocke and Blythe Durbin A Model for Measurement Error for Gene Expression Arrays . . . . . . . . . . . 557--569 Ting Chen and Jacob D. Jaffe and George M. Church Algorithms for Identifying Protein Cross-Links via Tandem Mass Spectrometry 571--583 Joachim Theilhaber and Steven Bushnell and Amanda Jackson and Rainer Fuchs Bayesian Estimation of Fold-Changes in the Analysis of Gene Expression: The PFOLD Algorithm . . . . . . . . . . . . 585--614 Winfried Just Computational Complexity of Multiple Sequence Alignment with SP-Score . . . . 615--623 Russell D. Wolfinger and Greg Gibson and Elizabeth D. Wolfinger and Lee Bennett and Hisham Hamadeh and Pierre Bushel and Cynthia Afshari and Richard S. Paules Assessing Gene Significance from cDNA Microarray Expression Data via Mixed Models . . . . . . . . . . . . . . . . . 625--637 Keith A. Baggerly and Kevin R. Coombes and Kenneth R. Hess and David N. Stivers and Lynne V. Abruzzo and Wei Zhang Identifying Differentially Expressed Genes in cDNA Microarray Experiments . . 639--659
Rimli Sengupta and Martin Tompa Quality Control in Manufacturing Oligo Arrays: a Combinatorial Design Approach 1--22 S. Rajasekaran and X. Jin and J. L. Spouge The Efficient Computation of Position-Specific Match Scores with the Fast Fourier Transform . . . . . . . . . 23--33 Jon M. Sorenson and Teresa Head-Gordon Protein Engineering Study of Protein L by Simulation . . . . . . . . . . . . . 35--54 Charles Kooperberg and Thomas G. Fazzio and Jeffrey J. Delrow and Toshio Tsukiyama Improved Background Correction for Spotted DNA Microarrays . . . . . . . . 55--66 Hidde de Jong Modeling and Simulation of Genetic Regulatory Systems: a Literature Review 67--103 Edward R. Dougherty and Junior Barrera and Marcel Brun and Seungchan Kim and Roberto M. Cesar and Yidong Chen and Michael Bittner and Jeffrey M. Trent Inference from Clustering with Application to Gene-Expression Microarrays . . . . . . . . . . . . . . 105--126 Seungchan Kim and Edward R. Dougherty and Junior Barrera and Yidong Chen and Michael L. Bittner and Jeffrey M. Trent Strong Feature Sets from Small Samples 127--146
Thomas Lengauer Preface: Special RECOMB 2001 Issue . . . 147--148 Nancy M. Amato and Guang Song Using Motion Planning to Study Protein Folding Pathways . . . . . . . . . . . . 149--168 Yoseph Barash and Nir Friedman Context-Specific Bayesian Clustering for Gene Expression Data . . . . . . . . . . 169--191 Yonatan Bilu and Michal Linial The Advantage of Functional Prediction Based on Clustering of Yeast Genes and Its Correlation with Non-Sequence Based Classifications . . . . . . . . . . . . 193--210 Mathieu Blanchette and Benno Schwikowski and Martin Tompa Algorithms for Phylogenetic Footprinting 211--223 Jeremy Buhler and Martin Tompa Finding Motifs Using Random Projections 225--242 Ralf Bundschuh Rapid Significance Estimation in Local Sequence Alignment with Gaps . . . . . . 243--260 Lenore Cowen and Phil Bradley and Matthew Menke and Jonathan King and Bonnie Berger Predicting the Beta-Helix Fold from Protein Sequence Data . . . . . . . . . 261--276 Miklós Csurös Fast Recovery of Evolutionary Trees with Thousands of Nodes . . . . . . . . . . . 277--297 Alon Efrat and Frank Hoffmann and Klaus Kriegel and Christof Schultz and Carola Wenk Geometric Algorithms for the Analysis of $2$D-Electrophoresis Gels . . . . . . . 299--315 Vladimir Filkov and Steven Skiena and Jizu Zhi Analysis Techniques for Microarray Time-Series Data . . . . . . . . . . . . 317--330 Nir Friedman and Matan Ninio and Itsik Pe'er and Tal Pupko A Structural EM Algorithm for Phylogenetic Inference . . . . . . . . . 331--353 Alan M. Frieze and Bjarni V. Halldórsson Optimal Sequencing by Hybridization in Rounds . . . . . . . . . . . . . . . . . 355--369 Tao Jiang and Guohui Lin and Bin Ma and Kaizhong Zhang A General Edit Distance between RNA Structures . . . . . . . . . . . . . . . 371--388 Lior Pachter and Marina Alexandersson and Simon Cawley Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems . . . . . . . . . . . . 389--399 Paul Pavlidis and Jason Weston and Jinsong Cai and William Stafford Noble Learning Gene Functional Classifications from Multiple Data Types . . . . . . . . 401--411 Ron Shamir and Dekel Tsur Large Scale Sequencing by Hybridization 413--428 Mengxiang Tang and Michael Waterman and Shibu Yooseph Zinc Finger Gene Clusters and Tandem Gene Duplication . . . . . . . . . . . . 429--446 Gert Thijs and Kathleen Marchal and Magali Lescot and Stephane Rombauts and Bart De Moor and Pierre Rouzé and Yves Moreau A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed Genes . . . . . . 447--464
Natalia Berloff and Markus Perola and Kenneth Lange Spline Methods for the Comparison of Physical and Genetic Maps . . . . . . . 465--475 Shi-Yi Shen and Jun Yang and Adam Yao and Pei-Ing Hwang Super Pairwise Alignment (SPA): an Efficient Approach to Global Alignment for Homologous Sequences . . . . . . . . 477--486 Jian Zhang Analysis of Information Content for Biological Sequences . . . . . . . . . . 487--503 Michael D. Radmacher and Lisa M. McShane and Richard Simon A Paradigm for Class Prediction Using Gene Expression Profiles . . . . . . . . 505--511 Terry Clark and Sanggyu Lee and L. Ridgway Scott and San Ming Wang Computational Analysis of Gene Identification with SAGE . . . . . . . . 513--526 Myong-Hee Sung and Yingdong Zhao and Roland Martin and Richard Simon T-Cell Epitope Prediction with Combinatorial Peptide Libraries . . . . 527--539 Markus E. Nebel Combinatorial Properties of RNA Secondary Structures . . . . . . . . . . 541--573 Timothy L. Bailey and Michael Gribskov Estimating and Evaluating the Statistics of Gapped Local-Alignment Scores . . . . 575--593 Anonymous Correction . . . . . . . . . . . . . . . 594--595
Ernst Althaus and Oliver Kohlbacher and Hans-Peter Lenhof and Peter Müller A Combinatorial Approach to Protein Docking with Flexible Side Chains . . . 597--612 Berrin Yanikoglu and Burak Erman Minimum Energy Configurations of the $2$-Dimensional HP-Model of Proteins by Self-Organizing Networks . . . . . . . . 613--620 Jorng-Tzong Horng and Hsien-Da Huang and Ming-Hui Jin and Li-Cheng Wu and Shir-Ly Huang The Repetitive Sequence Database and Mining Putative Regulatory Elements in Gene Promoter Regions . . . . . . . . . 621--640 Alberto Mercatanti and Giuseppe Rainaldi and Laura Mariani and Roberto Marangoni and Lorenzo Citti A Method for Prediction of Accessible Sites on an mRNA Sequence for Target Selection of Hammerhead Ribozymes . . . 641--653 Kevin R. Coombes and W. Edward Highsmith and Tammy A. Krogmann and Keith A. Baggerly and David N. Stivers and Lynne V. Abruzzo Identifying and Quantifying Sources of Variation in Microarray Data Using High-Density cDNA Membrane Arrays . . . 655--669 Philippe Broët and Sylvia Richardson and François Radvanyi Bayesian Hierarchical Model for Identifying Changes in Gene Expression from Microarray Experiments . . . . . . 671--683 Anonymous Correction . . . . . . . . . . . . . . . 685--685
Richard Desper and Olivier Gascuel Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle . . . . . . 687--705 Giri Narasimhan and Changsong Bu and Yuan Gao and Xuning Wang and Ning Xu and Kalai Mathee Mining Protein Sequences for Motifs . . 707--720 James Aspnes and Julia Hartling and Ming-Yang Kao and Junhyong Kim and Gauri Shah A Combinatorial Toolbox for Protein Sequence Design and Landscape Analysis in the Grand Canonical Model . . . . . . 721--741 João Meidanis and Maria M. T. Walter and Zanoni Dias A Lower Bound on the Reversal and Transposition Diameter . . . . . . . . . 743--745 Rainer Spang and Marc Rehmsmeier and Jens Stoye A Novel Approach to Remote Homology Detection: Jumping Alignments . . . . . 747--760
S. Robin and J.-J. Daudin and H. Richard and M.-F. Sagot and S. Schbath Occurrence Probability of Structured Motifs in Random Sequences . . . . . . . 761--773 Eleazar Eskin and William Stafford Noble and Yoram Singer Using Substitution Matrices to Estimate Probability Distributions for Biological Sequences . . . . . . . . . . . . . . . 775--791 Kajsa Ljungberg and Sverker Holmgren and Örjan Carlborg Efficient Algorithms for Quantitative Trait Loci Mapping Problems . . . . . . 793--804 Thomas L. York and Richard Durrett and Rasmus Nielsen Bayesian Estimation of the Number of Inversions in the History of Two Chromosomes . . . . . . . . . . . . . . 805--818 D. V. Raje and H. J. Purohit and R. N. Singh Distinguishing Features of 16S rDNA Gene for Five Dominating Bacterial Genus Observed in Bioremediation . . . . . . . 819--829 Didier Piau Mutation--Replication Statistics of Polymerase Chain Reactions . . . . . . . 831--847 Scott Doniger and Thomas Hofmann and Joanne Yeh Predicting CNS Permeability of Drug Molecules: Comparison of Neural Network and Support Vector Machine Algorithms 849--864
Bingwen Lu and Ting Chen A Suboptimal Algorithm for \em De Novo Peptide Sequencing via Tandem Mass Spectrometry . . . . . . . . . . . . . . 1--12 Russell Schwartz and Bjarni V. Halldórsson and Vineet Bafna and Andrew G. Clark and Sorin Istrail Robustness of Inference of Haplotype Block Structure . . . . . . . . . . . . 13--19 Agatha H. Liu and Andrea Califano CASTOR: Clustering Algorithm for Sequence Taxonomical Organization and Relationships . . . . . . . . . . . . . 21--45 Xueliang Li and Zimao Li and Lusheng Wang The Inverse Problems for Some Topological Indices in Combinatorial Chemistry . . . . . . . . . . . . . . . 47--55 Joseph S. Oliveira and Colin G. Bailey and Janet B. Jones-Oliveira and David A. Dixon and Dean W. Gull and Mary L. Chandler A Computational Model for the Identification of Biochemical Pathways in the Krebs Cycle . . . . . . . . . . . 57--82 Sujay Chattopadhyay and Jayprokas Chakrabarti Temporal Changes in Phosphoglycerate Kinase Coding Sequences: a Quantitative Measure . . . . . . . . . . . . . . . . 83--93 Magnus Åstrand Contrast Normalization of Oligonucleotide Arrays . . . . . . . . . 95--102
Gene Myers and Richard Durbin A Table-Driven, Full-Sensitivity Similarity Search Algorithm . . . . . . 103--117 Sayan Mukherjee and Pablo Tamayo and Simon Rogers and Ryan Rifkin and Anna Engle and Colin Campbell and Todd R. Golub and Jill P. Mesirov Estimating Dataset Size Requirements for Classifying DNA Microarray Data . . . . 119--142 Yinglei Lai and Deepali Shinde and Norman Arnheim and Fengzhu Sun The Mutation Process of Microsatellites During the Polymerase Chain Reaction . . 143--155 Yaning Yang and Josephine Hoh and Clemens Broger and Martin Neeb and Joanne Edington and Klaus Lindpaintner and Jurg Ott Statistical Methods for Analyzing Microarray Feature Data with Replications . . . . . . . . . . . . . . 157--169 Honghui Wan and Lugang Li and Scott Federhen and John C. Wootton Discovering Simple Regions in Biological Sequences Associated with Scoring Schemes . . . . . . . . . . . . . . . . 171--185 Eleazar Eskin and William Stafford Noble and Yoram Singer Protein Family Classification Using Sparse Markov Transducers . . . . . . . 187--213 Robert Penchovsky and Jörg Ackermann DNA Library Design for Molecular Computation . . . . . . . . . . . . . . 215--229 F. K. Hwang and Y. C. Liu Error-Tolerant Pooling Designs with Inhibitors . . . . . . . . . . . . . . . 231--236
Eugene W. Myers Special RECOMB 2002 Issue . . . . . . . 237--237 Nancy M. Amato and Ken A. Dill and Guang Song Using Motion Planning to Map Protein Folding Landscapes and Analyze Folding Kinetics of Known Native Structures . . 239--255 Mehmet Serkan Apaydin and Douglas L. Brutlag and Carlos Guestrin and David Hsu and Jean-Claude Latombe and Chris Varma Stochastic Roadmap Simulation: an Efficient Representation and Algorithm for Analyzing Molecular Motion . . . . . 257--281 Alberto Apostolico and Mary Ellen Bock and Stefano Lonardi Monotony of Surprise and Large-Scale Quest for Unusual Words . . . . . . . . 283--311 Peter F. Arndt and Christopher B. Burge and Terence Hwa DNA Sequence Evolution with Neighbor-Dependent Mutation . . . . . . 313--322 Vineet Bafna and Dan Gusfield and Giuseppe Lancia and Shibu Yooseph Haplotyping as Perfect Phylogeny: a Direct Approach . . . . . . . . . . . . 323--340 Ziv Bar-Joseph and Georg K. Gerber and David K. Gifford and Tommi S. Jaakkola and Itamar Simon Continuous Representations of Time-Series Gene Expression Data . . . . 341--356 S\`everine Bérard and Eric Rivals Comparison of Minisatellites . . . . . . 357--372 Amir Ben-Dor and Benny Chor and Richard Karp and Zohar Yakhini Discovering Local Structure in Gene Expression Data: The Order-Preserving Submatrix Problem . . . . . . . . . . . 373--384 Amir Ben-Dor and Richard M. Karp and Benno Schwikowski and Ron Shamir The Restriction Scaffold Problem . . . . 385--398 Jeremy Buhler Provably Sensitive Indexing Strategies for Biosequence Similarity Search . . . 399--417 Barry Cohen and Steven Skiena Natural Selection and Algorithmic Design of mRNA . . . . . . . . . . . . . . . . 419--432 Ron O. Dror and Jonathan G. Murnick and Nicola J. Rinaldi and Voichita D. Marinescu and Ryan M. Rifkin and Richard A. Young Bayesian Estimation of Transcript Levels Using a General Model of Array Measurement Noise . . . . . . . . . . . 433--452 Dannie Durand and David Sankoff Tests for Gene Clustering . . . . . . . 453--482 Eran Halperin and Shay Halperin and Tzvika Hartman and Ron Shamir Handling Long Targets and Errors in Sequencing by Hybridization . . . . . . 483--497 Samuel A. Heath and Franco P. Preparata and Joel Young Sequencing by Hybridization by Cooperating Direct and Reverse Spectra 499--508 Fumei Lam and Marina Alexandersson and Lior Pachter Picking Alignments from (Steiner) Trees 509--520 Christopher James Langmead and Anthony K. Yan and C. Robertson McClung and Bruce Randall Donald Phase-Independent Rhythmic Analysis of Genome-Wide Expression Patterns . . . . 521--536 Jia Li and Webb Miller Significance of Interspecies Matches when Evolutionary Rate Varies . . . . . 537--554 Brendan M. Mumey and Brian W. Bailey and Bonnie Kirkpatrick and Algirdas J. Jesaitis and Thomas Angel and Edward A. Dratz A New Method for Mapping Discontinuous Antibody Epitopes to Reveal Structural Features of Proteins . . . . . . . . . . 555--567 Jurg Ott and Josephine Hoh Set Association Analysis of SNP Case-Control and Microarray Data . . . . 569--574 Adam C. Siepel An Algorithm to Enumerate Sorting Reversals for Signed Permutations . . . 575--597 Saurabh Sinha Discriminative Motifs . . . . . . . . . 599--615 Miguel L. Teodoro and George N. Phillips, Jr. and Lydia E. Kavraki Understanding Protein Flexibility through Dimensionality Reduction . . . . 617--634 Andy Wildenberg and Steven Skiena and Pavel Sumazin Deconvolving Sequence Variation in Mixed DNA Populations . . . . . . . . . . . . 635--652 Alexander Zien and Juliane Fluck and Ralf Zimmer and Thomas Lengauer Microarrays: How Many Do You Need? . . . 653--667
Elchanan Mossel On the Impossibility of Reconstructing Ancestral Data and Phylogenies . . . . . 669--676 Fan Chung and Linyuan Lu and T. Gregory Dewey and David J. Galas Duplication Models for Biological Networks . . . . . . . . . . . . . . . . 677--687 George Michailidis and Kerby Shedden The Application of Rule-Based Methods to Class Prediction Problems in Genomics 689--698 Yonghong Wang and Hongyu Ou and Fengbiao Guo Recognition of Translation Initiation Sites of Eukaryotic Genes Based on an EM Algorithm . . . . . . . . . . . . . . . 699--708 Wei-Fu Lu and Wen-Lian Hsu A Test for the Consecutive Ones Property on Noisy Data --- Application to Physical Mapping and Sequence Assembly 709--735 Henrik Jönsson and Bo Söderberg An Approximate Maximum Likelihood Approach, Applied to Phylogenetic Trees 737--749 D. Faller and H. U. Voss and J. Timmer and U. Hobohm Normalization of DNA-Microarray Data by Nonlinear Correlation Maximization . . . 751--762 Antonio Piccolboni and Dan Gusfield On the Complexity of Fundamental Computational Problems in Pedigree Analysis . . . . . . . . . . . . . . . . 763--773 Lenwood S. Heath and John Paul C. Vergara Sorting by Short Swaps . . . . . . . . . 775--789 N. Pisanti and R. Marangoni and P. Ferragina and A. Frangioni and A. Savona and C. Pisanelli and F. Luccio PaTre: a Method for Paralogy Trees Construction . . . . . . . . . . . . . . 791--802
Yu Zhang and Michael S. Waterman An Eulerian Path Approach to Global Multiple Alignment for DNA Sequences . . 803--819 Hagit Shatkay and Ronen Feldman Mining the Biomedical Literature in the Genomic Era: An Overview . . . . . . . . 821--855 Li Liao and William Stafford Noble Combining Pairwise Sequence Similarity and Support Vector Machines for Detecting Remote Protein Evolutionary and Structural Relationships . . . . . . 857--868 G. A. Lunter and I. Miklós and Y. S. Song and J. Hein An Efficient Algorithm for Statistical Multiple Alignment on Arbitrary Phylogenetic Trees . . . . . . . . . . . 869--889 M. Kathleen Kerr Linear Models for Microarray Data Analysis: Hidden Similarities and Differences . . . . . . . . . . . . . . 891--901 Gonzalo Navarro and Mathieu Raffinot Fast and Simple Character Classes and Bounded Gaps Pattern Matching, with Applications to Protein Searching . . . 903--923 Ryan H. Lilien and Hany Farid and Bruce R. Donald Probabilistic Disease Classification of Expression-Dependent Proteomic Data from Mass Spectrometry of Human Serum . . . . 925--946 Minghua Deng and Kui Zhang and Shipra Mehta and Ting Chen and Fengzhu Sun Prediction of Protein Function Using Protein--Protein Interaction Data . . . 947--960 Mark R. Segal and Kam D. Dahlquist and Bruce R. Conklin Regression Approaches for Microarray Data Analysis . . . . . . . . . . . . . 961--980 Samuel Ieong and Ming-Yang Kao and Tak-Wah Lam and Wing-Kin Sung and Siu-Ming Yiu Predicting RNA Secondary Structures with Arbitrary Pseudoknots by Maximizing the Number of Stacking Pairs . . . . . . . . 981--995 Shalini Veerassamy and Andrew Smith and Elisabeth R. M. Tillier A Transition Probability Model for Amino Acid Substitutions from Blocks . . . . . 997--1010
Haiyan Huang and Ming-Chih J. Kao and Xianghong Zhou and Jun S. Liu and Wing H. Wong Determination of Local Statistical Significance of Patterns in Markov Sequences with Application to Promoter Element Identification . . . . . . . . . 1--14 Alberto Apostolico and Laxmi Parida Incremental Paradigms of Motif Discovery 15--25 Alberto Caprara and Robert Carr and Sorin Istrail and Giuseppe Lancia and Brian Walenz 1001 Optimal PDB Structure Alignments: Integer Programming Methods for Finding the Maximum Contact Map Overlap . . . . 27--52 Andreas Wagner Reconstructing Pathways in Large Genetic Networks from Genetic Perturbations . . 53--60 Peter A. Spiro and Natasa Macura A Local Alignment Metric for Accelerating Biosequence Database Search 61--82 Maxim Shatsky and Ruth Nussinov and Haim J. Wolfson FlexProt: Alignment of Flexible Protein Structures Without a Predefinition of Hinge Regions . . . . . . . . . . . . . 83--106 Leo Wang-Kit Cheung Use of Runs Statistics for Pattern Recognition in Genomic DNA Sequences . . 107--124 Myong-Hee Sung and Richard Simon Genomewide Conserved Epitope Profiles of HIV-1 Predicted by Biophysical Properties of MHC Binding Peptides . . . 125--145 Xiaobo Zhou and Xiaodong Wang and Edward R. Dougherty and Daniel Russ and Edward Suh Gene Clustering Based on Clusterwide Mutual Information . . . . . . . . . . . 147--161 R. W. Adamiak and J. Blazewicz and P. Formanowicz and Z. Gdaniec and M. Kasprzak and M. Popenda and M. Szachniuk An Algorithm for an Automatic NOE Pathways Analysis of $2$D NMR Spectra of RNA Duplexes . . . . . . . . . . . . . . 163--179 Markus Wistrand and Erik L. L. Sonnhammer Transition Priors for Protein Hidden Markov Models: An Empirical Study towards Maximum Discrimination . . . . . 181--193 Vladimir Makarenkov and Pierre Legendre From a Phylogenetic Tree to a Reticulated Network . . . . . . . . . . 195--212
Webb Miller and Martin Vingron Special RECOMB 2003 Issue . . . . . . . 213--213 Wentian Li and Fengzhu Sun and Ivo Grosse Extreme Value Distribution Based Gene Selection Criteria for Discriminant Microarray Data Analysis Using Logistic Regression . . . . . . . . . . . . . . . 215--226 Balaji Krishnapuram and Lawrence Carin and Alexander J. Hartemink Joint Classifier and Feature Optimization for Comprehensive Cancer Diagnosis Using Gene Expression Data . . 227--242 Chen-Hsiang Yeang and Trey Ideker and Tommi Jaakkola Physical Network Models . . . . . . . . 243--262 Maayan Fishelson and Dan Geiger Optimizing Exact Genetic Linkage Computations . . . . . . . . . . . . . . 263--275 Christopher James Langmead and Anthony Yan and Ryan Lilien and Lincong Wang and Bruce Randall Donald A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments . . . . . . . . . 277--298 Itay Lotan and Fabian Schwarzer Approximation of Protein Structure for Fast Similarity Measures . . . . . . . . 299--317 Manolis Kellis and Nick Patterson and Bruce Birren and Bonnie Berger and Eric S. Lander Methods in Comparative Genomics: Genome Correspondence, Gene Identification and Regulatory Motif Discovery . . . . . . . 319--355 Amos Tanay and Ron Shamir Multilevel Modeling and Inference of Transcription Regulation . . . . . . . . 357--375 Gene Yeo and Christopher B. Burge Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing Signals . . . . . . . . . . . . 377--394 Krishna M. Roskin and Mark Diekhans and David Haussler Score Functions for Determining Regional Conservation in Two-Species Local Alignments . . . . . . . . . . . . . . . 395--411 Adam Siepel and David Haussler Combining Phylogenetic and Hidden Markov Models in Biosequence Analysis . . . . . 413--428 Andrew B. Kahng and Ion I. M\uandoiu and Pavel A. Pevzner and Sherief Reda and Alexander Z. Zelikovsky Scalable Heuristics for Design of DNA Probe Arrays . . . . . . . . . . . . . . 429--447 Tatsuya Akutsu Efficient Extraction of Mapping Rules of Atoms from Enzymatic Reaction Data . . . 449--462 Minghua Deng and Ting Chen and Fengzhu Sun An Integrated Probabilistic Model for Functional Prediction of Proteins . . . 463--475 Amir Ben-Dor and Tzvika Hartman and Richard M. Karp and Benno Schwikowski and Roded Sharan and Zohar Yakhini Towards Optimally Multiplexed Applications of Universal Arrays . . . . 476--492 Gideon Greenspan and Dan Geiger Model-Based Inference of Haplotype Block Variation . . . . . . . . . . . . . . . 493--504 Lei M. Li and Jong Hyun Kim and Michael S. Waterman Haplotype Reconstruction from SNP Alignment . . . . . . . . . . . . . . . 505--516
Craig J. Benham and Chengpeng Bi The Analysis of Stress-Induced Duplex Destabilization in Long Genomic DNA Sequences . . . . . . . . . . . . . . . 519--543 Kevin A. Janes and Jason R. Kelly and Suzanne Gaudet and John G. Albeck and Peter K. Sorger and Douglas A. Lauffenburger Cue-Signal-Response Analysis of TNF-Induced Apoptosis by Partial Least Squares Regression of Dynamic Multivariate Data . . . . . . . . . . . 544--561 Rongling Wu and Chang-Xing Ma and George Casella A Mixed Polyploid Model for Linkage Analysis in Outcrossing Tetraploids Using a Pseudo-Test Backcross Design . . 562--580 Paul Helman and Robert Veroff and Susan R. Atlas and Cheryl Willman A Bayesian Network Classification Methodology for Gene Expression Data . . 581--615 Hilary S. Booth and John H. Maindonald and Susan R. Wilson and Jill E. Gready An Efficient $Z$-Score Algorithm for Assessing Sequence Alignments . . . . . 616--625 Dan Levy and Mariel Vazquez and Michael Cornforth and Bradford Loucas and Rainer K. Sachs and Javier Arsuaga Comparing DNA Damage-Processing Pathways by Computer Analysis of Chromosome Painting Data . . . . . . . . . . . . . 626--641 Jason Ku and Xiao-Jiang Feng and Herschel Rabitz Closed-Loop Learning Control of Bio-Networks . . . . . . . . . . . . . . 642--659 Ciprian Doru Giurc\uarneanu and Ioan T\uabu\cs and Jaakko Astola and Juha Ollila and Mauno Vihinen Fast Iterative Gene Clustering Based on Information Theoretic Criteria for Selecting the Cluster Structure . . . . 660--682 Lin Zhihua and Wu Yuzhang and Zhu Bo and Ni Bing and Wang Li Toward the Quantitative Prediction of T-Cell Epitopes: QSAR Studies on Peptides Having Affinity with the Class I MHC Molecular HLA-A*0201 . . . . . . . 683--694 T. L. Bergemann and R. J. Laws and F. Quiaoit and L. P. Zhao A Statistically Driven Approach for Image Segmentation and Signal Extraction in cDNA Microarrays . . . . . . . . . . 695--713 Sue-Jane Wang and James J. Chen Sample Size for Identifying Differentially Expressed Genes in Microarray Experiments . . . . . . . . . 714--726 N. Galtier and A. Jean-Marie Markov-Modulated Markov Chains and the Covarion Process of Molecular Evolution 727--733 Michael Roberts and Brian R. Hunt and James A. Yorke and Randall A. Bolanos and Arthur L. Delcher A Preprocessor for Shotgun Assembly of Large Genomes . . . . . . . . . . . . . 734--752 Franco P. Preparata and John S. Oliver DNA Sequencing by Hybridization Using Semi-Degenerate Bases . . . . . . . . . 753--765 Piotr Berman and Paul Bertone and Bhaskar Dasgupta and Mark Gerstein and Ming-Yang Kao and Michael Snyder Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search . . . . . . . . . . . . 766--785
Yuting Jia and T. Gregory Dewey and Ilya N. Shindyalov and Philip E. Bourne A New Scoring Function and Associated Statistical Significance for Structure Alignment by CE . . . . . . . . . . . . 787--799 Hagit Shatkay and Jason Miller and Clark Mobarry and Michael Flanigan and Shibu Yooseph and Granger Sutton ThurGood: Evaluating Assembly-to-Assembly Mapping . . . . . . 800--811 Joseph S. Oliveira and Janet B. Jones-Oliveira and David A. Dixon and Colin G. Bailey and Dean W. Gull Hyperdigraph-Theoretic Analysis of the EGFR Signaling Network: Initial Steps Leading to GTP:Ras Complex Formation . . 812--842 Andreas Heger and Michael Lappe and Liisa Holm Accurate Detection of Very Sparse Sequence Motifs . . . . . . . . . . . . 843--857 Vineet Bafna and Dan Gusfield and Sridhar Hannenhalli and Shibu Yooseph A Note on Efficient Computation of Haplotypes via Perfect Phylogeny . . . . 858--866 Gill Bejerano and Nir Friedman and Naftali Tishby Efficient Exact $p$-Value Computation for Small Sample, Sparse, and Surprising Categorical Data . . . . . . . . . . . . 867--886 Andres Figueroa and James Borneman and Tao Jiang Clustering Binary Fingerprint Vectors with Missing Values for DNA Array Data Analysis . . . . . . . . . . . . . . . . 887--901 Itay Lotan and Fabian Schwarzer and Dan Halperin and Jean-Claude Latombe Algorithm and Data Structures for Efficient Energy Maintenance during Monte Carlo Simulation of Proteins . . . 902--932 Can Alkan and Evan E. Eichler and Jeffrey A. Bailey and S. Cenk \cSahinalp and Eray Tüzün The Role of Unequal Crossover in Alpha-Satellite DNA Evolution: a Computational Analysis . . . . . . . . . 933--944 Kaleigh Smith and Mike Hallett Towards Quality Control for DNA Microarrays . . . . . . . . . . . . . . 945--970 S. D. Bay and L. Chrisman and A. Pohorille and J. Shrager Temporal Aggregation Bias and Inference of Causal Regulatory Networks . . . . . 971--985 Jieping Ye and Ravi Janardan Approximate Multiple Protein Structure Alignment Using the Sum-of-Pairs Distance . . . . . . . . . . . . . . . . 986--1000 Miklós Csürös and Aleksandar Milosavljevic Pooled Genomic Indexing (PGI): Analysis and Design of Experiments . . . . . . . 1001--1021
G. Nuel LD-SPatt: Large Deviations Statistics for Patterns on Markov Chains . . . . . 1023--1033 Irit Gat-Viks and Amos Tanay and Ron Shamir Modeling and Analysis of Heterogeneous Regulation in Biological Networks . . . 1034--1049 Revital Eres and Gad M. Landau and Laxmi Parida Permutation Pattern Discovery in Biosequences . . . . . . . . . . . . . . 1050--1060 Matteo Comin and Concettina Guerra and Giuseppe Zanotti PROuST: a Comparison Method of Three-Dimensional Structures of Proteins Using Indexing Techniques . . . . . . . 1061--1072 C. Bhattacharyya and L. R. Grate and M. I. Jordan and L. El Ghaoui and I. S. Mian Robust Sparse Hyperplane Classifiers: Application to Uncertain Molecular Profiling Data . . . . . . . . . . . . . 1073--1089 P. Chiappetta and M. C. Roubaud and B. Torrésani Blind Source Separation and the Analysis of Microarray Data . . . . . . . . . . . 1090--1109 Sebastian Böcker Sequencing from Compomers: Using Mass Spectrometry for DNA \em de novo Sequencing of 200+ nt . . . . . . . . . 1110--1134 Mathäus Dejori and Martin Stetter Identifying Interventional and Pathogenic Mechanisms by Generative Inverse Modeling of Gene Expression Profiles . . . . . . . . . . . . . . . . 1135--1148 Ahmet Palazoglu and Attila Gursoy and Yaman Arkun and Burak Erman Folding Dynamics of Proteins from Denatured to Native State: Principal Component Analysis . . . . . . . . . . . 1149--1168 Danny Barash Spectral Decomposition for the Search and Analysis of RNA Secondary Structure 1169--1174 Nanxiang Ge and Charles B. Epstein An Empirical Bayesian Significance Test of cDNA Library Data . . . . . . . . . . 1175--1188 Darrell Conklin Recognition of the Helical Cytokine Fold 1189--1200
Andrei Rodin and Thomas H. Mosley, Jr. and Andrew G. Clark and Charles F. Sing and Eric Boerwinkle Mining Genetic Epidemiology Data with Bayesian Networks Application to \em APOE Gene Variation and Plasma Lipid Levels . . . . . . . . . . . . . . . . . 1--11 Golan Yona and Klara Kedem The URMS-RMS Hybrid Algorithm for Fast and Sensitive Local Protein Structure Alignment . . . . . . . . . . . . . . . 12--32 Elodie Nédélec and Thomas Moncion and Elisabeth Gassiat and Bruno Bossard and Guillemette Duchateau-Nguyen and Alain Denise and Michel Termier A Pairwise Alignment Algorithm Which Favors Clusters of Blocks . . . . . . . 33--47 Jason W. Zwolak and John J. Tyson and Layne T. Watson Parameter Estimation for a Mathematical Model of the Cell Cycle in Frog Eggs . . 48--63 Konstantinos Blekas and Dimitrios I. Fotiadis and Aristidis Likas Motif-Based Protein Sequence Classification Using Neural Networks . . 64--82 P. Clote An Efficient Algorithm to Compute the Landscape of Locally Optimal RNA Secondary Structures with Respect to the Nussinov--Jacobson Energy Model . . . . 83--101 Ying Chih Lin and Chin Lung Lu and Hwan-You Chang and Chuan Yi Tang An Efficient Algorithm for Sorting by Block-Interchanges and Its Application to the Evolution of Vibrio Species . . . 102--112
Joël R. Pradines and Victor Farutin and Steve Rowley and Vlado Dan\vcík Analyzing Protein Lists with Large Networks: Edge-Count Probabilities in Random Graphs with Given Expected Degrees . . . . . . . . . . . . . . . . 113--128 Zhi-Zhong Chen and Guohui Lin and Romeo Rizzi and Jianjun Wen and Dong Xu and Ying Xu and Tao Jiang More Reliable Protein NMR Peak Assignment via Improved $2$-Interval Scheduling . . . . . . . . . . . . . . . 129--146 Yun S. Song and Jotun Hein Constructing Minimal Ancestral Recombination Graphs . . . . . . . . . . 147--169 Lei M. Li and Henry Horng-Shing Lu Explore Biological Pathways from Noisy Array Data by Directed Acyclic Boolean Networks . . . . . . . . . . . . . . . . 170--185 Asger Hobolth and Jens Ledet Jensen Applications of Hidden Markov Models for Characterization of Homologous DNA Sequences with a Common Gene . . . . . . 186--203 Bernd Sturmfels and Seth Sullivant Toric Ideals of Phylogenetic Invariants 204--228 Biao Xing and Mark J. van der Laan A Statistical Method for Constructing Transcriptional Regulatory Networks Using Gene Expression and Sequence Data 229--246 Yuval Nov and Lawrence M. Wein Modeling and Analysis of Protein Design under Resource Constraints . . . . . . . 247--282
Michael C. Wendl Probabilistic Assessment of Clone Overlaps in DNA Fingerprint Mapping via a Priori Models . . . . . . . . . . . . 283--297 Yuting Jia and T. Gregory Dewey A Random Polymer Model of the Statistical Significance of Structure Alignment . . . . . . . . . . . . . . . 298--313 Libi Hertzberg and Or Zuk and Gad Getz and Eytan Domany Finding Motifs in Promoter Regions . . . 314--330 Ming-Ying Leung and Kwok Pui Choi and Aihua Xia and Louis H. Y. Chen Nonrandom Clusters of Palindromes in Herpesvirus Genomes . . . . . . . . . . 331--354 Michael Wagner and Rafa\l Adamczak and Aleksey Porollo and Jaros\law Meller Linear Regression Models for Solvent Accessibility Prediction in Proteins . . 355--369 Lang Li and Huidong Shi and Constantin Yiannoutsos and Tim Hui-Ming Huang and Kenneth P. Nephew Epigenetic Hypothesis Tests for Methylation and Acetylation in a Triple Microarray System . . . . . . . . . . . 370--390
Dabao Zhang and Martin T. Wells and Christine D. Smart and William E. Fry Bayesian Normalization and Identification for Differential Gene Expression Data . . . . . . . . . . . . 391--406 Ross A. Lippert Space-Efficient Whole Genome Comparisons with Burrows--Wheeler Transforms . . . . 407--415 Uri Keich sFFT: a Faster Accurate Computation of the $p$-Value of the Entropy Score . . . 416--430 Chaim Linhart and Ron Shamir The Degenerate Primer Design Problem: Theory and Applications . . . . . . . . 431--456 Bernd Sturmfels and Seth Sullivant Toric Ideals of Phylogenetic Invariants 457--481 Stan Pounds and Cheng Cheng Statistical Development and Evaluation of Microarray Gene Expression Data Filters . . . . . . . . . . . . . . . . 482--495
Ian M. Dew and Brian Walenz and Granger Sutton A Tool for Analyzing Mate Pairs in Assemblies (TAMPA) . . . . . . . . . . . 497--513 Roded Sharan and Jens Gramm and Zohar Yakhini and Amir Ben-Dor Multiplexing Schemes for Generic SNP Genotyping Assays . . . . . . . . . . . 514--533 Daniel Berrar and Brian Sturgeon and Ian Bradbury and C. Stephen Downes and Werner Dubitzky Survival Trees for Analyzing Clinical Outcome in Lung Adenocarcinomas Based on Gene Expression Profiles: Identification of Neogenin and Diacylglycerol Kinase $ \alpha $ Expression as Critical Factors 534--544 Manuel Dehnert and Rainer Plaumann and Werner E. Helm and Marc-Th. Hütt Genome Phylogeny Based on Short-Range Correlations in DNA Sequences . . . . . 545--553 Martijn J. Schuemie and Jan A. Kors and Barend Mons Word Sense Disambiguation in the Biomedical Domain: An Overview . . . . . 554--565
Dan Gusfield Preface: Special RECOMB 2004 Issue . . . 567--568 Chris Bailey-Kellogg and Sheetal Chainraj and Gopal Pandurangan A Random Graph Approach to NMR Sequential Assignment . . . . . . . . . 569--583 Niko Beerenwinkel and Jörg Rahnenführer and Martin Däumer and Daniel Hoffmann and Rolf Kaiser and Joachim Selbig and Thomas Lengauer Learning Multiple Evolutionary Pathways from Cross-Sectional Data . . . . . . . 584--598 Sourav Chatterji and Lior Pachter Large Multiple Organism Gene Finding by Collapsed Gibbs Sampling . . . . . . . . 599--608 Michael A. Erdmann Protein Similarity from Knot Theory: Geometric Convolution and Line Weavings 609--637 Xin He and Michael H. Goldwasser Identifying Conserved Gene Clusters in the Presence of Homology Families . . . 638--656 Jun Huan and Deepak Bandyopadhyay and Wei Wang and Jack Snoeyink and Jan Prins and Alexander Tropsha Comparing Graph Representations of Protein Structure for Mining Family-Specific Residue-Based Packing Motifs . . . . . . . . . . . . . . . . . 657--671 Sabrina Ledent and Stéphane Robin Checking Homogeneity of Motifs' Distribution in Heterogeneous Sequences 672--685 Henry C. M. Leung and Francis Y. L. Chin and S. M. Yiu and Roni Rosenfeld and W. W. Tsang Finding Motifs with Insufficient Number of Strong Binding Sites . . . . . . . . 686--701 Haifeng Li and Tao Jiang A Class of Edit Kernels for SVMs to Predict Translation Initiation Sites in Eukaryotic mRNAs . . . . . . . . . . . . 702--718 Jing Li and Tao Jiang Computing the Minimum Recombinant Haplotype Configuration from Incomplete Genotype Data on a Pedigree by Integer Linear Programming . . . . . . . . . . . 719--739 Ryan H. Lilien and Brian W. Stevens and Amy C. Anderson and Bruce R. Donald A Novel Ensemble-Based Scoring and Search Algorithm for Protein Redesign and Its Application to Modify the Substrate Specificity of the Gramicidin Synthetase A Phenylalanine Adenylation Enzyme . . . . . . . . . . . . . . . . . 740--761 Ross A. Lippert and Xiaoyue Zhao and Liliana Florea and Clark Mobarry and Sorin Istrail Finding Anchors for Genomic Sequence Comparison . . . . . . . . . . . . . . . 762--776 Matthew Menke and Jonathan King and Bonnie Berger and Lenore Cowen Wrap-and-Pack: a New Paradigm for Beta Structural Motif Recognition with Application to Recognizing Beta Trefoils 777--795 Luay Nakhleh and Tandy Warnow and C. Randal Linder and Katherine St.John Reconstructing Reticulate Evolution in Species --- Theory and Practice . . . . 796--811 David Sankoff and Phil Trinh Chromosomal Breakpoint Reuse in Genome Sequence Rearrangement . . . . . . . . . 812--821 Eran Segal and Roded Sharan A Discriminative Model for Identifying Spatial cis-Regulatory Modules . . . . . 822--834 Roded Sharan and Trey Ideker and Brian Kelley and Ron Shamir and Richard M. Karp Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data . . . 835--846 Yanni Sun and Jeremy Buhler Designing Multiple Simultaneous Seeds for DNA Similarity Search . . . . . . . 847--861 Xinyu Tang and Bonnie Kirkpatrick and Shawna Thomas and Guang Song and Nancy M. Amato Using Motion Planning to Study RNA Folding Kinetics . . . . . . . . . . . . 862--881 Zhijin Wu and Rafael A. Irizarry Stochastic Models Inspired by Hybridization Theory for Short Oligonucleotide Arrays . . . . . . . . . 882--893 Xiaoyue Zhao and Haiyan Huang and Terence P. Speed Finding Short DNA Motifs Using Permuted Markov Models . . . . . . . . . . . . . 894--906 Anonymous Correction . . . . . . . . . . . . . . . 907--907
Alexis Battle and Eran Segal and Daphne Koller Probabilistic Discovery of Overlapping Cellular Processes and Their Regulation 909--927 Ydo Wexler and Zohar Yakhini and Yechezkel Kashi and Dan Geiger Finding Approximate Tandem Repeats in Genomic Sequences . . . . . . . . . . . 928--942 Ross A. Lippert and Clark M. Mobarry and Brian P. Walenz A Space-Efficient Construction of the Burrows--Wheeler Transform for Genomic Data . . . . . . . . . . . . . . . . . . 943--951 Jun Xie and Nak-Kyeong Kim Bayesian Models and Markov Chain Monte Carlo Methods for Protein Motifs with the Secondary Characteristics . . . . . 952--970 Jian Liu and Ming Li Finding Cancer Biomarkers from Mass Spectrometry Data by Decision Lists . . 971--979 Itai Sharon and Aaron Birkland and Kuan Chang and Ran El-Yaniv and Golan Yona Correcting BLAST $e$-Values for Low-Complexity Segments . . . . . . . . 980--1003 Robert F. Tichy and Stephan Wagner Extremal Problems for Topological Indices in Combinatorial Chemistry . . . 1004--1013 Menachem Kaufman and David Bloch and Naomi Zurgil and Yana Shafran and Mordechai Deutsch A Cluster Pattern Algorithm for the Analysis of Multiparametric Cell Assays 1014--1028 Dongxiao Zhu and Alfred O. Hero and Zhaohui S. Qin and Anand Swaroop High Throughput Screening of Co-Expressed Gene Pairs with Controlled False Discovery Rate (FDR) and Minimum Acceptable Strength (MAS) . . . . . . . 1029--1045
Sheng Zhao and Russell D. Fernald Comprehensive Algorithm for Quantitative Real-Time Polymerase Chain Reaction . . 1047--1064 Michele Morgante and Alberto Policriti and Nicola Vitacolonna and Andrea Zuccolo Structured Motifs Search . . . . . . . . 1065--1082 Rose Hoberman and David Sankoff and Dannie Durand The Statistical Analysis of Spatially Clustered Genes under the Maximum Gap Criterion . . . . . . . . . . . . . . . 1083--1102 Albert C.-C. Yang and Ary L. Goldberger and C.-K. Peng Genomic Classification Using an Information-Based Similarity Index: Application to the SARS Coronavirus . . 1103--1116 S. Rajasekaran and S. Balla and C.-H. Huang Exact Algorithms for Planted Motif Problems . . . . . . . . . . . . . . . . 1117--1128 A. D'Yachkov and Frank Hwang and Antony Macula and Pavel Vilenkin and Chih-Wen Weng A Construction of Pooling Designs with Some Happy Surprises . . . . . . . . . . 1129--1136
Franco P. Preparata and Louxin Zhang and Kwok Pui Choi Quick, Practical Selection of Effective Seeds for Homology Search . . . . . . . 1137--1152 Changchuan Yin and Stephen S.-T. Yau A Fourier Characteristic of Coding Sequences: Origins and a Non-Fourier Approximation . . . . . . . . . . . . . 1153--1165 Ole F. Christensen and Asger Hobolth and Jens L. Jensen Pseudo-Likelihood Analysis of Codon Substitution Models with Neighbor-Dependent Rates . . . . . . . . 1166--1182 Noah A. Rosenberg Algorithms for Selecting Informative Marker Panels for Population Assignment 1183--1201 Chu-Wen Yang and Chin-Fu Hsiao and Chen-Kung Chou Evaluation of Experimental Designs for Two-Color cDNA Microarrays . . . . . . . 1202--1220 Zeyar Aung and Kian-Lee Tan Automatic $3$D Protein Structure Classification without Structural Alignment . . . . . . . . . . . . . . . 1221--1241
Gad Kimmel and Ron Shamir A Block-Free Hidden Markov Model for Genotypes and Its Application to Disease Association . . . . . . . . . . . . . . 1243--1260 Yao-Ting Huang and Kun-Mao Chao and Ting Chen An Approximation Algorithm for Haplotype Inference by Maximum Parsimony . . . . . 1261--1274 Daniel M. Dunlavy and Dianne P. O'leary and Dmitri Klimov and D. Thirumalai HOPE: a Homotopy Optimization Method for Protein Structure Prediction . . . . . . 1275--1288 Gad M. Landau and Laxmi Parida and Oren Weimann Gene Proximity Analysis across Whole Genomes via PQ Trees$^1$ . . . . . . . . 1289--1306 Wolfram Liebermeister Predicting Physiological Concentrations of Metabolites from Their Molecular Structure . . . . . . . . . . . . . . . 1307--1315 Silvio C. E. Tosatto The Victor/FRST Function for Model Quality Estimation . . . . . . . . . . . 1316--1327 Arvind Gupta and Ján Ma\vnuch and Ladislav Stacho Structure-Approximating Inverse Protein Folding Problem in the $2$D HP Model . . 1328--1345
Joseph West and John Healy and Michael Wigler and William Casey and Bud Mishra Validation of \bionameS. Pombe Sequence Assembly by Microarray Hybridization . . 1--20 David Chiang and Aravind K. Joshi and Ken A. Dill A Grammatical Theory for the Conformational Changes of Simple Helix Bundles . . . . . . . . . . . . . . . . 21--42 Jakob Vesterstròm and William R. Taylor Flexible Secondary Structure Based Protein Structure Comparison Applied to the Detection of Circular Permutation 43--63 Moshe Havilio Signal Deconvolution Based Expression-Detection and Background Adjustment for Microarray Data . . . . . 63--80 Anna Gambin and Jerzy Tiuryn and Jerzy Tyszkiewicz Alignment with Context Dependent Scoring Function . . . . . . . . . . . . . . . . 81--101 Manoj Bhasin and Ellis L. Reinherz and Pedro A. Reche Recognition and Classification of Histones Using Support Vector Machine 102--112 Tim Hohm and Philipp Limbourg and Daniel Hoffmann A Multiobjective Evolutionary Method for the Design of Peptidic Mimotopes . . . . 113--125 Joanne I. Yeh and Lisong Mao Prediction of Membrane Proteins in \bionameMycobacterium tuberculosis Using a Support Vector Machine Algorithm . . . 126--129
Satoru Miyano Preface: Special RECOMB 2005 Issue . . . 131--132 Jacob Scott and Trey Ideker and Richard M. Karp and Roded Sharan Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks . . . . . . . . . . 133--144 Ariel Jaimovich and Gal Elidan and Hanah Margalit and Nir Friedman Towards an Integrated Protein--Protein Interaction Network: a Relational Markov Network Approach . . . . . . . . . . . . 145--164 Irit Gat-Viks and Amos Tanay and Daniela Raijman and Ron Shamir A Probabilistic Methodology for Integrating Knowledge and Experiments on Biological Networks . . . . . . . . . . 165--181 Mehmet Koyutürk and Yohan Kim and Umut Topkara and Shankar Subramaniam and Wojciech Szpankowski and Ananth Grama Pairwise Alignment of Protein Interaction Networks . . . . . . . . . . 182--199 Brendan J. Frey and Quaid D. Morris and Timothy R. Hughes GenRate: a Generative Model that Reveals Novel Transcripts in Genome-Tiling Microarray Data . . . . . . . . . . . . 200--214 Doron Lipson and Yonatan Aumann and Amir Ben-Dor and Nathan Linial and Zohar Yakhini Efficient Calculation of Interval Scores for DNA Copy Number Data Analysis . . . 215--228 Kun-Pin Wu and Jia-Ming Chang and Jun-Bo Chen and Chi-Fon Chang and Wen-Jin Wu and Tai-Huang Huang and Ting-Yi Sung and Wen-Lian Hsu RIBRA --- An Error-Tolerant Algorithm for the NMR Backbone Assignment Problem 229--244 Chaya Ben-Zaken Zilberstein and Michal Ziv-Ukelson and Ron Y. Pinter and Zohar Yakhini A High-Throughput Approach for Associating MicroRNAs with Their Activity Conditions . . . . . . . . . . 245--266 Can Alkan and Emre Karakoç and Joseph H. Nadeau and S. Cenk Sahinalp and Kaizhong Zhang RNA--RNA Interaction Prediction and Antisense RNA Target Search . . . . . . 267--282 Vineet Bafna and Haixu Tang and Shaojie Zhang Consensus Folding of Unaligned RNA Sequences Revisited . . . . . . . . . . 283--295 Kim R. Rasmussen and Jens Stoye and Eugene W. Myers Efficient $q$-Gram Filters for Finding All $ \epsilon $-Matches over a Given Length . . . . . . . . . . . . . . . . . 296--308 Sing-Hoi Sze and Yue Lu and Qingwu Yang A Polynomial Time Solvable Formulation of Multiple Sequence Alignment . . . . . 309--319 Dannie Durand and Bjarni V. Halldórsson and Benjamin Vernot A Hybrid Micro--Macroevolutionary Approach to Gene Tree Reconstruction . . 320--335 Igor Ulitsky and David Burstein and Tamir Tuller and Benny Chor The Average Common Substring Approach to Phylogenomic Reconstruction . . . . . . 336--350 Teresa Przytycka and George Davis and Nan Song and Dannie Durand Graph Theoretical Insights into Evolution of Multidomain Proteins . . . 351--363 Marshall Bern and David Goldberg \em De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning . . . . . . . . . . . . . . 364--378 Samuel S. Gross and Michael R. Brent Using Multiple Alignments to Improve Gene Prediction . . . . . . . . . . . . 379--393 Yan Liu and Jaime Carbonell and Peter Weigele and Vanathi Gopalakrishnan Protein Fold Recognition Using Segmentation Conditional Random Fields (SCRFs) . . . . . . . . . . . . . . . . 394--406 Maxim Shatsky and Alexandra Shulman-Peleg and Ruth Nussinov and Haim J. Wolfson The Multiple Common Point Set Problem and Its Application to Molecule Binding Pattern Detection . . . . . . . . . . . 407--428 Nicholas Chia and Ralf Bundschuh A Practical Approach to Significance Assessment in Alignment with Gaps . . . 429--441 Anton Valouev and Lei Li and Yu-Chi Liu and David C. Schwartz and Yi Yang and Yu Zhang and Michael S. Waterman Alignment of Optical Maps . . . . . . . 442--462 Chen-Hsiang Yeang and Tommi Jaakkola Modeling the Combinatorial Functions of Multiple Transcription Factors . . . . . 463--480 Eran Halperin and Elad Hazan HAPLOFREQ --- Estimating Haplotype Frequencies Efficiently . . . . . . . . 481--500 Vineet Bafna and Vikas Bansal Inference about Recombination from Haplotype Data: Lower Bounds and Recombination Hotspots . . . . . . . . . 501--521 Zhihong Ding and Vladimir Filkov and Dan Gusfield A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem . . 522--553 Matthew Mazowita and Lani Haque and David Sankoff Stability of Rearrangement Measures in the Comparison of Genome Sequences . . . 554--566 Anne Bergeron and Julia Mixtacki and Jens Stoye On Sorting by Translocations . . . . . . 567--578
Sündüz Kele\cs and Mark J. Van Der Laan and Sandrine Dudoit and Simon E. Cawley Multiple Testing Methods For ChIP--Chip High Density Oligonucleotide Array Data 579--613 Florian A. Potra and Xing Liu and Françoise Seillier-Moiseiwitsch and Anindya Roy and Yaming Hang and Mark R. Marten and Babu Raman and Carol Whisnant Protein Image Alignment via Piecewise Affine Transformations . . . . . . . . . 614--630 Gianluca Pollastri and Alessandro Vullo and Paolo Frasconi and Pierre Baldi Modular DAG--RNN Architectures for Assembling Coarse Protein Structures . . 631--650 Pierre Nicolas and Anne-Sophie Tocquet and Vincent Miele and Florence Muri A Reversible Jump Markov Chain Monte Carlo Algorithm for Bacterial Promoter Motifs Discovery . . . . . . . . . . . . 651--667 Arun S. Konagurthu and Peter J. Stuckey Optimal Sum-of-Pairs Multiple Sequence Alignment Using Incremental Carrillo and Lipman Bounds . . . . . . . . . . . . . 668--685 Jonathan M. Carlson and Arijit Chakravarty and Robert H. Gross BEAM: a Beam Search Algorithm for the Identification of \em Cis-Regulatory Elements in Groups of Genes . . . . . . 686--701 Jesper Jansson and Ngo Trung Hieu and Wing-Kin Sung Local Gapped Subforest Alignment and Its Application in Finding RNA Structural Motifs . . . . . . . . . . . . . . . . . 702--718 Sébastien Ferré and Ross D. King Finding Motifs in Protein Secondary Structure for Use in Function Prediction 719--731 Ion I. M\uandoiu and Drago\cs Trinc\ua Exact and Approximation Algorithms for DNA Tag Set Design . . . . . . . . . . . 732--744 Chandan K. Reddy and Hsiao-Dong Chiang A Stability Boundary Based Method for Finding Saddle Points on Potential Energy Surfaces . . . . . . . . . . . . 745--766 Kristin L. Ayers and Chiara Sabatti and Kenneth Lange Reconstructing Ancestral Haplotypes with a Dictionary Model . . . . . . . . . . . 767--785 Shuguang Huang and Yongming Qu The Loss in Power When the Test of Differential Expression Is Performed under a Wrong Scale . . . . . . . . . . 786--797 N. Raghavan and D. Amaratunga and J. Cabrera and A. Nie and J. Qin and M. McMillian On Methods for Gene Function Scoring as a Means of Facilitating the Interpretation of Microarray Results . . 798--809 Raya Khanin and Ernst Wit How Scale-Free Are Biological Networks 810--818 Benny Chor and Amit Khetan and Sagi Snir Maximum Likelihood Molecular Clock Comb: Analytic Solutions . . . . . . . . . . . 819--837 Andrew Golightly and Darren J. Wilkinson Bayesian Sequential Inference for Stochastic Kinetic Biochemical Network Models . . . . . . . . . . . . . . . . . 838--851
Marcus Hjelm and Mattias Höglund and Jens Lagergren New Probabilistic Network Models and Algorithms for Oncogenesis . . . . . . . 853--865 Arkadii G. D'Yachkov and Anthony J. Macula and Wendy K. Pogozelski and Thomas E. Renz and Vyacheslav V. Rykov and David C. Torney New $t$-Gap Insertion-Deletion-Like Metrics for DNA Hybridization Thermodynamic Modeling . . . . . . . . . 866--881 Dirk Metzler Robust $E$-Values for Gapped Local Alignments . . . . . . . . . . . . . . . 882--896 Ravi Vijayasatya and Amar Mukherjee An Optimal Algorithm for Perfect Phylogeny Haplotyping . . . . . . . . . 897--928 Sumedha Gunewardena and Peter Jeavons and Zhaolei Zhang Enhancing the Prediction of Transcription Factor Binding Sites by Incorporating Structural Properties and Nucleotide Covariations . . . . . . . . 929--945 Vera P. Turutina and Andrew A. Laskin and Nikolay A. Kudryashov and Konstantin G. Skryabin and Eugene V. Korotkov Identification of Amino Acid Latent Periodicity within 94 Protein Families 946--964 Michael Cameron and Hugh E. Williams and Adam Cannane A Deterministic Finite Automaton for Faster Protein Hit Detection in BLAST 965--978 Justin Colannino and Mirela Damian and Ferran Hurtado and John Iacono and Henk Meijer and Suneeta Ramaswami and Godfried Toussaint An $ O(n \log n) $-Time Algorithm for the Restriction Scaffold Assignment Problem . . . . . . . . . . . . . . . . 979--989 Ding-Zhu Du and F. K. Hwang and Weili Wu and Taieb Znati New Construction for Transversal Design 990--995 E. Chudin and S. Kruglyak and S. C. Baker and S. Oeser and D. Barker and T. K. McDaniel A Model of Technical Variation of Microarray Signals . . . . . . . . . . . 996--1003
David Sankoff and Lani Haque The Distribution of Genomic Distance between Random Genomes . . . . . . . . . 1005--1012 Carmel Kent and Gad M. Landau and Michal Ziv-Ukelson On the Complexity of Sparse Exon Assembly . . . . . . . . . . . . . . . . 1013--1027 Aleksandr Morgulis and E. Michael Gertz and Alejandro A. Schäffer and Richa Agarwala A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences . . 1028--1040 Tatiana Maximova and Chen Keasar A Novel Algorithm for Non-Bonded-List Updating in Molecular Simulations . . . 1041--1048 John Goutsias and Seungchan Kim Stochastic Transcriptional Regulatory Systems with Time Delays: a Mean-Field Approximation . . . . . . . . . . . . . 1049--1076 David Chiang and Aravind K. Joshi and David B. Searls Grammatical Representations of Macromolecular Structure . . . . . . . . 1077--1100 Elizabeth S. Allman and John A. Rhodes The Identifiability of Tree Topology for Phylogenetic Models, Including Covarion and Mixture Models . . . . . . . . . . . 1101--1113 Bradley J. Beattie and Peter N. Robinson Binary State Pattern Clustering: a Digital Paradigm for Class and Biomarker Discovery in Gene Microarray Studies of Cancer . . . . . . . . . . . . . . . . . 1114--1130
Angela P. Presson and Eric Sobel and Kenneth Lange and Jeanette C. Papp Merging Microsatellite Data . . . . . . 1131--1147 Jing Wu and David Haussler Coding Exon Detection Using Comparative Sequences . . . . . . . . . . . . . . . 1148--1164 Yair Horesh and Ramit Mehr and Ron Unger Designing an $ A* $ Algorithm for Calculating Edit Distance between Rooted-Unordered Trees . . . . . . . . . 1165--1176 Michael C. Wendl A General Coverage Theory for Shotgun DNA Sequencing . . . . . . . . . . . . . 1177--1196 Einar Andreas Ròdland Pseudoknots in RNA Secondary Structures: Representation, Enumeration, and Prevalence . . . . . . . . . . . . . . . 1197--1213 M. Christodoulakis and C. Iliopoulos and L. Mouchard and K. Perdikuri and A. Tsakalidis and K. Tsichlas Computation of Repetitions and Regularities of Biologically Weighted Sequences . . . . . . . . . . . . . . . 1214--1231 Meera Sitharam and Mavis Agbandje-Mckenna Modeling Virus Self-Assembly Pathways: Avoiding Dynamics Using Geometric Constraint Decomposition . . . . . . . . 1232--1265
Lincong Wang and Ramgopal R. Mettu and Bruce Randall Donald A Polynomial-Time Algorithm for \em De Novo Protein Backbone Structure Determination from Nuclear Magnetic Resonance Data . . . . . . . . . . . . . 1267--1288 Adrian D. Haimovich and Bruce Byrne and Ramakrishna Ramaswamy and William J. Welsh Wavelet Analysis of DNA Walks . . . . . 1289--1298 Mehmet Koyutürk and Yohan Kim and Shankar Subramaniam and Wojciech Szpankowski and Ananth Grama Detecting Conserved Interaction Patterns in Biological Networks . . . . . . . . . 1299--1322 Isaac Elias Settling the Intractability of Multiple Alignment . . . . . . . . . . . . . . . 1323--1339 Anne Bergeron and Jens Stoye On the Similarity of Sets of Permutations and Its Applications to Genome Comparison . . . . . . . . . . . 1340--1354 Jinbo Xu and Daniel Brown and Ming Li and Bin Ma Optimizing Multiple Spaced Seeds for Homology Search . . . . . . . . . . . . 1355--1368 Jonathan M. Keith Segmenting Eukaryotic Genomes with the Generalized Gibbs Sampler . . . . . . . 1369--1383 Florian A. Potra and Xing Liu Aligning Families of Two-Dimensional Gels by a Combined Multiresolution Forward-Inverse Transformation Approach 1384--1395
Firas Swidan and Michal Ziv-Ukelson and Ron Y. Pinter On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem . . . . . . 1397--1418 Maria Luisa Bonet and Katherine St.John and Ruchi Mahindru and Nina Amenta Approximating Subtree Distances Between Phylogenies . . . . . . . . . . . . . . 1419--1434 Winfried Just Reverse Engineering Discrete Dynamical Systems from Data Sets with Random Input Vectors . . . . . . . . . . . . . . . . 1435--1456 Joel E. Richardson fjoin: Simple and Efficient Computation of Feature Overlaps . . . . . . . . . . 1457--1464 Gilles Didier and Ivan Laprevotte and Maude Pupin and Alain Hénaut Local Decoding of Sequences and Alignment-Free Comparison . . . . . . . 1465--1476 Giulia Menconi and Roberto Marangoni A Compression-Based Approach for Coding Sequences Identification. I. Application to Prokaryotic Genomes . . . . . . . . . 1477--1488 Catherine Mooney and Alessandro Vullo and Gianluca Pollastri Protein Structural Motif Prediction in Multidimensional $ \phi $--$ \psi $ Space Leads to Improved Secondary Structure Prediction . . . . . . . . . . 1489--1502 Frank Emmert-Streib Algorithmic Computation of Knot Polynomials of Secondary Structure Elements of Proteins . . . . . . . . . . 1503--1512
B. Moerkerke and E. Goetghebeur Selecting ``Significant'' Differentially Expressed Genes from the Combined Perspective of the Null and the Alternative . . . . . . . . . . . . . . 1513--1531 Peter C. Y. Chen A Discrete-Event Approach to Transcription Control with Dynamic Event-Controllability . . . . . . . . . 1532--1545 Derek A. Ruths and Luay Nakhleh and M. Sriram Iyengar and Shrikanth A. G. Reddy and Prahlad T. Ram Hypothesis Generation in Signaling Networks . . . . . . . . . . . . . . . . 1546--1557 Ga\vsper Jakli\vc and Toma\vz Pisanski and Milan Randi\'c Characterization of Complex Biological Systems by Matrix Invariants . . . . . . 1558--1564 Yu Chen and Gordon M. Crippen Fold Recognition via a Tree . . . . . . 1565--1573 William J. Bruno and John E. Pearson Transformations that Preserve Detailed Balance in Markov Models . . . . . . . . 1574--1578 Pengfei Han and Xiuzhen Zhang and Raymond S. Norton and Zhi-Ping Feng Predicting Disordered Regions in Proteins Based on Decision Trees of Reduced Amino Acid Composition . . . . . 1579--1590 Bart J. A. Mertens and M. E. De Noo and R. A. E. M. Tollenaar and A. M. Deelder Mass Spectrometry Proteomic Diagnosis: Enacting the Double Cross-Validatory Paradigm . . . . . . . . . . . . . . . . 1591--1605 Zhenqiu Liu and Shili Lin and Ming Tan Genome-Wide Tagging SNPs with Entropy-Based Monte Carlo Method . . . . 1606--1614 Nak-Kyeong Kim and Jun Xie Protein Multiple Alignment Incorporating Primary and Secondary Structure Information . . . . . . . . . . . . . . 1615--1629 Andre Ribeiro and Rui Zhu and Stuart A. Kauffman A General Modeling Strategy for Gene Regulatory Networks with Stochastic Dynamics . . . . . . . . . . . . . . . . 1630--1639 P. Clote Combinatorics of Saturated Secondary Structures of RNA . . . . . . . . . . . 1640--1657
Noga Alon and Vera Asodi and Charles Cantor and Simon Kasif and John Rachlin Multi-Node Graphs: a Framework for Multiplexed Biological Assays . . . . . 1659--1672 Lu-yong Wang and Dorin Comaniciu and Daniel Fasulo Exploiting Interactions among Polymorphisms Contributing to Complex Disease Traits with Boosted Generative Modeling . . . . . . . . . . . . . . . . 1673--1684 Laxmi Parida Using PQ Structures for Genomic Rearrangement Phylogeny . . . . . . . . 1685--1700 Nicolas Lartillot Conjugate Gibbs Sampling for Bayesian Phylogenetic Models . . . . . . . . . . 1701--1722 Pengfei Han and Xiuzhen Zhang and Raymond S. Norton and Zhi-Ping Feng Predicting Disordered Regions in Proteins Based on Decision Trees of Reduced Amino Acid Composition . . . . . 1723--1734 Nak-Kyeong Kim and Jun Xie Protein Multiple Alignment Incorporating Primary and Secondary Structure Information . . . . . . . . . . . . . . 1735--1748 Sushmita Roy and Terran Lane and Chris Allen and Anthony D. Aragon and Margaret Werner-Washburne A Hidden-State Markov Model for Cell Population Deconvolution . . . . . . . . 1749--1774 Chun-Min Hung and Yueh-Min Huang and Ming-Shi Chang CSAM: Using Clustering-Hashing-Signal Anchoring Method to Explore Human Novel Genes . . . . . . . . . . . . . . . . . 1775--1789
Ilan Gronau and Shlomo Moran Neighbor Joining Algorithms for Inferring Phylogenies via LCA Distances 1--15 Baharak Rastegari and Anne Condon Parsing Nucleic Acid Pseudoknotted Secondary Structure: Algorithm and Applications . . . . . . . . . . . . . . 16--32 Sven Siebert and Rolf Backofen A Dynamic Programming Approach for Finding Common Patterns in RNAs . . . . 33--44 Laxmi Parida Gapped Permutation Pattern Discovery for Gene Order Comparisons . . . . . . . . . 45--55 Qingwu Yang and Sing-Hoi Sze Path Matching and Graph Matching in Biological Networks . . . . . . . . . . 56--67 Karen Lees and Stephen Roberts and Pari Skamnioti and Sarah Gurr Gene Microarray Analysis Using Angular Distribution Decomposition . . . . . . . 68--83 Morgan Bishop and Anthony J. Macula and Kayla Nimmo and Lauren Wood and Wendy K. Pogozelski and Thomas E. Renz Group Testing to Annihilate Pairs Applied to DNA Cross-Hybridization Elimination Using SYBR Green I . . . . . 84--96 Nilanjan Saha and Layne T. Watson and Karen Kafadar and Naren Ramakrishnan and Alexey Onufriev and Shrinivasrao Mane and Cecilia Vasquez-Robinet Validation and Estimation of Parameters for a General Probabilistic Model of the PCR Process . . . . . . . . . . . . . . 97--112
Leming Zhou and Liliana Florea Designing Sensitive and Specific Spaced Seeds for Cross-Species mRNA-to-Genome Alignment . . . . . . . . . . . . . . . 113--130 Pankaj K. Agarwal and Nabil H. Mustafa and Yusu Wang Fast Molecular Shape Matching Using Contact Maps . . . . . . . . . . . . . . 131--143 Dan Levy and Christopher Reeder and Bradford Loucas and Lynn Hlatky and Allen Chen and Michael Cornforth and Rainer Sachs Interpreting Chromosome Aberration Spectra . . . . . . . . . . . . . . . . 144--155 Daniel \vStefankovi\vc and Eric Vigoda Phylogeny of Mixture Models: Robustness of Maximum Likelihood and Non-Identifiable Distributions . . . . . 156--189 J. Waldispühl and P. Clote Computing the Partition Function and Sampling for Saturated Secondary Structures of RNA, with Respect to the Turner Energy Model . . . . . . . . . . 190--215 Isaac Elias and Tamir Tuller Reconstruction of Ancestral Genomic Sequences Using Likelihood . . . . . . . 216--237 Yong Kong Generalized Correlation Functions and Their Applications in Selection of Optimal Multiple Spaced Seeds for Homology Search . . . . . . . . . . . . 238--254
Haifeng Li and Anton Valouev and David C. Schwartz and Michael S. Waterman and Lei M. Li A Quantile Method for Sizing Optical Maps . . . . . . . . . . . . . . . . . . 255--266 Eric P. Xing and Michael I. Jordan and Roded Sharan Bayesian Haplotype Inference via the Dirichlet Process . . . . . . . . . . . 267--284 Mary Ellen Bock and Claudio Garutti and Concettina Guerra Discovery of Similar Regions on Protein Surfaces . . . . . . . . . . . . . . . . 285--299 Laxmi Parida Discovering Topological Motifs Using a Compact Notation . . . . . . . . . . . . 300--323 Naftali Kaminski and Ziv Bar-Joseph A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies 324--338 Grzegorz A. Rempala and Kenneth S. Ramos and Ted Kalbfleisch and Ivo Teneng Validation of a Mathematical Model of Gene Transcription in Aggregated Cellular Systems: Application to L1 Retrotransposition . . . . . . . . . . . 339--349 Mariusz Lubomirski and Michael R. D'Andrea and Stanley M. Belkowski and Javier Cabrera and James M. Dixon and Dhammika Amaratunga A Consolidated Approach to Analyzing Data from High-Throughput Protein Microarrays with an Application to Immune Response Profiling in Humans . . 350--359 Noah A. Rosenberg Counting Coalescent Histories . . . . . 360--377
Sébastien Angibaud and Guillaume Fertin and Irena Rusu and Stéphane Vialette A Pseudo-Boolean Framework for Computing Rearrangement Distances between Genomes with Duplicates . . . . . . . . . . . . 379--393 Guillaume Blin and Eric Blais and Danny Hermelin and Pierre Guillon and Mathieu Blanchette and Nadia El-Mabrouk Gene Maps Linearization Using Genomic Rearrangement Distances . . . . . . . . 394--407 Michal Ozery-Flato and Ron Shamir Sorting by Reciprocal Translocations via Reversals Theory . . . . . . . . . . . . 408--422 Wei Xu and Chunfang Zheng and David Sankoff Paths and Cycles in Breakpoint Graph of Random Multichromosomal Genomes . . . . 423--435 Zaky Adam and Monique Turmel and Claude Lemieux and David Sankoff Common Intervals and Symmetric Difference in a Model-Free Phylogenomics, with an Application to Streptophyte Evolution . . . . . . . . . 436--445 Abdoulaye Banire Diallo and Vladimir Makarenkov and Mathieu Blanchette Exact and Heuristic Algorithms for the Indel Maximum Likelihood Problem . . . . 446--461 Mathieu Lajoie and Denis Bertrand and Nadia El-Mabrouk and Olivier Gascuel Duplication and Inversion History of a Tandemly Repeated Genes Family . . . . . 462--478 Damian Wójtowicz and Jerzy Tiuryn Evolution of Gene Families Based on Gene Duplication, Loss, Accumulated Change, and Innovation . . . . . . . . . . . . . 479--495 N. Song and R. D. Sedgewick and D. Durand Domain Architecture Comparison for Multidomain Homology Identification . . 496--516 Cuong Than and Derek Ruths and Hideki Innan and Luay Nakhleh Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions . . . . . . . . . 517--535
Alberto Apostolico Preface . . . . . . . . . . . . . . . . 537--538 Teresa Przytycka Stability of Characters and Construction of Phylogenetic Trees . . . . . . . . . 539--549 Jim C. Huang and Quaid D. Morris and Brendan J. Frey Bayesian Inference of MicroRNA Targets from Sequence and Expression Data . . . 550--563 Jinbo Xu and Feng Jiao and Bonnie Berger A Parameterized Algorithm for Protein Structure Alignment . . . . . . . . . . 564--577 Tsung-Han Chiang and Mehmet Serkan Apaydin and Douglas L. Brutlag and David Hsu and Jean-Claude Latombe Using Stochastic Roadmap Simulation to Predict Experimental Quantities in Protein Folding Kinetics: Folding Rates and Phi-Values . . . . . . . . . . . . . 578--593 Michael Cameron and Yaniv Bernstein and Hugh E. Williams Clustered Sequence Representation for Fast Homology Search . . . . . . . . . . 594--614 Martin Bader and Enno Ohlebusch Sorting by Weighted Reversals, Transpositions, and Inverted Transpositions . . . . . . . . . . . . . 615--636 Wei Xie and Nikolaos V. Sahinidis A Reduction-Based Exact Algorithm for the Contact Map Overlap Problem . . . . 637--654 Philipp W. Messer and Ralf Bundschuh and Martin Vingron and Peter F. Arndt Effects of Long-Range Correlations in DNA on Sequence Alignment Score Statistics . . . . . . . . . . . . . . . 655--668 Stefanie Scheid and Rainer Spang Compensating for Unknown Confounders in Microarray Data Analysis Using Filtered Permutations . . . . . . . . . . . . . . 669--681 Samuel A. Andersson and Jens Lagergren Motif Yggdrasil: Sampling Sequence Motifs from a Tree Mixture Model . . . . 682--697
Alberto Apostolico Preface . . . . . . . . . . . . . . . . 699--700 Stanislav Angelov and Boulos Harb and Sampath Kannan and Sanjeev Khanna and Junhyong Kim Efficient Enumeration of Phylogenetically Informative Substrings 701--723 Nicholas D. Pattengale and Eric J. Gottlieb and Bernard M. E. Moret Efficiently Computing the Robinson--Foulds Metric . . . . . . . . 724--735 David Heckerman and Carl Kadie and Jennifer Listgarten Leveraging Information Across HLA Alleles/Supertypes Improves Epitope Prediction . . . . . . . . . . . . . . . 736--746 Mehmet Koyutürk and Wojciech Szpankowski and Ananth Grama Assessing Significance of Connectivity and Conservation in Protein Interaction Networks . . . . . . . . . . . . . . . . 747--764 Chakra Chennubhotla and Ivet Bahar Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics . . . . . . . . . . . . . . . . 765--776 Xiaoduan Ye and Alan M. Friedman and Chris Bailey-Kellogg Hypergraph Model of Multi-Residue Interactions in Proteins: Sequentially-Constrained Partitioning Algorithms for Optimization of Site-Directed Protein Recombination . . 777--790 Brian Y. Chen and Viacheslav Y. Fofanov and Drew H. Bryant and Bradley D. Dodson and David M. Kristensen and Andreas M. Lisewski and Marek Kimmel and Olivier Lichtarge and Lydia E. Kavraki The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of $3$D Motifs . . 791--816 Benny Chor and Tamir Tuller Biological Networks: Comparison, Conservation, and Evolution via Relative Description Length . . . . . . . . . . . 817--838 Shawna Thomas and Xinyu Tang and Lydia Tapia and Nancy M. Amato Simulating Protein Motions with Rigidity Analysis . . . . . . . . . . . . . . . . 839--855 Ydo Wexler and Chaya Zilberstein and Michal Ziv-Ukelson A Study of Accessible Motifs and RNA Folding Complexity . . . . . . . . . . . 856--872
Nevzat Onur Domaniç and Franco P. Preparata A Novel Approach to the Detection of Genomic Approximate Tandem Repeats in the Levenshtein Metric . . . . . . . . . 873--891 Manikandan Narayanan and Richard M. Karp Comparing Protein Interaction Networks via a Graph Match-and-Split Algorithm 892--907 Isana Veksler-Lublinsky and Michal Ziv-Ukelson and Danny Barash and Klara Kedem A Structure-Based Flexible Search Method for Motifs in RNA . . . . . . . . . . . 908--926 Réka Albert and Bhaskar DasGupta and Riccardo Dondi and Sema Kachalo and Eduardo Sontag and Alexander Zelikovsky and Kelly Westbrooks A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence . . . . . . . . . 927--949 Liqing Zhang and Layne T. Watson Note on the Computation of Critical Effective Population Sizes . . . . . . . 950--960 Frank Emmert-Streib The Chronic Fatigue Syndrome: a Comparative Pathway Analysis . . . . . . 961--972 M. Andrecut and S. A. Kauffman A Physical Analogy of the Genetic Toggle Switch . . . . . . . . . . . . . . . . . 973--983 Stefan Zeiser and Johannes Müller and Volkmar Liebscher Modeling the Hes1 Oscillator . . . . . . 984--1000 Manolis Christodoulakis and G. Brian Golding and Costas S. Iliopoulos and Yoan José Pinzón Ardila and William F. Smyth Efficient Algorithms for Counting and Reporting Segregating Sites in Genomic Sequences . . . . . . . . . . . . . . . 1001--1010 Yi Y. Shi and Gerald A. Miller and Oleg Denisenko and Hong Qian and Karol Bomsztyk Quantitative Model for Binary Measurements of Protein-Protein Interactions . . . . . . . . . . . . . . 1011--1023
Xue Wu and Chau-Wen Tseng and Nathan Edwards HMMatch: Peptide Identification by Spectral Matching of Tandem Mass Spectra Using Hidden Markov Models . . . . . . . 1025--1043 Zakharia M. Frenkel and Edward N. Trifonov Evolutionary Networks in the Formatted Protein Sequence Space . . . . . . . . . 1044--1057 Beckett Sterner and Rohit Singh and Bonnie Berger Predicting and Annotating Catalytic Residues: An Information Theoretic Approach . . . . . . . . . . . . . . . . 1058--1073 Rolf Backofen and Shihyen Chen and Danny Hermelin and Gad M. Landau and Mikhail A. Roytberg and Oren Weimann and Kaizhong Zhang Locality and Gaps in RNA Comparison . . 1074--1087 Morgan A. Bishop and Arkadii G. D'Yachkov and Anthony J. Macula and Thomas E. Renz and Vyacheslav V. Rykov Free Energy Gap and Statistical Thermodynamic Fidelity of DNA Codes . . 1088--1104 Koen Deforche and Ricardo Camacho and Kristel Van Laethem and Beth Shapiro and Yves Moreau and Andrew Rambaut and Anne-Mieke Vandamme and Philippe Lemey Estimating the Relative Contribution of dNTP Pool Imbalance and APOBEC3G/3F Editing to HIV Evolution \em In Vivo . . 1105--1114 Aleksandar Stojmirovi\'c and Yi-Kuo Yu Information Flow in Interaction Networks 1115--1143
Laxmi Parida Statistical Significance of Large Gene Clusters . . . . . . . . . . . . . . . . 1145--1159 Zheng Fu and Xin Chen and Vladimir Vacic and Peng Nan and Yang Zhong and Tao Jiang MSOAR: a High-Throughput Ortholog Assignment System Based on Genome Rearrangement . . . . . . . . . . . . . 1160--1175 Francis L. Martin and Matthew J. German and Ernst Wit and Thomas Fearn and Narasimhan Ragavan and Hubert M. Pollock Identifying Variables Responsible for Clustering in Discriminant Analysis of Data from Infrared Microspectroscopy of a Biological Sample . . . . . . . . . . 1176--1184 Hendrik Fuß and Werner Dubitzky and C. Stephen Downes and Mary Jo Kurth Deactivation of Src Family Kinases: Hypothesis Testing Using a Monte Carlo Sensitivity Analysis of Systems-Level Properties . . . . . . . . . . . . . . . 1185--1200 Tetsuo Shibuya Efficient Substructure RMSD Query Algorithms . . . . . . . . . . . . . . . 1201--1207 Yongxi Cheng and Ding-Zhu Du Efficient Constructions of Disjunct Matrices with Applications to DNA Library Screening . . . . . . . . . . . 1208--1216 Achim Tresch and T. Beissbarth and H. Sültmann and R. Kuner and A. Poustka and A. Buness Discrimination of Direct and Indirect Interactions in a Network of Regulatory Effects . . . . . . . . . . . . . . . . 1217--1228 Ilkka Havukkala and Stijn Vanderlooy On the Reliable Identification of Plant Sequences Containing a Polyadenylation Site . . . . . . . . . . . . . . . . . . 1229--1245
Dan Gusfield and Vikas Bansal and Vineet Bafna and Yun S. Song A Decomposition Theory for Phylogenetic Networks and Incompatible Characters . . 1247--1272 Yun S. Song and Zhihong Ding and Dan Gusfield and Charles H. Langley and Yufeng Wu Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations . . . . . . . . 1273--1286 Scott C. Schmidler and Joseph E. Lucas and Terrence G. Oas Statistical Estimation of Statistical Mechanical Models: Helix-Coil Theory and Peptide Helicity Prediction . . . . . . 1287--1310 Dongxiao Zhu and Alfred O. Hero III Bayesian Hierarchical Model for Large-Scale Covariance Matrix Estimation 1311--1326 Michael Hirsch and Stephen Swift and Xiohui Liu Optimal Search Space for Clustering Gene Expression Data via Consensus . . . . . 1327--1341 Binhai Zhu Protein Local Structure Alignment Under the Discrete Fréchet Distance . . . . . . 1343--1351 Magnus Åstrand and Petter Mostad and Mats Rudemo Improved Covariance Matrix Estimators for Weighted Analysis of Microarray Data 1353--1367
F. Picard and J.-J. Daudin and M. Koskas and S. Schbath and S. Robin Assessing the Exceptionality of Network Motifs . . . . . . . . . . . . . . . . . 1--20 M. Andrecut and S. A. Kauffman On the Sparse Reconstruction of Gene Networks . . . . . . . . . . . . . . . . 21--30 W. A. Lorenz and Y. Ponty and P. Clote Asymptotics of RNA Shapes . . . . . . . 31--63 Rosemarie Swanson and Ioannis Kagiampakis and Jerry W. Tsai An Information Measure of the Quality of Protein Secondary Structure Prediction 65--79 Dumitru Brinza and Alexander Zelikovsky Design and Validation of Methods Searching for Risk Factors in Genotype Case-Control Studies . . . . . . . . . . 81--90 Sagi Snir and Tandy Warnow and Satish Rao Short Quartet Puzzling: a New Quartet-Based Phylogeny Reconstruction Algorithm . . . . . . . . . . . . . . . 91--103 C. Bidot and F. Gruy and C.-S. Haudin and F. El Hentati and B. Guy and C. Lambert Mathematical Modeling of T-Cell Activation Kinetic . . . . . . . . . . . 105--128
Xiaoqiu Huang Sequence Alignment with an Appropriate Substitution Matrix . . . . . . . . . . 129--138 Hosna Jabbari and Anne Condon and Shelly Zhao Novel and Efficient RNA Secondary Structure Prediction Using Hierarchical Folding . . . . . . . . . . . . . . . . 139--163 Ramu Anandakrishnan and Alexey Onufriev Analysis of Basic Clustering Algorithms for Numerical Estimation of Statistical Averages in Biomolecules . . . . . . . . 165--184 Jutta Gebert and Susanne Motameny and Ulrich Faigle and Christian V. Forst and Rainer Schrader Identifying Genes of Gene Regulatory Networks Using Formal Concept Analysis 185--194 Yongxi Cheng and Ding-Zhu Du New Constructions of One- and Two-Stage Pooling Designs . . . . . . . . . . . . 195--205 Guzmán Santafé and Jose A. Lozano and Pedro Larrañaga Inference of Population Structure Using Genetic Markers and a Bayesian Model Averaging Approach for Clustering . . . 207--220 Thomas Stolte and Volker Hösel and Johannes Müller and Michael Speicher Modeling Clonal Expansion from M-FISH Experiments . . . . . . . . . . . . . . 221--230
George Nicola and Colin A. Smith and Ruben Abagyan New Method for the Assessment of All Drug-Like Pockets Across a Structural Genome . . . . . . . . . . . . . . . . . 231--240 Jing Li Prioritize and Select SNPs for Association Studies with Multi-Stage Designs . . . . . . . . . . . . . . . . 241--257 Utz-Uwe Haus and Steffen Klamt and Tamon Stephen Computing Knock-Out Strategies in Metabolic Networks . . . . . . . . . . . 259--268 A. J. Adewale and I. Dinu and J. D. Potter and Q. Liu and Y. Yasui Pathway Analysis of Microarray Data via Regression . . . . . . . . . . . . . . . 269--277 Jing Wu and Jun Xie Computation-Based Discovery of \em Cis-Regulatory Modules by Hidden Markov Model . . . . . . . . . . . . . . . . . 279--290 Mikael Bodén and Rohan D. Teasdale Determining Nucleolar Association from Sequence by Leveraging Protein-Protein Interactions . . . . . . . . . . . . . . 291--304 Raya Khanin and Veronica Vinciotti Computational Modeling of Post-Transcriptional Gene Regulation by MicroRNAs . . . . . . . . . . . . . . . 305--316 James O. Wrabl and Nick V. Grishin Statistics of Random Protein Superpositions: $p$-Values for Pairwise Structure Alignment . . . . . . . . . . 317--355
Enno Ohlebusch and Stefan Kurtz Space Efficient Computation of Rare Maximal Exact Matches between Multiple Sequences . . . . . . . . . . . . . . . 357--377 Valery Polyanovsky and Mikhail A. Roytberg and Vladimir G. Tumanyan Reconstruction of Genuine Pair-Wise Sequence Alignment . . . . . . . . . . . 379--391 Vladimir Filkov and Nameeta Shah A Simple Model of the Modular Structure of Transcriptional Regulation in Yeast 393--405 Jonathan M. Keith and Peter Adams and Stuart Stephen and John S. Mattick Delineating Slowly and Rapidly Evolving Fractions of the \bionameDrosophila Genome . . . . . . . . . . . . . . . . . 407--430 Patrick C. H. Ma and Keith C. C. Chan UPSEC: an Algorithm for Classifying Unaligned Protein Sequences into Functional Families . . . . . . . . . . 431--443 Olga Tcheremenskaia and Alessandro Giuliani and Maurizio Tomasi PROFALIGN Algorithm Identifies the Regions Containing Folding Determinants by Scoring Pairs of Hydrophobic Profiles of Remotely Related Proteins . . . . . . 445--455 Jian Feng and Daniel Q. Naiman and Bret Cooper Combined Dynamic Arrays for Storing and Searching Semi-Ordered Tandem Mass Spectrometry Data . . . . . . . . . . . 457--468
Huy Hoang Do and Kwok Pui Choi and Franco P. Preparata and Wing Kin Sung and Louxin Zhang Spectrum-Based \em De Novo Repeat Detection in Genomic Sequences . . . . . 469--488 Buhm Han and Banu Dost and Vineet Bafna and Shaojie Zhang Structural Alignment of Pseudoknotted RNA . . . . . . . . . . . . . . . . . . 489--504 Zhiyu Zhao and Bin Fu and Francisco J. Alanis and Christopher M. Summa Feedback Algorithm and Web-Server for Protein Structure Alignment . . . . . . 505--524 Anthony J. Macula and Alexander Schliep and Morgan A. Bishop and Thomas E. Renz New, Improved, and Practical $k$-Stem Sequence Similarity Measures for Probe Design . . . . . . . . . . . . . . . . . 525--534 Zhixiang Chen and Bin Fu and Robert Schweller and Boting Yang and Zhiyu Zhao and Binhai Zhu Linear Time Probabilistic Algorithms for the Singular Haplotype Reconstruction Problem from SNP Fragments . . . . . . . 535--546
Utz J. Pape and Sven Rahmann and Fengzhu Sun and Martin Vingron Compound Poisson Approximation of the Number of Occurrences of a Position Frequency Matrix (PFM) on Both Strands 547--564 Torsten Blum and Oliver Kohlbacher Using Atom Mapping Rules for an Improved Detection of Relevant Routes in Weighted Metabolic Networks . . . . . . . . . . . 565--576 Anne Kupczok and Arndt Von Haeseler and Steffen Klaere An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees . . 577--591 Xu Ling and Xin He and Dong Xin and Jiawei Han Efficiently Identifying Max-Gap Clusters in Pairwise Genome Comparison . . . . . 593--609 David Gold and Bani Mallick and Kevin Coombes Real-Time Gene Expression: Statistical Challenges in Design and Inference . . . 611--623 Andrew K. C. Wong and Wai-Ho Au and Keith C. C. Chan Discovering High-Order Patterns of Gene Expression Levels . . . . . . . . . . . 625--637 Katharina T. Huber and Martin Lott and Vincent Moulton and Andreas Spillner The Complexity of Deriving Multi-Labeled Trees from Bipartitions . . . . . . . . 639--651
Terry Speed Preface . . . . . . . . . . . . . . . . 653--653 Anthony A. Philippakis and Aaron M. Qureshi and Michael F. Berger and Martha L. Bulyk Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments . . . . . . . . . 655--665 Yufeng Wu Association Mapping of Complex Diseases with Ancestral Recombination Graphs: Models and Efficient Algorithms . . . . 667--684 Ole Schulz-Trieglaff and Rene Hussong and Clemens Gröpl and Andreas Leinenbach and Andreas Hildebrandt and Christian Huber and Knut Reinert Computational Quantification of Peptides from LC-MS Data . . . . . . . . . . . . 685--704 Marshall Bern and David Goldberg Improved Ranking Functions for Protein and Modification-Site Identifications 705--719 Ydo Wexler and Dan Geiger Variational Upper and Lower Bounds for Probabilistic Graphical Models . . . . . 721--735 Dina Schneidman-Duhovny and Oranit Dror and Yuval Inbar and Ruth Nussinov and Haim J. Wolfson Deterministic Pharmacophore Detection via Multiple Flexible Alignment of Drug-Like Molecules . . . . . . . . . . 737--754 Hetunandan Kamisetty and Eric P. Xing and Christopher J. Langmead Free Energy Estimates of All-Atom Protein Structures Using Generalized Belief Propagation . . . . . . . . . . . 755--766 Yue Lu and Sing-Hoi Sze Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences . . . . . . . . . . . . . . . 767--777 Hiroyuki Kuwahara and Chris J. Myers Production-Passage-Time Approximation: a New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions . . . . . . . . . . . . . . . 779--792 Michal Ozery-Flato and Ron Shamir Sorting Genomes with Centromeres by Translocations . . . . . . . . . . . . . 793--812 Anshul Nigham and David Hsu Protein Conformational Flexibility Analysis with Noisy Data . . . . . . . . 813--828 T. M. Murali and Corban G. Rivera Network Legos: Building Blocks of Cellular Wiring Diagrams . . . . . . . . 829--844 Antonio Piccolboni Multivariate Segmentation in the Analysis of Transcription Tiling Array Data . . . . . . . . . . . . . . . . . . 845--856 Wenyi Wang and Benilton Carvalho and Nathaniel D. Miller and Jonathan Pevsner and Aravinda Chakravarti and Rafael A. Irizarry Estimating Genome-Wide Copy Number Using Allele-Specific Mixture Models . . . . . 857--866 Chun-Nam John Yu and Thorsten Joachims and Ron Elber and Jaroslaw Pillardy Support Vector Training of Protein Alignment Models . . . . . . . . . . . . 867--880 Wah-Heng Lee and Wing-Kin Sung RB-Finder: an Improved Distance-Based Sliding Window Method to Detect Recombination Breakpoints . . . . . . . 881--898 Chen Yanover and Ora Schueler-Furman and Yair Weiss Minimizing and Learning Energy Functions for Side-Chain Prediction . . . . . . . 899--911 Banu Dost and Tomer Shlomi and Nitin Gupta and Eytan Ruppin and Vineet Bafna and Roded Sharan QNet: a Tool for Querying Protein Interaction Networks . . . . . . . . . . 913--925 Noah Zaitlen and Manuel Reyes-Gomez and David Heckerman and Nebojsa Jojic Shift-Invariant Adaptive Double Threading: Learning MHC II--Peptide Binding . . . . . . . . . . . . . . . . 927--942
Glenn Tesler and Dannie Durand Preface . . . . . . . . . . . . . . . . 943--946 Chunfang Zheng and Qian Zhu and David Sankoff Descendants of Whole Genome Duplication within Gene Order Phylogeny . . . . . . 947--964 Ai Xia and Maria V. Sharakhova and Igor V. Sharakhov Reconstructing Ancestral Autosomal Arrangements in the \bionameAnopheles gambiae Complex . . . . . . . . . . . . 965--980 Benjamin Vernot and Maureen Stolzer and Aiton Goldman and Dannie Durand Reconciliation with Non-Binary Species Trees . . . . . . . . . . . . . . . . . 981--1006 Jian Ma and Aakrosh Ratan and Brian J. Raney and Bernard B. Suh and Louxin Zhang and Webb Miller and David Haussler DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications . . 1007--1027 Simon Gog and Martin Bader Fast Algorithms for Transforming Back and Forth between a Signed Permutation and Its Equivalent Simple Permutation 1029--1041 Cedric Chauve and Jean-Philippe Doyon and Nadia El-Mabrouk Gene Family Evolution by Duplication, Speciation, and Loss . . . . . . . . . . 1043--1062 Denis Bertrand and Mathieu Lajoie and Nadia El-Mabrouk Inferring Ancestral Gene Orders for a Family of Tandemly Arrayed Genes . . . . 1063--1077 William Arndt and Jijun Tang Improving Reversal Median Computation Using Commuting Reversals and Cycle Information . . . . . . . . . . . . . . 1079--1092 Sébastien Angibaud and Guillaume Fertin and Irena Rusu and Annelyse Thévenin and Stéphane Vialette Efficient Tools for Computing the Number of Breakpoints and the Number of Adjacencies between Two Genomes with Duplicate Genes . . . . . . . . . . . . 1093--1115 Max A. Alekseyev Multi-Break Rearrangements and Breakpoint Re-Uses: From Circular to Linear Genomes . . . . . . . . . . . . . 1117--1131 Anonymous Correction . . . . . . . . . . . . . . . 1132--1132
Laxmi Parida and Marta Melé and Francesc Calafell and Jaume Bertranpetit Estimating the Ancestral Recombinations Graph (ARG) as Compatible Networks of SNP Patterns . . . . . . . . . . . . . . 1133--1153 Justin Kennedy and Ion M\uandoiu and Bogdan Pa\csaniuc Genotype Error Detection Using Hidden Markov Models of Haplotype Diversity . . 1155--1171 M. Andrecut and S. Huang and S. A. Kauffman Heuristic Approach to Sparse Approximation of Gene Regulatory Networks . . . . . . . . . . . . . . . . 1173--1186 Lee A. Newberg Significance of Gapped Sequence Alignments . . . . . . . . . . . . . . . 1187--1194 Hillary S. W. Han and Christian M. Reidys Pseudoknot RNA Structures with Arc-Length $ \geq 4 $ . . . . . . . . . 1195--1208 Kanti V. Mardia and Vysaul B. Nyirongo Simulating Virtual Protein $ C_\alpha $ Traces with Applications . . . . . . . . 1209--1220 María Elena Díaz and Guillermo Ayala and Teresa León and Roberto Zoncu and Derek Toomre Analyzing Protein-Protein Spatial-Temporal Dependencies from Image Sequences Using Fuzzy Temporal Random Sets . . . . . . . . . . . . . . . . . . 1221--1236
Xianyang Jiang and Dominique Lavenier and Stephen S.-T. Yau Coding Region Prediction Based on a Universal DNA Sequence Representation Method . . . . . . . . . . . . . . . . . 1237--1256 Gang Ma and Christian M. Reidys Canonical RNA Pseudoknot Structures . . 1257--1273 Jing Xiao and Lusheng Wang and Xiaowen Liu and Tao Jiang An Efficient Voting Algorithm for Finding Additive Biclusters with Random Background . . . . . . . . . . . . . . . 1275--1293 Jialiang Yang and Louxin Zhang Run Probabilities of Seed-Like Patterns and Identifying Good Transition Seeds 1295--1313 Antonio Lijoi and Ramsés H. Mena and Igor Prünster A Bayesian Nonparametric Approach for Comparing Clustering Structures in EST Libraries . . . . . . . . . . . . . . . 1315--1327 Miranda van Uitert and Wouter Meuleman and Lodewyk Wessels Biclustering Sparse Binary Genomic Data 1329--1345 Man-Hung Eric Tang and Anders Krogh and Ole Winther BayesMD: Flexible Biological Modeling for Motif Discovery . . . . . . . . . . 1347--1363 Riccardo Porreca and Samuel Drulhe and Hidde de Jong and Giancarlo Ferrari-Trecate Structural Identification of Piecewise-Linear Models of Genetic Regulatory Networks . . . . . . . . . . 1365--1380
Lee A. Newberg and Charles E. Lawrence Exact Calculation of Distributions on Integers, with Application to Sequence Alignment . . . . . . . . . . . . . . . 1--18 Alireza Hadj Khodabakhshi and Ján Ma\vnuch and Arash Rafiey and Arvind Gupta Stable Structure-Approximating Inverse Protein Folding in $2$D Hydrophobic-Polar-Cysteine (HPC) Model 19--30 Yong Kong Statistical Distributions of Pyrosequencing . . . . . . . . . . . . . 31--42 Paola Bonizzoni and Giancarlo Mauri and Graziano Pesole and Ernesto Picardi and Yuri Pirola and Raffaella Rizzi Detecting Alternative Gene Structures from Spliced ESTs: a Computational Approach . . . . . . . . . . . . . . . . 43--66 Valéria Lima Passos and Frans E. S. Tan and Bjorn Winkens and Martijn P. F. Berger Optimal Designs for One- and Two-Color Microarrays Using Mixed Models: a Comparative Evaluation of Their Efficiencies . . . . . . . . . . . . . . 67--83 Tamjidul Hoque and Madhu Chetty and Abdul Sattar Extended HP Model for Protein Structure Prediction . . . . . . . . . . . . . . . 85--103 Ran Libeskind-Hadas and Michael A. Charleston On the Computational Complexity of the Reticulate Cophylogeny Reconstruction Problem . . . . . . . . . . . . . . . . 105--117 Hao Ge and Min Qian Boolean Network Approach to Negative Feedback Loops of the p53 Pathways: Synchronized Dynamics and Stochastic Limit Cycles . . . . . . . . . . . . . . 119--132
Henry C. M. Leung and Qian Xiang and S. M. Yiu and Francis Y. L. Chin Predicting Protein Complexes from PPI Data: a Core-Attachment Approach . . . . 133--144 Xiaoning Qian and Sing-Hoi Sze and Byung-Jun Yoon Querying Pathways in Protein Interaction Networks Based on Hidden Markov Models 145--157 Fereydoun Hormozdiari and Raheleh Salari and Michael Hsing and Alexander Schönhuth and Simon K. Chan and S. Cenk Sahinalp and Artem Cherkasov The Effect of Insertions and Deletions on Wirings in Protein-Protein Interaction Networks: a Large-Scale Study . . . . . . . . . . . . . . . . . 159--167 Jason E. McDermott and Ronald C. Taylor and Hyunjin Yoon and Fred Heffron Bottlenecks and Hubs in Inferred Networks Are Important for Virulence in \bionameSalmonella typhimurium . . . . . 169--180 Shaul Karni and Hermona Soreq and Roded Sharan A Network-Based Method for Predicting Disease-Causing Genes . . . . . . . . . 181--189 Elhanan Borenstein and Marcus W. Feldman Topological Signatures of Species Interactions in Metabolic Networks . . . 191--200 Karen Sachs and Solomon Itani and Jennifer Carlisle and Garry P. Nolan and Dana Pe'er and Douglas A. Lauffenburger Learning Signaling Network Structures with Sparsely Distributed Data . . . . . 201--212 Robert Castelo and Alberto Roverato Reverse Engineering Molecular Regulatory Networks from Microarray Data with qp-Graphs . . . . . . . . . . . . . . . 213--227 Daniel Marbach and Thomas Schaffter and Claudio Mattiussi and Dario Floreano Generating Realistic \em In Silico Gene Networks for Performance Assessment of Reverse Engineering Methods . . . . . . 229--239 Francesco Iorio and Roberto Tagliaferri and Diego di Bernardo Identifying Network of Drug Mode of Action by Gene Expression Profiling . . 241--251 Saket Navlakha and Michael C. Schatz and Carl Kingsford Revealing Biological Modules via Graph Summarization . . . . . . . . . . . . . 253--264 Xi Chen and Lily Wang Integrating Biological Knowledge with Gene Expression Profiles for Survival Prediction of Cancer . . . . . . . . . . 265--278 Gal Chechik and Daphne Koller Timing of Gene Expression Responses to Environmental Changes . . . . . . . . . 279--290 Balaji Veeramani and Joel S. Bader Metabolic Flux Correlations, Genetic Interactions, and Disease . . . . . . . 291--302 Tamir Tuller and Udi Rubinstein and Dani Bar and Michael Gurevitch and Eytan Ruppin and Martin Kupiec Higher-Order Genomic Organization of Cellular Functions in Yeast . . . . . . 303--316 Leping Li GADEM: a Genetic Algorithm Guided Formation of Spaced Dyads Coupled with an EM Algorithm for Motif Discovery . . 317--329 J. William Lee and Tomasz Zemojtel and Eugene Shakhnovich Systems-Level Evidence of Transcriptional Co-Regulation of Yeast Protein Complexes . . . . . . . . . . . 331--339 Guo-Cheng Yuan Targeted Recruitment of Histone Modifications in Humans Predicted by Genomic Sequences . . . . . . . . . . . 341--355 Zhen Xuan Yeo and Hock Chuan Yeo and Joan Keng Suan Yeo and Ai Li Yeo and Ye Li and Neil D. Clarke Inferring Transcription Factor Targets from Gene Expression Changes and Predicted Promoter Occupancy . . . . . . 357--368 Albert Erives Non-Homologous Structured CRMs from the \bionameCiona Genome . . . . . . . . . . 369--377 G. Russo and M. Di Bernardo How to Synchronize Biological Clocks . . 379--393 Bogusaw Kluge and Anna Gambin and Wojciech Niemiro Modeling Exopeptidase Activity from LC-MS Data . . . . . . . . . . . . . . . 395--406
Ali Shojaie and George Michailidis Analysis of Gene Sets Based on the Underlying Regulatory Network . . . . . 407--426 Junfeng Gu and Honglin Li and Hualiang Jiang and Xicheng Wang Optimizing Energy Potential for Protein Fold Recognition with Parametric Evaluation Function . . . . . . . . . . 427--442 Michelle R. Lacey and Jason Calmes A Sharp Error Probability Estimate for the Reconstruction of Phylogenetic Quartets by the Four-Point Method . . . 443--456 Renqiang Min and Anthony Bonner and Jingjing Li and Zhaolei Zhang Learned Random-Walk Kernels and Empirical-Map Kernels for Protein Sequence Classification . . . . . . . . 457--474 Juliette Blanchet and Matthieu Vignes A Model-Based Approach to Gene Clustering with Missing Observation Reconstruction in a Markov Random Field Framework . . . . . . . . . . . . . . . 475--486 Scott Grandison and Carl Roberts and Richard J. Morris The Application of $3$D Zernike Moments for the Description of ``Model-Free'' Molecular Structure, Functional Motion, and Structural Reliability . . . . . . . 487--500 David Soloveichik Robust Stochastic Chemical Reaction Networks and Bounded Tau-Leaping . . . . 501--522
David Dynerman and Erick Butzlaff and Julie C. Mitchell CUSA and CUDE: GPU-Accelerated Methods for Estimating Solvent Accessible Surface Area and Desolvation . . . . . . 523--537 Andre S. Ribeiro and Olli-Pekka Smolander and Tiina Rajala and Antti Häkkinen and Olli Yli-Harja Delayed Stochastic Model of Transcription at the Single Nucleotide Level . . . . . . . . . . . . . . . . . 539--553 Andrey Ilatovskiy and Michael Petukhov Genome-Wide Search for Local DNA Segments with Anomalous GC-Content . . . 555--564 Waibhav D. Tembe and John V. Pearson and Nils Homer and James Lowey and Edward Suh and David W. Craig Statistical Comparison Framework and Visualization Scheme for Ranking-Based Algorithms in High-Throughput Genome-Wide Studies . . . . . . . . . . 565--577 Aleksandar Stojmirovi\'c and Yi-Kuo Yu Geometric Aspects of Biological Sequence Comparison . . . . . . . . . . . . . . . 579--610 József Dombi and Attila Kertész-Farkas Applying Fuzzy Technologies to Equivalence Learning in Protein Classification . . . . . . . . . . . . . 611--623 Lucinda K. Southworth and Stuart K. Kim and Art B. Owen Properties of Balanced Permutations . . 625--638
Yan Liu and Jaime Carbonell and Vanathi Gopalakrishnan and Peter Weigele Conditional Graphical Models for Protein Structural Motif Recognition . . . . . . 639--657 Sang-Cheol Seok and Michael Evans and Veronica J. Vieland Fast and Accurate Calculation of a Computationally Intensive Statistic for Mapping Disease Genes . . . . . . . . . 659--676 Christine De Mol and Sofia Mosci and Magali Traskine and Alessandro Verri A Regularized Method for Selecting Nested Groups of Relevant Genes from Microarray Data . . . . . . . . . . . . 677--690 Zheng Rong Yang Predict Collagen Hydroxyproline Sites Using Support Vector Machines . . . . . 691--702 Alexander G. Georgiev Interpretable Numerical Descriptors of Amino Acid Space . . . . . . . . . . . . 703--723 Utz-Uwe Haus and Kathrin Niermann and Klaus Truemper and Robert Weismantel Logic Integer Programming Models for Signaling Networks . . . . . . . . . . . 725--743 Ye-In Chang and Jiun-Rung Chen and Yueh-Chi Tsai Mining Subspace Clusters from DNA Microarray Data Using Large Itemset Techniques . . . . . . . . . . . . . . . 745--768
Alireza Hadj Khodabakhshi and Ján Ma\vnuch and Arash Rafiey and Arvind Gupta Inverse Protein Folding in $3$D Hexagonal Prism Lattice under HPC Model 769--802 Ho-Lin Chen and Anne Condon and Hosna Jabbari An $O$ ( $ n^5$ ) Algorithm for MFE Prediction of Kissing Hairpins and $4$-Chains in Nucleic Acids . . . . . . 803--815 Yong Kong Statistical Distributions of Sequencing by Synthesis with Probabilistic Nucleotide Incorporation . . . . . . . . 817--827 Jörn Behre and Stefan Schuster Modeling Signal Transduction in Enzyme Cascades with the Concept of Elementary Flux Modes . . . . . . . . . . . . . . . 829--844 Niels Richard Hansen Statistical Models for Local Occurrences of RNA Structures . . . . . . . . . . . 845--858 Filippo Geraci and Mauro Leoncini and Manuela Montangero and Marco Pellegrini and M. Elena Renda K-Boost: a Scalable Algorithm for High-Quality Clustering of Microarray Gene Expression Data . . . . . . . . . . 859--873 Elias August and Antonis Papachristodoulou A New Computational Tool for Establishing Model Parameter Identifiability . . . . . . . . . . . . 875--885 Anonymous Correction . . . . . . . . . . . . . . . 886--886
Xiaoqiu Huang and Martin Vingron Maximum Similarity: a New Formulation of Phylogenetic Reconstruction . . . . . . 887--896 Niranjan Nagarajan and Mihai Pop Parametric Complexity of Sequence Assembly: Theory and Applications to Next Generation Sequencing . . . . . . . 897--908 M. Andrecut and D. Foster and H. Carteret and S. A. Kauffman Maximal Information Transfer and Behavior Diversity in Random Threshold Networks . . . . . . . . . . . . . . . . 909--916 Xiaodong Cai and Zhi-Min Yuan Stochastic Modeling and Simulation of the p53-MDM2/MDMX Loop . . . . . . . . . 917--933 Peng Qiu and Sylvia K. Plevritis Simultaneous Class Discovery and Classification of Microarray Data Using Spectral Analysis . . . . . . . . . . . 935--944 Yuki Kato and Tatsuya Akutsu and Hiroyuki Seki Dynamic Programming Algorithms and Grammatical Modeling for Protein Beta-Sheet Prediction . . . . . . . . . 945--957 Kilian Bartholomé and Clemens Kreutz and Jens Timmer Estimation of Gene Induction Enables a Relevance-Based Ranking of Gene Sets . . 959--967
Anonymous Special RECOMB 2008 Issue . . . . . . . 969--969 Caroline C. Friedel and Jan Krumsiek and Ralf Zimmer Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast . . . . . . . . . . . 971--987 Maxim Kalaev and Vineet Bafna and Roded Sharan Fast and Accurate Alignment of Multiple Protein Networks . . . . . . . . . . . . 989--999 Jason Flannick and Antal Novak and Chuong B. Do and Balaji S. Srinivasan and Serafim Batzoglou Automatic Parameter Learning for Multiple Local Network Alignment . . . . 1001--1022 Michael R. Mehan and Juan Nunez-Iglesias and Mrinal Kalakrishnan and Michael S. Waterman and Xianghong Jasmine Zhou An Integrative Network Approach to Map the Transcriptome to the Phenome . . . . 1023--1034 Yanxin Shi and Michael Klutstein and Itamar Simon and Tom Mitchell and Ziv Bar-Joseph A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors . . . . . . . . . 1035--1049 Yu Zhang and Giltae Song and Tomá\vs Vina\vr and Eric D. Green and Adam Siepel and Webb Miller Evolutionary History Reconstruction for Mammalian Complex Gene Clusters . . . . 1051--1070 J. G. Burleigh and M. S. Bansal and A. Wehe and O. Eulenstein Locating Large-Scale Gene Duplication Events through Reconciled Trees: Implications for Identifying Ancient Polyploidy Events in Plants . . . . . . 1071--1083 Sebastian Böcker and Katharina Jahn and Julia Mixtacki and Jens Stoye Computation of Median Gene Clusters . . 1085--1099 Paul Medvedev and Michael Brudno Maximum Likelihood Genome Assembly . . . 1101--1116 Michael Sammeth Complete Alternative Splicing Events Are Bubbles in Splicing Graphs . . . . . . . 1117--1140 Sivan Bercovici and Dan Geiger Inferring Ancestries Efficiently in Admixed Populations with Linkage Disequilibrium . . . . . . . . . . . . . 1141--1150 Wei Zheng and Alan M. Friedman and Chris Bailey-Kellogg Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins . . . . . . . . . . . . . . . . 1151--1168 Ritendra Datta and Marshall Bern Spectrum Fusion: Using Multiple Mass Spectra for De Novo Peptide Sequencing 1169--1182 Yong Fuga Li and Randy J. Arnold and Yixue Li and Predrag Radivojac and Quanhu Sheng and Haixu Tang A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics . . . . . 1183--1193
Mary Sehl and Alexander V. Alekseyenko and Kenneth L. Lange Accurate Stochastic Simulation via the Step Anticipation $ \tau $-Leaping (SAL) Algorithm . . . . . . . . . . . . . . . 1195--1208 Jens Ledet Jensen A Note on the Linear Memory Baum--Welch Algorithm . . . . . . . . . . . . . . . 1209--1210 Catherine Eng and Charu Asthana and Bertrand Aigle and Sébastien Hergalant and Jean-François Mari and Pierre Leblond A New Data Mining Approach for the Detection of Bacterial Promoters Combining Stochastic and Combinatorial Methods . . . . . . . . . . . . . . . . 1211--1225 Hanen Ben Hassen and Afif Masmoudi and Ahmed Rebai Inference in Signal Transduction Pathways Using EM Algorithm and an Implicit Algorithm: Incomplete Data Case 1227--1240 Qiang Cheng and Jie Cheng Sparsity Optimization Method for Multivariate Feature Screening for Gene Expression Analysis . . . . . . . . . . 1241--1252 Jin Jun and Paul Ryvkin and Edward Hemphill and Craig Nelson Duplication Mechanism and Disruptions in Flanking Regions Determine the Fate of Mammalian Gene Duplicates . . . . . . . 1253--1266 Géraldine Jean and David James Sherman and Macha Nikolski Mining the Semantics of Genome Super-Blocks to Infer Ancestral Architectures . . . . . . . . . . . . . 1267--1284
Craig Nelson and Stéphane Vialette RECOMB--Comparative Genomics Special Issue . . . . . . . . . . . . . . . . . 1285--1286 S\`everine Bérard and Annie Chateau and Cedric Chauve and Christophe Paul and Eric Tannier Computation of Perfect DCJ Rearrangement Scenarios with Linear and Circular Chromosomes . . . . . . . . . . . . . . 1287--1309 Sophia Yancopoulos and Richard Friedberg DCJ Path Formulation for Genome Transformations which Include Insertions, Deletions, and Duplications 1311--1338 Krister M. Swenson and Yu Lin and Vaibhav Rajan and Bernard M. E. Moret Hurdles and Sorting by Inversions: Combinatorial, Statistical, and Experimental Results . . . . . . . . . . 1339--1351 David Sankoff and Chunfang Zheng and P. Kerr Wall and Claude dePamphilis and Jim Leebens-Mack and Victor A. Albert Towards Improved Reconstruction of Ancestral Gene Order in Angiosperm Phylogeny . . . . . . . . . . . . . . . 1353--1367 Andrew Wei Xu A Fast and Exact Algorithm for the Median of Three Problem: a Graph Decomposition Approach . . . . . . . . . 1369--1381 Melvin Zhang and Hon Wai Leong Gene Team Tree: a Hierarchical Representation of Gene Teams for All Gap Lengths . . . . . . . . . . . . . . . . 1383--1398 Jean-Philippe Doyon and Cedric Chauve and Sylvie Hamel Space of Gene/Species Trees Reconciliations and Parsimonious Models 1399--1418 Daniel R. Schrider and James C. Costello and Matthew W. Hahn All Human-Specific Gene Losses Are Present in the Genome as Pseudogenes . . 1419--1427 Jin Jun and Paul Ryvkin and Edward Hemphill and Ion Mandoiu and Craig Nelson The Birth of New Genes by RNA- and DNA-Mediated Duplication during Mammalian Evolution . . . . . . . . . . 1429--1444 Michal Ozery-Flato and Ron Shamir Sorting Cancer Karyotypes by Elementary Operations . . . . . . . . . . . . . . . 1445--1460 Abdoulaye Baniré Diallo and Dunarel Badescu and Mathieu Blanchette and Vladimir Makarenkov A Whole Genome Study and Identification of Specific Carcinogenic Regions of the Human Papilloma Viruses . . . . . . . . 1461--1473 Denis Bertrand and Mathieu Blanchette and Nadia El-Mabrouk Genetic Map Refinement Using a Comparative Genomic Approach . . . . . . 1475--1486 Bernhard Haubold and Peter Pfaffelhuber and Mirjana Domazet-Los\=o and Thomas Wiehe Estimating Mutation Distances from Unaligned Genomes . . . . . . . . . . . 1487--1500
Yunxia Sui and Xiaoyue Zhao and Terence P. Speed and Zhijin Wu Background Adjustment for DNA Microarrays Using a Database of Microarray Experiments . . . . . . . . . 1501--1515 John P. McCrow Alignment of Phylogenetically Unambiguous Indels in \bionameShewanella 1517--1528 Yongxi Cheng and Ding-Zhu Du and Ker-I Ko and Guohui Lin On the Parameterized Complexity of Pooling Design . . . . . . . . . . . . . 1529--1537 Ming-Wei Su and Hsiu-Man Lin and Hanna S. Yuan and Woei-Chyn Chu Categorizing Host-Dependent RNA Viruses by Principal Component Analysis of Their Codon Usage Preferences . . . . . . . . 1539--1547 Fenix W. D. Huang and Wade W. J. Peng and Christian M. Reidys Folding $3$-Noncrossing RNA Pseudoknot Structures . . . . . . . . . . . . . . . 1549--1575 Matteo Comin and Concettina Guerra and Frank Dellaert Binding Balls: Fast Detection of Binding Sites Using a Property of Spherical Fourier Transform . . . . . . . . . . . 1577--1591 M. Andrecut Parallel GPU Implementation of Iterative PCA Algorithms . . . . . . . . . . . . . 1593--1599 Kouichi Kimura and Yutaka Suzuki and Sumio Sugano and Asako Koike Computation of Rank and Select Functions on Hierarchical Binary String and Its Application to Genome Mapping Problems for Short-Read DNA Sequences . . . . . . 1601--1613
Gesine Reinert and David Chew and Fengzhu Sun and Michael S. Waterman Alignment-Free Sequence Comparison (I): Statistics and Power . . . . . . . . . . 1615--1634 Nadia Pisanti and Henry Soldano and Mathilde Carpentier and Joel Pothier A Relational Extension of the Notion of Motifs: Application to the Common $3$D Protein Substructures Searching Problem 1635--1660 Zhenqiu Liu and Ronald B. Gartenhaus and Xue-Wen Chen and Charles D. Howell and Ming Tan Survival Prediction and Gene Identification with Penalized Global AUC Maximization . . . . . . . . . . . . . . 1661--1670 Huixiao Hong and Qilong Hong and Roger Perkins and Leming Shi and Hong Fang and Zhenqiang Su and Yvonne Dragan and James C. Fuscoe and Weida Tong The Accurate Prediction of Protein Family from Amino Acid Sequence by Measuring Features of Sequence Fragments 1671--1688 Li-Yeh Chuang and Cheng-Huei Yang and Cheng-Hong Yang Tabu Search and Binary Particle Swarm Optimization for Feature Selection Using Microarray Data . . . . . . . . . . . . 1689--1703 Andrei S. Rodin and Anatoliy Litvinenko and Kathy Klos and Alanna C. Morrison and Trevor Woodage and Josef Coresh and Eric Boerwinkle Use of Wrapper Algorithms Coupled with a Random Forests Classifier for Variable Selection in Large-Scale Genomic Association Studies . . . . . . . . . . 1705--1718 Yi He and Changjun Chen and Yi Xiao United-Residue (UNRES) Langevin Dynamics Simulations of trpzip2 Folding . . . . . 1719--1730 Li-Ching Wu and Jorng-Tzong Horng and Yong-An Chen A Computation to Integrate the Analysis of Genetic Variations Occurring within Regulatory Elements and Their Possible Effects . . . . . . . . . . . . . . . . 1731--1747
Alexander Schönhuth and Raheleh Salari and Fereydoun Hormozdiari and Artem Cherkasov and S. Cenk Sahinalp Towards Improved Assessment of Functional Similarity in Large-Scale Screens: a Study on Indel Length . . . . 1--20 Lan Liu and Yonghui Wu and Stefano Lonardi and Tao Jiang Efficient Genome-Wide TagSNP Selection Across Populations via the Linkage Disequilibrium Criterion . . . . . . . . 21--37 Regina Samaga and Axel Von Kamp and Steffen Klamt Computing Combinatorial Intervention Strategies and Failure Modes in Signaling Networks . . . . . . . . . . . 39--53 Vladimir Vacic and Lilia M. Iakoucheva and Stefano Lonardi and Predrag Radivojac Graphlet Kernels for Prediction of Functional Residues in Protein Structures . . . . . . . . . . . . . . . 55--72 Nirmalya Bandyopadhyay and Tamer Kahveci GBA Manager: an Online Tool for Querying Low-Complexity Regions in Proteins . . . 73--77 Scott Mann and Jinyan Li and Yi-Ping Phoebe Chen Insights into Bacterial Genome Composition through Variable Target GC Content Profiling . . . . . . . . . . . 79--96 Juhyun Jung and Taewoo Ryu and Yongdeuk Hwang and Eunjung Lee and Doheon Lee Prediction of Extracellular Matrix Proteins Based on Distinctive Sequence and Domain Characteristics . . . . . . . 97--105
Dimitrije Jevremovic and Cong T. Trinh and Friedrich Srienc and Daniel Boley On Algebraic Properties of Extreme Pathways in Metabolic Networks . . . . . 107--119 Hyungwon Choi and Zhaohui S. Qin and Debashis Ghosh A Double-Layered Mixture Model for the Joint Analysis of DNA Copy Number and Gene Expression Data . . . . . . . . . . 121--137 Nha Nguyen and Heng Huang and Soontorn Oraintara and An Vo Stationary Wavelet Packet Transform and Dependent Laplacian Bivariate Shrinkage Estimator for Array-CGH Data Smoothing 139--152 Mert Karaka\cs and Nils Woetzel and Jens Meiler BCL::Contact --- Low Confidence Fold Recognition Hits Boost Protein Contact Prediction and \em De Novo Structure Determination . . . . . . . . . . . . . 153--168 Peng Qiu and Andrew J. Gentles and Sylvia K. Plevritis Reducing the Computational Complexity of Information Theoretic Approaches for Reconstructing Gene Regulatory Networks 169--176 Shuo Jiao and Shunpu Zhang Estimating the Proportion of Equivalently Expressed Genes in Microarray Data Based on Transformed Test Statistics . . . . . . . . . . . . 177--187 M. N. Steijaert and J. H. K. Van Den Brink and A. M. L. Liekens and P. A. J. Hilbers and H. M. M. Ten Eikelder Computing the Stochastic Dynamics of Phosphorylation Networks . . . . . . . . 189--199
Anonymous RECOMB Main Conference 2009 . . . . . . 201--201 Tetsuo Shibuya Searching Protein $3$-D Structures in Linear Time . . . . . . . . . . . . . . 203--219 Zengyou He and Chao Yang and Can Yang and Robert Z. Qi and Jason Po-Ming Tam and Weichuan Yu Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification . . . . . . . . . . . . . 221--235 Sharon Bruckner and Falk Hüffner and Richard M. Karp and Ron Shamir and Roded Sharan Topology-Free Querying of Protein Interaction Networks . . . . . . . . . . 237--252 Yong Lu and Roni Rosenfeld and Gerard J. Nau and Ziv Bar-Joseph Cross Species Expression Analysis of Innate Immune Response . . . . . . . . . 253--268 Bonnie Kirkpatrick and Eran Halperin and Richard M. Karp Haplotype Inference in Complex Pedigrees 269--280 Veli Mäkinen and Gonzalo Navarro and Jouni Sirén and Niko Välimäki Storage and Retrieval of Highly Repetitive Sequence Collections . . . . 281--308 Arvind Ramanathan and Pratul K. Agarwal and Maria Kurnikova and Christopher J. Langmead An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations . . . . . . . . . . . . . . 309--324 Alexandre Donzé and Gilles Clermont and Christopher J. Langmead Parameter Synthesis in Nonlinear Dynamical Systems: Application to Systems Biology . . . . . . . . . . . . 325--336 Nicholas D. Pattengale and Masoud Alipour and Olaf R. P. Bininda-Emonds and Bernard M. E. Moret and Alexandros Stamatakis How Many Bootstrap Replicates Are Necessary? . . . . . . . . . . . . . . . 337--354 Oliver Stegle and Katherine J. Denby and Emma J. Cooke and David L. Wild and Zoubin Ghahramani and Karsten M. Borgwardt A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series . . 355--367 Ali Bashir and Qing Lu and Dennis Carson and Benjamin J. Raphael and Yu-Tsueng Liu and Vineet Bafna Optimizing PCR Assays for DNA-Based Cancer Diagnostics . . . . . . . . . . . 369--381 Dan Gusfield The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory . . . . . . . . . . 383--399 Xiang Zhang and Feng Pan and Yuying Xie and Fei Zou and Wei Wang COE: a General Approach for Efficient Genome-Wide Two-Locus Epistasis Test in Disease Association Study . . . . . . . 401--415 Osvaldo Zagordi and Lukas Geyrhofer and Volker Roth and Niko Beerenwinkel Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction 417--428 Mathias Möhl and Sebastian Will and Rolf Backofen Lifting Prediction to Alignment of RNA Pseudoknots . . . . . . . . . . . . . . 429--442 Mathieu Lavallée-Adam and Benoit Coulombe and Mathieu Blanchette Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks . . . . . . . . . . . . . . . . 443--457 Wei Zheng and Karl E. Griswold and Chris Bailey-Kellogg Protein Fragment Swapping: a Method for Asymmetric, Selective Site-Directed Recombination . . . . . . . . . . . . . 459--475 B. J. Hescott and M. D. M. Leiserson and L. J. Cowen and D. K. Slonim Evaluating Between-Pathway Models with Expression Data . . . . . . . . . . . . 477--487 Krister M. Swenson and Vaibhav Rajan and Yu Lin and Bernard M. E. Moret Sorting Signed Permutations by Inversions in $ O(n \log n) $ Time . . . 489--501 Saket Navlakha and James White and Niranjan Nagarajan and Mihai Pop and Carl Kingsford Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information . . . . . . . . . . . . . . 503--516 Suzanne S. Sindi and Benjamin J. Raphael Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data . . . . . . . . . . . . . 517--531 Eun Yong Kang and Chun Ye and Ilya Shpitser and Eleazar Eskin Detecting the Presence and Absence of Causal Relationships between Expression of Yeast Genes with Very Few Samples . . 533--546 Hyun Min Kang and Noah A. Zaitlen and Eleazar Eskin EMINIM: an Adaptive and Memory-Efficient Algorithm for Genotype Imputation . . . 547--560 John Kececioglu and Eagu Kim and Travis Wheeler Aligning Protein Sequences with Predicted Secondary Structure . . . . . 561--580
Zhiyuan Zhai and Shih-Yen Ku and Yihui Luan and Gesine Reinert and Michael S. Waterman and Fengzhu Sun The Power of Detecting Enriched Patterns: an HMM Approach . . . . . . . 581--592 Tetsuo Shibuya Searching Protein Three-Dimensional Structures in Faster Than Linear Time 593--602 Haixiang Shi and Bertil Schmidt and Weiguo Liu and Wolfgang Müller-Wittig A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware 603--615 Mikael Bodén and Graham Dellaire and Kevin Burrage and Timothy L. Bailey A Bayesian Network Model of Proteins' Association with Promyelocytic Leukemia (PML) Nuclear Bodies . . . . . . . . . . 617--630 Gang Wu and Ying Zhang and Yimin Wei Krylov Subspace Algorithms for Computing GeneRank for the Analysis of Microarray Data Mining . . . . . . . . . . . . . . 631--646 Namsu Ahn and Sungsoo Park Finding an Upper Bound for the Number of Contacts in Hydrophobic-Hydrophilic Protein Structure Prediction Model . . . 647--656
Qingwu Yang and Gangman Yi and Fenghui Zhang and Michael R. Thon and Sing-Hoi Sze Identifying Gene Clusters within Localized Regions in Multiple Genomes 657--668 Fereydoun Hormozdiari and Raheleh Salari and Vineet Bafna and S. Cenk Sahinalp Protein-Protein Interaction Network Evaluation for Identifying Potential Drug Targets . . . . . . . . . . . . . . 669--684 Yen-Lin Huang and Chin Lung Lu Sorting by Reversals, Generalized Transpositions, and Translocations Using Permutation Groups . . . . . . . . . . . 685--705 Antonio Cardone and R. Wayne Albers and Ram D. Sriram and Harish C. Pant Evaluation of the Interaction of Cyclin-Dependent Kinase 5 with Activator p25 and with p25-Derived Inhibitor CIP 707--721 Claude Berge and Nicolas Froloff and Ravi Kiran Reddy Kalathur and Myriam Maumy and Olivier Poch and Wolfgang Raffelsberger and Nicolas Wicker Multidimensional Fitting for Multivariate Data Analysis . . . . . . . 723--732 Patrick C. H. Ma and Keith C. C. Chan Discovering Interesting Motif-Sets for Multi-Class Protein Sequence Classification . . . . . . . . . . . . . 733--743 Myung-Hoon Chung and Chul Koo Kim Non-Random Mating Involving Inheritance of Social Status . . . . . . . . . . . . 745--754 Ivan Molineris and Gabriele Sales and Federico Bianchi and Ferdinando Di Cunto and Michele Caselle A New Approach for the Identification of Processed Pseudogenes . . . . . . . . . 755--765
Fumei Lam and Ryan Tarpine and Sorin Istrail The Imperfect Ancestral Recombination Graph Reconstruction Problem: Upper Bounds for Recombination and Homoplasy 767--781 Feng Zhao and Jian Peng and Joe Debartolo and Karl F. Freed and Tobin R. Sosnick and Jinbo Xu A Probabilistic and Continuous Model of Protein Conformational Space for Template-Free Modeling . . . . . . . . . 783--798 Frederick A. Matsen constNJ: an Algorithm to Reconstruct Sets of Phylogenetic Trees Satisfying Pairwise Topological Constraints . . . . 799--818 Mats Aspnäs and Kimmo Mattila and Kristoffer Osowski and Jan Westerholm Code Optimization of the Subroutine to Remove Near Identical Matches in the Sequence Database Homology Search Tool PSI-BLAST . . . . . . . . . . . . . . . 819--823 Howsun Jow and Madhuchhanda Bhattacharjee and Richard Boys and Darren Wilkinson The Integration of Genetic Maps Using Bayesian Inference . . . . . . . . . . . 825--840 Ján Ma\vnuch and Ladislav Stacho and Christine Stoll Two Lower Bounds for Self-Assemblies at Temperature 1 . . . . . . . . . . . . . 841--852 Elena S. Dimitrova and M. Paola Vera Licona and John McGee and Reinhard Laubenbacher Discretization of Time Series Data . . . 853--868
Adrián López García De Lomana and Qasim K. Beg and G. De Fabritiis and Jordi Vill\`a-Freixa Statistical Analysis of Global Connectivity and Activity Distributions in Cellular Networks . . . . . . . . . . 869--878 Shuguang Huang Statistical Issues in Subpopulation Analysis of High Content Imaging Data 879--894 Scott C. James and Varun Boriah Modeling Algae Growth in an Open-Channel Raceway . . . . . . . . . . . . . . . . 895--906 Lusheng Wang and Binhai Zhu On the Tractability of Maximal Strip Recovery . . . . . . . . . . . . . . . . 907--914 Minghui Jiang and Pedro J. Tejada and Ramoni O. Lasisi and Shanhong Cheng and D. Scott Fechser $K$-Partite RNA Secondary Structures . . 915--925 Huilan Chang and Hong-Bin Chen and Hung-Lin Fu Identification and Classification Problems on Pooling Designs for Inhibitor Models . . . . . . . . . . . . 927--941 Marcos R. Betancourt Comparison between Molecular Dynamic Based and Knowledge Based Potentials for Protein Side Chains . . . . . . . . . . 943--952
Ewa Szczurek and Przemys\law Biecek and Jerzy Tiuryn and Martin Vingron Introducing Knowledge into Differential Expression Analysis . . . . . . . . . . 953--967 Ana Graça and Inês Lynce and João Marques-Silva and Arlindo L. Oliveira Haplotype Inference by Pure Parsimony: a Survey . . . . . . . . . . . . . . . . . 969--992 Peter Minary and Michael Levitt Conformational Optimization with Natural Degrees of Freedom: a Novel Stochastic Chain Closure Algorithm . . . . . . . . 993--1010 Alberto Apostolico and Fabio Cunial The Subsequence Composition of Polypeptides . . . . . . . . . . . . . . 1011--1049 Michal Ziv-Ukelson and Irit Gat-Viks and Ydo Wexler and Ron Shamir A Faster Algorithm for Simultaneous Alignment and Folding of RNA . . . . . . 1051--1065 Bong-Rae Kim and Timothy McMurry and Wei Zhao and Rongling Wu and Arthur Berg Wavelet-Based Functional Clustering for Patterns of High-Dimensional Dynamic Gene Expression . . . . . . . . . . . . 1067--1080 Xiaodong Pang and Linxiang Zhou and Mingjun Zhang and Fang Xie and Long Yu and Lili Zhang and Lina Xu and Xinyi Zhang A Mathematical Model for Peptide Inhibitor Design . . . . . . . . . . . . 1081--1093
Anonymous Preface . . . . . . . . . . . . . . . . 1095--1096 Cedric Chauve and Haris Gavranovic and Aida Ouangraoua and Eric Tannier Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods II . . . . . . . . . . . . . . . 1097--1112 Zhenyu Yang and David Sankoff Natural Parameter Values for Generalized Gene Adjacency . . . . . . . . . . . . . 1113--1128 A\"\ida Ouangraoua and Anne Bergeron Combinatorial Structure of Genome Rearrangements Scenarios . . . . . . . . 1129--1144 Marília D. V. Braga and Jens Stoye The Solution Space of Sorting by DCJ . . 1145--1165 Cedric Chauve and Utz-Uwe Haus and Tamon Stephen and Vivija P. You Minimal Conflicting Sets for the Consecutive Ones Property in Ancestral Genome Reconstruction . . . . . . . . . 1167--1181 Guillaume Blin and David Faye and Jens Stoye Finding Nested Common Intervals Efficiently . . . . . . . . . . . . . . 1183--1194 Andrew Wei Xu The Median Problems on Linear Multichromosomal Genomes: Graph Representation and Fast Exact Solutions 1195--1211 Anne Bergeron and Paul Medvedev and Jens Stoye Rearrangement Models and Single-Cut Operations . . . . . . . . . . . . . . . 1213--1225 Giltae Song and Louxin Zhang and Tomas Vinar and Webb Miller CAGE: Combinatorial Analysis of Gene-Cluster Evolution . . . . . . . . . 1227--1242 João Delgado and Inês Lynce and Vasco Manquinho Computing the Summed Adjacency Disruption Number between Two Genomes with Duplicate Genes . . . . . . . . . . 1243--1265 Tomá\vs Vina\vr and Bro\vna Brejová and Giltae Song and Adam Siepel Reconstructing Histories of Complex Gene Clusters on a Phylogeny . . . . . . . . 1267--1279 Chih-Hao Hsu and Yu Zhang and Ross C. Hardison and Eric D. Green and Webb Miller An Effective Method for Detecting Gene Conversion Events in Whole Genomes . . . 1281--1297 Zaky Adam and David Sankoff A Statistically Fair Comparison of Ancestral Genome Reconstructions, Based on Breakpoint and Rearrangement Distances . . . . . . . . . . . . . . . 1299--1314 Mahdi Belcaid and Anne Bergeron and Guylaine Poisson Mosaic Graphs and Comparative Genomics in Phage Communities . . . . . . . . . . 1315--1326 Tamir Tuller and Hadas Birin and Martin Kupiec and Eytan Ruppin Reconstructing Ancestral Genomic Sequences by Co-Evolution: Formal Definitions, Computational Issues, and Biological Examples . . . . . . . . . . 1327--1344
Laxmi Parida Ancestral Recombinations Graph: a Reconstructability Perspective Using Random-Graphs Framework . . . . . . . . 1345--1370 Ben Grainger and Michael I. Sadowski and William R. Taylor Re-Evaluating the ``Rules'' of Protein Topology . . . . . . . . . . . . . . . . 1371--1384 Zhijin Wu and Martin J. Aryee Subset Quantile Normalization Using Negative Control Features . . . . . . . 1385--1395 Eldar Giladi and John Healy and Gene Myers and Chris Hart and Philipp Kapranov and Doron Lipson and Steve Roels and Edward Thayer and Stan Letovsky Error Tolerant Indexing and Alignment of Short Reads with Covering Template Families . . . . . . . . . . . . . . . . 1397--1411 Zengti Li and Suogang Gao and Hongjie Du and Feng Zou and Weili Wu Efficient Error-Correcting Pooling Designs Constructed from Pseudo-Symplectic Spaces Over a Finite Field . . . . . . . . . . . . . . . . . 1413--1423 Haiying Zhang and Bing Zhou On the Maximal Interval Subgraph of a Tree . . . . . . . . . . . . . . . . . . 1425--1433 Arvind Gupta and Mohammad M. Karimi and Ján Ma\vnuch and Ladislav Stacho and Xiaohong Zhao Haplotype Inferring via Galled-Tree Networks Is NP-Complete . . . . . . . . 1435--1449 Duong D. Doan and Patricia A. Evans and Joseph D. Horton A Near-Linear Time Algorithm for Haplotype Determination on General Pedigrees . . . . . . . . . . . . . . . 1451--1465
Lin Wan and Gesine Reinert and Fengzhu Sun and Michael S. Waterman Alignment-Free Sequence Comparison (II): Theoretical Power of Comparison Statistics . . . . . . . . . . . . . . . 1467--1490 Nikita A. Sakhanenko and David J. Galas Markov Logic Networks in the Analysis of Genetic Data . . . . . . . . . . . . . . 1491--1508 Ilan Gronau and Shlomo Moran and Irad Yavneh Adaptive Distance Measures for Resolving K2P Quartets: Metric Separation versus Stochastic Noise . . . . . . . . . . . . 1509--1518 Sébastien Boisvert and François Laviolette and Jacques Corbeil Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies . . . . . . . . . . . . . . 1519--1533 Sagi Snir and Edward Trifonov A Novel Technique for Detecting Putative Horizontal Gene Transfer in the Sequence Space . . . . . . . . . . . . . . . . . 1535--1548 Xiaohong Zhao and Lance E. Palmer and Randall Bolanos and Cristian Mircean and Dan Fasulo and Gayle M. Wittenberg EDAR: an Efficient Error Detection and Removal Algorithm for Next Generation Sequencing Data . . . . . . . . . . . . 1549--1560 Xin Chen and Jian-Yi Yang Constructing Consensus Genetic Maps in Comparative Analysis . . . . . . . . . . 1561--1573 Christian M. Reidys and Rita R. Wang Shapes of RNA Pseudoknot Structures . . 1575--1590
Sarah Behrens and Martin Vingron Studying the Evolution of Promoter Sequences: a Waiting Time Problem . . . 1591--1606 Xugang Ye and Yi-Kuo Yu and Stephen F. Altschul Compositional Adjustment of Dirichlet Mixture Priors . . . . . . . . . . . . . 1607--1620 Qing Zhou On Weight Matrix and Free Energy Models for Sequence Motif Detection . . . . . . 1621--1638 Marc Herant and Micah Dembo Cytopede: a Three-Dimensional Tool for Modeling Cell Motility on a Flat Surface 1639--1677 Xin Liu and Ya-Pu Zhao Substitution Matrices of Residue Triplets Derived from Protein Blocks . . 1679--1687 Xinan Zhang and Yingdong Zhao and Avidan U. Neumann Partial Immunity and Vaccination for Influenza . . . . . . . . . . . . . . . 1689--1696 Hock Peng Chan and Nancy Ruonan Zhang and Louis H. Y. Chen Importance Sampling of Word Patterns in DNA and Protein Sequences . . . . . . . 1697--1709 Oscar Luaces and José R. Quevedo and Miguel Pérez-Enciso and Jorge Díez and Juan José Del Coz and Antonio Bahamonde Explaining the Genetic Basis of Complex Quantitative Traits through Prediction Models . . . . . . . . . . . . . . . . . 1711--1723
Cuong V. Than and Noah A. Rosenberg Consistency Properties of Species Tree Inference by Minimizing Deep Coalescences . . . . . . . . . . . . . . 1--15 Ryan Day and Xiaotao Qu and Rosemarie Swanson and Zach Bohannan and Robert Bliss and Jerry Tsai Relative Packing Groups in Template-Based Structure Prediction: Cooperative Effects of True Positive Constraints . . . . . . . . . . . . . . 17--26 Rumen Andonov and Noël Malod-Dognin and Nicola Yanev Maximum Contact Map Overlap Revisited 27--41 Markus Heinonen and Sampsa Lappalainen and Taneli Mielikäinen and Juho Rousu Computing Atom Mappings for Biochemical Reactions without Subgraph Isomorphism 43--58 Y. Ovadia and D. Fielder and C. Conow and R. Libeskind-Hadas The Cophylogeny Reconstruction Problem Is NP-Complete . . . . . . . . . . . . . 59--65 J. F. Weng and D. A. Thomas and I. Mareels Maximum Parsimony, Substitution Model, and Probability Phylogenetic Trees . . . 67--80 Elisabetta Marras and Antonella Travaglione and Enrico Capobianco Manifold Learning in Protein Interactomes . . . . . . . . . . . . . . 81--96 Thomas K. F. Wong and T. W. Lam and Wing-Kin Sung and Brenda W. Y. Cheung and S. M. Yiu Structural Alignment of RNA with Complex Pseudoknot Structure . . . . . . . . . . 97--108 Paul A. Jenkins and Robert C. Griffiths Inference from Samples of DNA Sequences Using a Two-Locus Model . . . . . . . . 109--127 Anonymous Correction . . . . . . . . . . . . . . . 129--129
Manolis Kellis and Andrea Califano and Ziv Bar-Joseph Preface . . . . . . . . . . . . . . . . 131--131 Liat Perlman and Assaf Gottlieb and Nir Atias and Eytan Ruppin and Roded Sharan Combining Drug and Gene Similarity Measures for Drug-Target Elucidation . . 133--145 Pradeep Bandaru and Mukesh Bansal and Ilya Nemenman Mass Conservation and Inference of Metabolic Networks from High-Throughput Mass Spectrometry Data . . . . . . . . . 147--154 Patrick Ng and Uri Keich Alignment Constrained Sampling . . . . . 155--168 Chang F. Quo and Richard A. Moffitt and Alfred H. Merrill, Jr. and May D. Wang Adaptive Control Model Reveals Systematic Feedback and Key Molecules in Metabolic Pathway Regulation . . . . . . 169--182 Alberto Corradin and Barbara Di Camillo and Vincenzo Ciminale and Gianna Toffolo and Claudio Cobelli Sensitivity Analysis of Retrovirus HTLV-1 Transactivation . . . . . . . . . 183--193 Athanasios Polynikis and Giulia Cuccato and Stefania Criscuolo and Stephen J. Hogan and Mario Di Bernardo and Diego Di Bernardo Design and Construction of a Versatile Synthetic Network for Bistable Gene Expression in Mammalian Systems . . . . 195--203
Bonnie Berger Preface: 14$^{th}$ International Conference on Research in Computational Molecular Biology (RECOMB 2010) . . . . 205--205 Nir Atias and Roded Sharan An Algorithmic Framework for Predicting Side Effects of Drugs . . . . . . . . . 207--218 Ferhat Ay and Manolis Kellis and Tamer Kahveci SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings . . . . . . . . . . 219--235 Sivan Bercovici and Dan Geiger Admixture Aberration Analysis: Application to Mapping in Admixed Population Using Pooled DNA . . . . . . 237--249 José Caldas and Samuel Kaski Hierarchical Generative Biclustering for MicroRNA Expression Analysis . . . . . . 251--261 Salim A. Chowdhury and Rod K. Nibbe and Mark R. Chance and Mehmet Koyutürk Subnetwork State Functions Define Dysregulated Subnetworks in Cancer . . . 263--281 Manfred Claassen and Ruedi Aebersold and Joachim M. Buhmann Proteome Coverage Prediction for Integrated Proteomics Datasets . . . . . 283--293 Timothy Danford and Robin Dowell and Sudeep Agarwala and Paula Grisafi and Gerald Fink and David Gifford Discovering Regulatory Overlapping RNA Transcripts . . . . . . . . . . . . . . 295--303 Jianxing Feng and Wei Li and Tao Jiang Inference of Isoforms from Short Sequence Reads . . . . . . . . . . . . . 305--321 Bjarni V. Halldórsson and Derek Aguiar and Ryan Tarpine and Sorin Istrail The Clark Phaseable Sample Size Problem: Long-Range Phasing and Loss of Heterozygosity in GWAS . . . . . . . . . 323--333 Michael Hirsch and Bernhard Schölkopf and Michael Habeck A Blind Deconvolution Approach for Improving the Resolution of Cryo-EM Density Maps . . . . . . . . . . . . . . 335--346 Richard Jang and Xin Gao and Ming Li Towards Fully Automated Structure-Based NMR Resonance Assignment of $^{15}$N-Labeled Proteins From Automatically Picked Peaks . . . . . . . 347--363 Wei-Chun Kao and Yun S. Song naiveBayesCall: an Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing . . . . . . . 365--377 David R. Kelley and Carl Kingsford Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression . . . . . . . . . . . . . . 379--390 Adam Kowalczyk and Justin Bedo and Thomas Conway and Bryan Beresford-Smith The Poisson Margin Test for Normalization-Free Significance Analysis of NGS Data . . . . . . . . . . . . . . 391--400 Christos Kozanitis and Chris Saunders and Semyon Kruglyak and Vineet Bafna and George Varghese Compressing Genomic Sequence Fragments Using SlimGene . . . . . . . . . . . . . 401--413 Fumei Lam and Charles H. Langley and Yun S. Song On the Genealogy of Asexual Diploids . . 415--428 Jonathan Laserson and Vladimir Jojic and Daphne Koller Genovo: \em De Novo Assembly for Metagenomes . . . . . . . . . . . . . . 429--443 Navodit Misra and Guy Blelloch and R. Ravi and Russell Schwartz Generalized Buneman Pruning for Inferring the Most Parsimonious Multi-State Phylogeny . . . . . . . . . 445--457 Bogdan Pa\csaniuc and Noah Zaitlen and Eran Halperin Accurate Estimation of Expression Levels of Homologous Genes in RNA-seq Experiments . . . . . . . . . . . . . . 459--468 Benedict Paten and Mark Diekhans and Dent Earl and John St.John and Jian Ma and Bernard Suh and David Haussler Cactus Graphs for Genome Comparisons . . 469--481 Manu N. Setty and Alexander Gusev and Itsik Pe'er HLA Type Inference via Haplotypes Identical by Descent . . . . . . . . . . 483--493 Itai Sharon and Sivan Bercovici and Ron Y. Pinter and Tomer Shlomi Pathway-Based Functional Analysis of Metagenomes . . . . . . . . . . . . . . 495--505 Fabio Vandin and Eli Upfal and Benjamin J. Raphael Algorithms for Detecting Significantly Mutated Pathways in Cancer . . . . . . . 507--522 Yu-Wei Wu and Yuzhen Ye A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using $l$-tuples . . . . . . . . . . . . . . . 523--534
Roberto Grossi and Andrea Pietracaprina and Nadia Pisanti and Geppino Pucci and Eli Upfal and Fabio Vandin MADMX: a Strategy for Maximal Dense Motif Extraction . . . . . . . . . . . . 535--545 Karin Noy and Fadi Towfic and Gayle M. Wittenberg and Daniel Fasulo Shape-Based Feature Matching Improves Protein Identification via LC-MS and Tandem MS . . . . . . . . . . . . . . . 547--557 A. Graudenzi and R. Serra and M. Villani and A. Colacci and S. A. Kauffman Robustness Analysis of a Boolean Model of Gene Regulatory Network with Memory 559--577 S. Grusea and E. Pardoux and O. Chabrol and P. Pontarotti Compound Poisson Approximation and Testing for Gene Clusters with Multigene Families . . . . . . . . . . . . . . . . 579--594 Valeria Fionda and Luigi Palopoli Biological Network Querying Techniques: Analysis and Comparison . . . . . . . . 595--625 Shu-Bo Zhang and Song-Yu Zhou and Jian-Guo He and Jian-Huang Lai Phylogeny Inference Based on Spectral Graph Clustering . . . . . . . . . . . . 627--637 Sajid A. Marhon and Stefan C. Kremer Gene Prediction Based on DNA Spectral Analysis: a Literature Review . . . . . 639--676
Lu Meng and Fengzhu Sun and Xuegong Zhang and Michael S. Waterman Sequence Alignment as Hypothesis Testing 677--691 Shuai Cheng Li and Dongbo Bu and Jinbo Xu and Ming Li Finding Nearly Optimal GDT Scores . . . 693--704 Nahla A. Belal and Lenwood S. Heath A Theoretical Model for Whole Genome Alignment . . . . . . . . . . . . . . . 705--728 Wessel N. Van Wieringen and Mark A. Van De Wiel Exploratory Factor Analysis of Pathway Copy Number Data with an Application Towards the Integration with Gene Expression Data . . . . . . . . . . . . 729--741 Lavanya Kannan and Hua Li and Arcady Mushegian A Polynomial-Time Algorithm Computing Lower and Upper Bounds of the Rooted Subtree Prune and Regraft Distance . . . 743--757 Xiaoyan Zhao and Sing-Hoi Sze Motif Finding in DNA Sequences Based on Skipping Nonconserved Positions in Background Markov Chains . . . . . . . . 759--770 Gregory Kucherov and Tamar Pinhas and Michal Ziv-Ukelson Regular Language Constrained Sequence Alignment Revisited . . . . . . . . . . 771--781
Alan Veliz-Cuba and Brandilyn Stigler Boolean Models Can Explain Bistability in the \bionamelac Operon . . . . . . . 783--794 Tade Souaiaia and Zach Frazier and Ting Chen ComB: SNP Calling and Mapping Analysis for Color and Nucleotide Space Platforms 795--807 Norbert Dojer and Przemys\law Biecek and Jerzy Tiuryn Bi-Billboard: Symmetrization and Careful Choice of Informant Species Results in Higher Accuracy of Regulatory Element Prediction . . . . . . . . . . . . . . . 809--819 Jacek Blazewicz and Marek Figlerowicz and Marta Kasprzak and Martyna Nowacka and Agnieszka Rybarczyk RNA Partial Degradation Problem: Motivation, Complexity, Algorithm . . . 821--834 Frans E. S. Tan and Valéria Lima Passos On the $A$-Optimality Criterion for Finding Two-Color Microarray Optimal Designs . . . . . . . . . . . . . . . . 835--841 Marcin Pacholczyk and Marek Kimmel Exploring the Landscape of Protein-Ligand Interaction Energy Using Probabilistic Approach . . . . . . . . . 843--850 Hong-Bin Chen and Annalisa De Bonis An Almost Optimal Algorithm for Generalized Threshold Group Testing with Inhibitors . . . . . . . . . . . . . . . 851--864
Pavel A. Pevzner and Ron Shamir Preface: 2$^{nd}$ Satellite Meeting on Bioinformatics Education, Research in Computational Molecular Biology (RECOMB--BE 2010) . . . . . . . . . . . 865--865 Jeff Elhai Humans, Computers, and the Route to Biological Insights: Regaining Our Capacity for Surprise . . . . . . . . . 867--878 Jian Ma Reconstructing the History of Large-Scale Genomic Changes: Biological Questions and Computational Challenges 879--893 Seung-Jin Sul and Tiffani L. Williams Big Cat Phylogenies, Consensus Trees, and Computational Thinking . . . . . . . 895--906 Bahar Taneri Is there Room for Ethics within Bioinformatics Education? . . . . . . . 907--916 Eugene V. Koonin and Pere Puigb\`o and Yuri I. Wolf Comparison of Phylogenetic Trees and Search for a Central Trend in the ``Forest of Life'' . . . . . . . . . . . 917--924
Yi-Kuo Yu and Stephen F. Altschul The Complexity of the Dirichlet Model for Multiple Alignment Data . . . . . . 925--939 Xugang Ye and Yi-Kuo Yu and Stephen F. Altschul On the Inference of Dirichlet Mixture Priors for Protein Sequence Comparison 941--954 Bjarni V. Halldórsson and Daníel F. Gudbjartsson An Algorithm for Detecting High Frequency Copy Number Polymorphisms Using SNP Arrays . . . . . . . . . . . . 955--966 Sagi Snir and Lior Pachter Tracing the Most Parsimonious Indel History . . . . . . . . . . . . . . . . 967--986 Valerio Freschi Improved Biological Network Reconstruction Using Graph Laplacian Regularization . . . . . . . . . . . . . 987--996 B. Knapp and S. Frantal and M. Cibena and W. Schreiner and P. Bauer Is an Intuitive Convergence Definition of Molecular Dynamics Simulations Solely Based on the Root Mean Square Deviation Possible? . . . . . . . . . . . . . . . 997--1005 Jesun Sahariar Firoz and Masud Hasan and Ashik Zinnat Khan and M. Sohel Rahman The 1.375 Approximation Algorithm for Sorting by Transpositions Can Run in $ O(n \log n) $ Time . . . . . . . . . . . 1007--1011 Hsien-Chi Kuo and Po-Yu Lin and Ting-Chiun Chung and Chin-Mei Chao and Liang-Chuan Lai and Mong-Hsun Tsai and Eric Y. Chuang DBCAT: Database of CpG Islands and Analytical Tools for Identifying Comprehensive Methylation Profiles in Cancer Cells . . . . . . . . . . . . . . 1013--1017
Anonymous Preface: Satellite Workshop on Comparative Genomics, Research in Computational Molecular Biology (RECOMB-CG 2010) . . . . . . . . . . . . 1019--1021 Roland Wittler and Ján Ma\vnuch and Murray Patterson and Jens Stoye Consistency of Sequence-Based Gene Clusters . . . . . . . . . . . . . . . . 1023--1039 A\"\ida Ouangraoua and Krister M. Swenson and Cedric Chauve A $2$-Approximation for the Minimum Duplication Speciation Problem . . . . . 1041--1053 Yu Lin and Bernard M. E. Moret A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses that Applies across Eukaryotes and Prokaryotes . . . . . . . . . . . . . . 1055--1064 Robert Warren and David Sankoff Genome Aliquoting Revisited . . . . . . 1065--1075 Minghui Jiang The Zero Exemplar Distance Problem . . . 1077--1086 Mukul S. Bansal and Guy Banay and J. Peter Gogarten and Ron Shamir Detecting Highways of Horizontal Gene Transfer . . . . . . . . . . . . . . . . 1087--1114 Emmanuel Mongin and Ken Dewar and Mathieu Blanchette Mapping Association between Long-Range cis-Regulatory Regions and Their Target Genes Using Synteny . . . . . . . 1115--1130 Y. Lin and V. Rajan and B. M. E. Moret Fast and Accurate Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Novel Robustness Estimator . . . . . . . . . . . . . . . 1131--1139 Raluca Uricaru and Alban Mancheron and Eric Rivals Novel Definition and Algorithm for Chaining Fragments with Proportional Overlaps . . . . . . . . . . . . . . . . 1141--1154 Hugo Devillers and Hél\`ene Chiapello and Sophie Schbath and Meriem El Karoui Robustness Assessment of Whole Bacterial Genome Segmentations . . . . . . . . . . 1155--1165 Marília D. V. Braga and Eyla Willing and Jens Stoye Double Cut and Join with Insertions and Deletions . . . . . . . . . . . . . . . 1167--1184 Olivier Tremblay Savard and Yves Gagnon and Denis Bertrand and Nadia El-Mabrouk Genome Halving and Double Distance with Losses . . . . . . . . . . . . . . . . . 1185--1199 Ghada Badr and Krister M. Swenson and David Sankoff Listing All Parsimonious Reversal Sequences: New Algorithms and Perspectives . . . . . . . . . . . . . . 1201--1210 Atheer A. Matroud and Christopher P. Tuffley and Michael D. Hendy An Algorithm to Solve the Motif Alignment Problem for Approximate Nested Tandem Repeats in Biological Sequences 1211--1218 A\"\ida Ouangraoua and Anne Bergeron and Krister M. Swenson Theory and Practice of Ultra-Perfection 1219--1230 Jakub Ková\vc and Robert Warren and Marília D. V. Braga and Jens Stoye Restricted DCJ Model: Rearrangement Problems with Chromosome Reincorporation 1231--1241 Ján Ma\vnuch and Murray Patterson The Complexity of the Gapped Consecutive-Ones Property Problem for Matrices of Bounded Maximum Degree . . . 1243--1253 Katharina Jahn Efficient Computation of Approximate Gene Clusters Based on Reference Occurrences . . . . . . . . . . . . . . 1255--1274
Tatsuya Akutsu and Avraham A. Melkman and Takeyuki Tamura and Masaki Yamamoto Determining a Singleton Attractor of a Boolean Network with Nested Canalyzing Functions . . . . . . . . . . . . . . . 1275--1290 Alex Graudenzi and Roberto Serra and Marco Villani and Chiara Damiani and Annamaria Colacci and Stuart A. Kauffman Dynamical Properties of a Boolean Model of Gene Regulatory Network with Memory 1291--1303 Joshua Collins and Simone Linz and Charles Semple Quantifying Hybridization in Realistic Time . . . . . . . . . . . . . . . . . . 1305--1318 Emiliano Barreto-Hernadez and Margarida Gama-Carvalho and Lisete Sousa Pre-Processing Optimization of RNA Immunoprecipitation Microarray Data . . 1319--1328 Hoon Kim and John Watkinson and Dimitris Anastassiou Biomarker Discovery Using Statistically Significant Gene Sets . . . . . . . . . 1329--1338 Cédric Saule and Mireille Régnier and Jean-Marc Steyaert and Alain Denise Counting RNA Pseudoknotted Structures 1339--1351 Fabrício M. Lopes and Roberto M. Cesar, Jr. and Luciano Da F.Costa Gene Expression Complex Networks: Synthesis, Identification, and Analysis 1353--1367
Vineet Bafna Preface: Research in Computational Molecular Biology (RECOMB 2011) . . . . 1369--1369 Hosein Mohimani and Wei-Ting Liu and Yu-Liang Yang and Susana P. Gaudêncio and William Fenical and Pieter C. Dorrestein and Pavel A. Pevzner Multiplex De Novo Sequencing of Peptide Antibiotics . . . . . . . . . . . . . . 1371--1381 Kerstin Scheubert and Franziska Hufsky and Florian Rasche and Sebastian Böcker Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data . . . . . . . . . . . . . . . . . . 1383--1397 Mark D. M. Leiserson and Diana Tatar and Lenore J. Cowen and Benjamin J. Hescott Inferring Mechanisms of Compensation from E-MAP and SGA Data Using Local Search Algorithms for Max Cut . . . . . 1399--1409 Xin Li and Jing Li Haplotype Reconstruction in Large Pedigrees with Untyped Individuals through IBD Inference . . . . . . . . . 1411--1421 Tobias Petri and Robert Küffner and Ralf Zimmer Experiment Specific Expression Patterns 1423--1435 Dana Silverbush and Michael Elberfeld and Roded Sharan Optimally Orienting Physical Networks 1437--1448 Glenn Hickey and Mathieu Blanchette A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels 1449--1464 Jérôme Waldispühl and Yann Ponty An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes Under Evolutionary Pressure 1465--1479 Bonnie Kirkpatrick and Shuai Cheng Li and Richard M. Karp and Eran Halperin Pedigree Reconstruction Using Identity by Descent . . . . . . . . . . . . . . . 1481--1493 Daniel Newkirk and Jacob Biesinger and Alvin Chon and Kyoko Yokomori and Xiaohui Xie AREM: Aligning Short Reads from ChIP-Sequencing by Expectation Maximization . . . . . . . . . . . . . . 1495--1505 Jeffrey W. Martin and Anthony K. Yan and Chris Bailey-Kellogg and Pei Zhou and Bruce R. Donald A Geometric Arrangement Algorithm for Structure Determination of Symmetric Protein Homo-Oligomers from NOEs and RDCs . . . . . . . . . . . . . . . . . . 1507--1523 Shay Zakov and Yoav Goldberg and Michael Elhadad and Michal Ziv-ukelson Rich Parameterization Improves RNA Structure Prediction . . . . . . . . . . 1525--1542 Yun Yu and Tandy Warnow and Luay Nakhleh Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles . . 1543--1559 Sinan Erten and Gurkan Bebek and Mehmet Koyutürk Vavien: an Algorithm for Prioritizing Candidate Disease Genes Based on Topological Similarity of Proteins in Interaction Networks . . . . . . . . . . 1561--1574 Allison P. Heath and George N. Bennett and Lydia E. Kavraki An Algorithm for Efficient Identification of Branched Metabolic Pathways . . . . . . . . . . . . . . . . 1575--1597 Navodit Misra and Guy Blelloch and R. Ravi and Russell Schwartz An Optimization-Based Sampling Scheme for Phylogenetic Trees . . . . . . . . . 1599--1609 Jae Hoon Sul and Buhm Han and Eleazar Eskin Increasing Power of Groupwise Association Test with Likelihood Ratio Test . . . . . . . . . . . . . . . . . . 1611--1624 Paul Medvedev and Son Pham and Mark Chaisson and Glenn Tesler and Pavel Pevzner Paired de Bruijn Graphs: a Novel Approach for Incorporating Mate Pair Information into Genome Assemblers . . . 1625--1634 Solomon Shenker and Charles W. O'Donnell and Srinivas Devadas and Bonnie Berger and Jérôme Waldispühl Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models . . . . . . . . . . . . . . . . . 1635--1647 Fabian L. Wauthier and Michael I. Jordan and Nebojsa Jojic Nonparametric Combinatorial Sequence Models . . . . . . . . . . . . . . . . . 1649--1660 Jianyang Zeng and Kyle E. Roberts and Pei Zhou and Bruce Randall Donald A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data . . . . . . . 1661--1679 Song Gao and Wing-Kin Sung and Niranjan Nagarajan Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences . . . . . . . . . . 1681--1691 Wei Li and Jianxing Feng and Tao Jiang IsoLasso: a LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly . . 1693--1707 Tien-Ho Lin and Ziv Bar-Joseph and Robert F. Murphy Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs 1709--1722 Amnon Amir and Or Zuk Bacterial Community Reconstruction Using Compressed Sensing . . . . . . . . . . . 1723--1741 Andrew S. Parker and Karl E. Griswold and Chris Bailey-Kellogg Optimization of Combinatorial Mutagenesis . . . . . . . . . . . . . . 1743--1756
Himanshu Chandola and Anthony K. Yan and Shobha Potluri and Bruce R. Donald and Chris Bailey-Kellogg NMR Structural Inference of Symmetric Homo-Oligomers . . . . . . . . . . . . . 1757--1775 Jiun-Rung Chen and Ye-In Chang An Up-Down Bit Pattern Approach to Coregulated and Negative-Coregulated Gene Clustering of Microarray Data . . . 1777--1791 Markus E. Nebel and Christian M. Reidys and Rita R. Wang Loops in Canonical RNA Pseudoknot Structures . . . . . . . . . . . . . . . 1793--1806 Rafa\l Adamczak and Jaroslaw Pillardy and Brinda K. Vallat and Jaroslaw Meller Fast Geometric Consensus Approach for Protein Model Quality Assessment . . . . 1807--1818 Matteo Comin and Davide Verzotto The Irredundant Class Method for Remote Homology Detection of Protein Sequences 1819--1829 Meng-Rong Li and Yu-Ju Lin and Tzong-Hann Shieh The Flux Model of the Movement of Tumor Cells and Healthy Cells Using a System of Nonlinear Heat Equations . . . . . . 1831--1839
Hugo Devillers and Sophie Schbath Separating Significant Matches from Spurious Matches in DNA Sequences . . . 1--12 Afshin Fayyaz Movaghar and Guillaume Launay and Sophie Schbath and Jean-François Gibrat and François Rodolphe Statistical Significance of Threading Scores . . . . . . . . . . . . . . . . . 13--29 Guy Karlebach and Ron Shamir Constructing Logical Models of Gene Regulatory Networks by Integrating Transcription Factor--DNA Interactions with Expression Data: an Entropy-Based Approach . . . . . . . . . . . . . . . . 30--41 Xiguo Yuan and David J. Miller and Junying Zhang and David Herrington and Yue Wang An Overview of Population Genetic Data Simulation . . . . . . . . . . . . . . . 42--54 Ritsuko Onuki and Ryo Yamada and Rui Yamaguchi and Minoru Kanehisa and Tetsuo Shibuya Population Model--Based Inter-Diplotype Similarity Measure for Accurate Diplotype Clustering . . . . . . . . . . 55--67 Li-Yeh Chuang and Cheng-Huei Yang and Jung-Chike Li and Cheng-Hong Yang A Hybrid BPSO-CGA Approach for Gene Selection and Classification of Microarray Data . . . . . . . . . . . . 68--82 Pawe\l Winter and Rasmus Fonseca Adjustable Chain Trees for Proteins . . 83--99
Andrea Califano and Manolis Kellis and Gustavo Stolovitzky Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2011 Special Issue . . . . . . . . . . . . . 101--101 Emanuel Gonçalves and Rui Pereira and Isabel Rocha and Miguel Rocha Optimization Approaches for the \em In Silico Discovery of Optimal Targets for Gene Over/Underexpression . . . . . . . 102--114 Roee Amit Anti-Cooperative and Cooperative Protein-Protein Interactions between TetR Isoforms on Synthetic Enhancers . . 115--125 Thomas Sakoparnig and Tobias Kockmann and Renato Paro and Christian Beisel and Niko Beerenwinkel Binding Profiles of Chromatin-Modifying Proteins Are Predictive for Transcriptional Activity and Promoter-Proximal Pausing . . . . . . . 126--138 Nnamdi E. Ihuegbu and Gary D. Stormo and Jeremy Buhler Fast, Sensitive Discovery of Conserved Genome-Wide Motifs . . . . . . . . . . . 139--147 Carlo Cosentino and Luca Salerno and Antonio Passanti and Alessio Merola and Declan G. Bates and Francesco Amato Structural Bistability of the GAL Regulatory Network and Characterization of its Domains of Attraction . . . . . . 148--162 Yael Silberberg and Assaf Gottlieb and Martin Kupiec and Eytan Ruppin and Roded Sharan Large-Scale Elucidation of Drug Response Pathways in Humans . . . . . . . . . . . 163--174 Xinyi Yang and Jennifer E. Dent and Christine Nardini An $S$-System Parameter Estimation Method (SPEM) for Biological Networks 175--187 Federica Eduati and Barbara di Camillo and Michael Karbiener and Marcel Scheideler and Davide Cor\`a and Michele Caselle and Gianna Toffolo Dynamic Modeling of miRNA-mediated Feed-Forward Loops . . . . . . . . . . . 188--199 Alexandra Dana and Tamir Tuller Efficient Manipulations of Synonymous Mutations for Controlling Translation Rate: an Analytical Approach . . . . . . 200--231 Liram Vardi and Eytan Ruppin and Roded Sharan A Linearized Constraint-Based Approach for Modeling Signaling Networks . . . . 232--240 Yi Wang and Henry C. M. Leung and S. M. Yiu and Francis Y. L. Chin MetaCluster 4.0: a Novel Binning Algorithm for NGS Reads and Huge Number of Species . . . . . . . . . . . . . . . 241--249
Kai Song and Ze Zhang and Tuo-Peng Tong and Fang Wu Classifier Assessment and Feature Selection for Recognizing Short Coding Sequences of Human Genes . . . . . . . . 251--260 Alberto Ceselli and Sandro Luciano Fornili and Giovanni Righini Algorithms for the Design of Maximum Hydropathic Complementarity Molecules 261--270 Olivier David and Catherine Larédo and Raphaël Leblois and Brigitte Schaeffer and Nicolas Vergne Coalescent-Based DNA Barcoding: Multilocus Analysis and Robustness . . . 271--278 Paolo Carnevali and Jonathan Baccash and Aaron L. Halpern and Igor Nazarenko and Geoffrey B. Nilsen and Krishna P. Pant and Jessica C. Ebert and Anushka Brownley and Matt Morenzoni and Vitali Karpinchyk and Bruce Martin and Dennis G. Ballinger and Radoje Drmanac Computational Techniques for Human Genome Resequencing Using Mated Gapped Reads . . . . . . . . . . . . . . . . . 279--292 Ethan M. Jewett and Noah A. Rosenberg iGLASS: an Improvement to the GLASS Method for Estimating Species Trees from Gene Trees . . . . . . . . . . . . . . . 293--315 Nikita A. Sakhanenko and David J. Galas Probabilistic Logic Methods and Some Applications to Biology and Medicine . . 316--336
Banu Dost and Nuno Bandeira and Xiangqian Li and Zhouxin Shen and Steven P. Briggs and Vineet Bafna Accurate Mass Spectrometry Based Protein Quantification via Shared Peptides . . . 337--348 Sébastien Li-Thiao-Té and Benno Schwikowski Feature Detection with Controlled Error Rates in LC/MS Images . . . . . . . . . 349--364 Thomas K. F. Wong and S. M. Yiu Structural Alignment of RNA with Triple Helix Structure . . . . . . . . . . . . 365--378 Aleksandar Stojmirovi\'c and Yi-kuo Yu Information Flow in Interaction Networks II: Channels, Path Lengths, and Potentials . . . . . . . . . . . . . . . 379--403 Yen Hung Chen The $k$ Partition-Distance Problem . . . 404--417 Serena Arima and Luca Tardella Improved Harmonic Mean Estimator for Phylogenetic Model Evidence . . . . . . 418--438 Arvind Gupta and Ján Ma\vnuch and Ladislav Stacho and Xiaohong Zhao Algorithm for Haplotype Inference via Galled-Tree Networks with Simple Galls 439--454
Anton Bankevich and Sergey Nurk and Dmitry Antipov and Alexey A. Gurevich and Mikhail Dvorkin and Alexander S. Kulikov and Valery M. Lesin and Sergey I. Nikolenko and Son Pham and Andrey D. Prjibelski and Alexey V. Pyshkin and Alexander V. Sirotkin and Nikolay Vyahhi and Glenn Tesler and Max A. Alekseyev and Pavel A. Pevzner SPAdes: a New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing . . . . . . . . . . . . . . . 455--477 Deepayan Sarkar and Steve Goldstein and David C. Schwartz and Michael A. Newton Statistical Significance of Optical Map Alignments . . . . . . . . . . . . . . . 478--492 Genki Terashi and Tetsuo Shibuya and Mayuko Takeda-Shitaka LB3D: a Protein Three-Dimensional Substructure Search Program Based on the Lower Bound of a Root Mean Square Deviation Value . . . . . . . . . . . . 493--503 Nimrod Bar-Yaakov and Zehava Grossman and Nathan Intrator Using Iterative Ridge Regression to Explore Associations Between Conditioned Variables . . . . . . . . . . . . . . . 504--518 Mikael Falconnet and Sarah Behrens Accurate Estimations of Evolutionary Times in the Context of Strong CpG Hypermutability . . . . . . . . . . . . 519--531 Michiaki Hamada and Kiyoshi Asai A Classification of Bioinformatics Algorithms from the Viewpoint of Maximizing Expected Accuracy (MEA) . . . 532--549 Sarah Behrens and Cyril Nicaud and Pierre Nicod\`eme An Automaton Approach for Waiting Times in DNA Evolution . . . . . . . . . . . . 550--562 Maysson Al-Haj Ibrahim and Sabah Jassim and Michael Anthony Cawthorne and Kenneth Langlands A Topology-Based Score for Pathway Enrichment . . . . . . . . . . . . . . . 563--573
Ting Chen and Paul Marjoram and Fengzhu Sun and Jasmine Xianghong Zhou Preface: Special Issue . . . . . . . . . 575--576 Derek Aguiar and Sorin Istrail HapCompass: a Fast Cycle Basis Algorithm for Accurate Haplotype Assembly of Sequence Data . . . . . . . . . . . . . 577--590 Md. Shamsuzzoha Bayzid and Tandy Warnow Estimating Optimal Species Trees from Incomplete Gene Trees Under Deep Coalescence . . . . . . . . . . . . . . 591--605 Zachary Frazier and Frank Alber A Computational Approach to Increase Time Scales in Brownian Dynamics--Based Reaction-Diffusion Modeling . . . . . . 606--618 Qinghui Gao and Christine Ho and Yingmin Jia and Jingyi Jessica Li and Haiyan Huang Biclustering of Linear Patterns In Gene Expression Data . . . . . . . . . . . . 619--631 Laura J. Helmkamp and Ethan M. Jewett and Noah A. Rosenberg Improvements to a Class of Distance Matrix Methods for Inferring Species Trees from Gene Trees . . . . . . . . . 632--649 Paul Joyce and Alan Genz and Erkan Ozge Buzbas Efficient Simulation and Likelihood Methods for Non-Neutral Multi-Allele Models . . . . . . . . . . . . . . . . . 650--661 Marcus Kinsella and Vineet Bafna Combinatorics of the Breakage--Fusion--Bridge Mechanism . . . 662--678 Yinglei Lai Change-Point Analysis of Paired Allele-Specific Copy Number Variation Data . . . . . . . . . . . . . . . . . . 679--693 Ofer Lavi and Gideon Dror and Ron Shamir Network-Induced Classification Kernels for Gene Expression Profile Analysis . . 694--709 Wenyuan Li and Chao Dai and Chun-Chi Liu and Xianghong Jasmine Zhou Algorithm to Identify Frequent Coupled Modules from Two-Layered Network Series: Application to Study Transcription and Splicing Coupling . . . . . . . . . . . 710--730 Li Luo and Yun Zhu and Momiao Xiong A Novel Genome-Information Content-Based Statistic for Genome-Wide Association Analysis Designed for Next-Generation Sequencing Data . . . . . . . . . . . . 731--744 Ioanna Manolopoulou and Brent C. Emerson Phylogeographic Ancestral Inference Using the Coalescent Model on Haplotype Trees . . . . . . . . . . . . . . . . . 745--755 Mary Sara McPeek BLUP Genotype Imputation for Case-Control Association Testing with Related Individuals and Missing Data . . 756--765 Shengyu Ni and Martin Vingron R2KS: a Novel Measure for Comparing Gene Expression Based on Ranked Gene Lists 766--775 Dhruv Grover and Juan Nunez-Iglesias Betamax: Towards Optimal Sampling Strategies for High-Throughput Screens 776--784 Tiago Rito and Charlotte M. Deane and Gesine Reinert The Importance of Age and High Degree, in Protein-Protein Interaction Networks 785--795 Sophie Schbath and Véronique Martin and Matthias Zytnicki and Julien Fayolle and Valentin Loux and Jean-François Gibrat Mapping Reads on a Genomic Sequence: an Algorithmic Overview and a Practical Comparative Analysis . . . . . . . . . . 796--813 Mingjie Wang and Yuzhen Ye and Haixu Tang A \em de Bruijn Graph Approach to the Quantification of Closely-Related Genomes in a Microbial Community . . . . 814--825 Jialin Xu and Yu Zhang A Generalized Linear Model for Peak Calling in ChIP-Seq Data . . . . . . . . 826--838 Zhiyuan Zhai and Gesine Reinert and Kai Song and Michael S. Waterman and Yihui Luan and Fengzhu Sun Normal and Compound Poisson Approximations for Pattern Occurrences in NGS Reads . . . . . . . . . . . . . . 839--854 Jing Zhang and C.-C. Jay Kuo and Liang Chen VERSE: a Varying Effect Regression for Splicing Elements Discovery . . . . . . 855--865
Hillary S. W. Han and Christian M. Reidys The 5'-3' Distance of RNA Secondary Structures . . . . . . . . . . . . . . . 867--878 Pawe\l Gniewek and Andrzej Kolinski and Dominik Gront Optimization of Profile-to-Profile Alignment Parameters for One-Dimensional Threading . . . . . . . . . . . . . . . 879--886 Torben Tvedebrink and Poul Svante Eriksen and Helle Smidt Mogensen and Niels Morling Identifying Contributors of DNA Mixtures by Means of Quantitative Information of STR Typing . . . . . . . . . . . . . . . 887--902 Yichao He and Haiyan Tian and Xinlu Zhang and Zhiwei Wang and Suogang Gao Nonadaptive Algorithms for Threshold Group Testing with Inhibitors and Error-Tolerance . . . . . . . . . . . . 903--910 Fabio Cunial and Alberto Apostolico Phylogeny Construction with Rigid Gapped Motifs . . . . . . . . . . . . . . . . . 911--927 Jòrgen E. Andersen and Fenix W. D. Huang and Robert C. Penner and Christian M. Reidys Topology of RNA-RNA Interaction Structures . . . . . . . . . . . . . . . 928--943
Eyal Cohen and Benny Chor Detecting Phylogenetic Signals in Eukaryotic Whole Genome Sequences . . . 945--956 Gangman Yi and Michael R. Thon and Sing-Hoi Sze Supervised Protein Family Classification and New Family Construction . . . . . . 957--967 Elias August Using Noise for Model-Testing . . . . . 968--977 Matthew Sperrin and Thomas Jaki Recovering Independent Associations in Genetics: a Comparison . . . . . . . . . 978--987
Hamid Bolouri and Walter L. Ruzzo Integration of 198 ChIP-seq Datasets Reveals Human \em cis-Regulatory Regions 989--997 Bonnie Kirkpatrick and Yakir Reshef and Hilary Finucane and Haitao Jiang and Binhai Zhu and Richard M. Karp Comparing Pedigree Graphs . . . . . . . 998--1014 M. González and C. Gutiérrez and R. Martínez Expectation-Maximization Algorithm for Determining Natural Selection of Y-Linked Genes Through Two-Sex Branching Processes . . . . . . . . . . . . . . . 1015--1026 Min Wu and Xiao-li Li and Chee-Keong Kwoh and See-Kiong Ng and Limsoon Wong Discovery of Protein Complexes with Core-Attachment Structures from Tandem Affinity Purification (TAP) Data . . . . 1027--1042 M. Shahriar Hossain and Monika Akbar and Nicholas F. Polys Narratives in the Network: Interactive Methods for Mining Cell Signaling Networks . . . . . . . . . . . . . . . . 1043--1059 Christina Schindler and Wolfgang B. Fischer Sequence Alignment of Viral Channel Proteins with Cellular Ion Channels . . 1060--1072 Yun Cui and Jesper Jansson and Wing-Kin Sung Polynomial-Time Algorithms for Building a Consensus MUL-Tree . . . . . . . . . . 1073--1088
Tomoya Mori and Takeyuki Tamura and Daiji Fukagawa and Atsuhiro Takasu and Etsuji Tomita and Tatsuya Akutsu A Clique-Based Method Using Dynamic Programming for Computing Edit Distance Between Unordered Trees . . . . . . . . 1089--1104 Hillary S. W. Han and Christian M. Reidys A Phase Transition in Energy-Filtered RNA Secondary Structures . . . . . . . . 1105--1119 Azadeh Saffarian and Mathieu Giraud and Antoine de Monte and Hél\`ene Touzet RNA Locally Optimal Secondary Structures 1120--1133 Markus E. Nebel and Frank Weinberg Algebraic and Combinatorial Properties of Common RNA Pseudoknot Classes with Applications . . . . . . . . . . . . . . 1134--1150 Huwaida S. Rabie and Ian W. Saunders A Simulation Study to Assess a Variable Selection Method for Selecting Single Nucleotide Polymorphisms Associated with Disease . . . . . . . . . . . . . . . . 1151--1161 Rajat S. Roy and Kevin C. Chen and Anirvan M. Sengupta and Alexander Schliep SLIQ: Simple Linear Inequalities for Efficient Contig Scaffolding . . . . . . 1162--1175 Narendra M. Dixit and Piyush Srivastava and Nisheeth K. Vishnoi A Finite Population Model of Molecular Evolution: Theory and Computation . . . 1176--1202 Rasmus Fonseca and Pawe\l Winter Bounding Volumes for Proteins: a Comparative Study . . . . . . . . . . . 1203--1213
I-Lin Lu and Hsiuying Wang Protein-specific Scoring Method for Ligand Discovery . . . . . . . . . . . . 1215--1226 Celine Scornavacca and Simone Linz and Benjamin Albrecht A First Step Toward Computing All Hybridization Networks For Two Rooted Binary Phylogenetic Trees . . . . . . . 1227--1242 M. Veselsky Order of Precedence and Age of Y-DNA Haplotypes . . . . . . . . . . . . . . . 1243--1250 M. Ehler and F. Filbir and H. N. Mhaskar Locally Learning Biomedical Data Using Diffusion Frames . . . . . . . . . . . . 1251--1264
Michiaki Hamada Direct Updating of an RNA Base-Pairing Probability Matrix with Marginal Probability Constraints . . . . . . . . 1265--1276 Hiroshi Toyoizumi and Hideo Tsubouchi Estimating the Number of Double-Strand Breaks Formed During Meiosis from Partial Observation . . . . . . . . . . 1277--1283 Jia-Hao Fan and Jianer Chen and Sing-Hoi Sze Identifying Complexes from Protein Interaction Networks According to Different Types of Neighborhood Density 1284--1294 R. Reyes and D. Gamermann and A. Montagud and D. Fuente and J. Triana and J. F. Urchueguía and P. Fernández de Córdoba Automation on the Generation of Genome-Scale Metabolic Models . . . . . 1295--1306 Young Hwan Chang and Joe Gray and Claire Tomlin Optimization-based Inference for Temporally Evolving Networks with Applications in Biology . . . . . . . . 1307--1323 Baikang Pei and Dong-Guk Shin Reconstruction of Biological Networks by Incorporating Prior Knowledge into Bayesian Network Models . . . . . . . . 1324--1334
Viet-An Nguyen and Jordan Boyd-Graber and Stephen F. Altschul Dirichlet Mixtures, the Dirichlet Process, and the Structure of Protein Space . . . . . . . . . . . . . . . . . 1--18 Lianping Yang and Xiangde Zhang and Tianming Wang and Hegui Zhu Large Local Analysis of the Unaligned Genome and Its Application . . . . . . . 19--29 Guilherme P. Telles and Nalvo F. Almeida and Rosane Minghim and Maria Emilia M. T. Walter Live Phylogeny . . . . . . . . . . . . . 30--37 Zhi-Zhong Chen and Lusheng Wang An Ultrafast Tool for Minimum Reticulate Networks . . . . . . . . . . . . . . . . 38--41 Hong Huang and Yongji Li MASTtreedist: Visualization of Tree Space Based on Maximum Agreement Subtree 42--49 Elizabeth S. Allman and James H. Degnan and John A. Rhodes Species Tree Inference by the STAR Method and Its Generalizations . . . . . 50--61
Benny Chor Preface: RECOMB 2012 . . . . . . . . . . 63--63 Kai Song and Jie Ren and Zhiyuan Zhai and Xuemei Liu and Minghua Deng and Fengzhu Sun Alignment-Free Sequence Comparison Based on Next-Generation Sequencing Reads . . 64--79 Dan He and Buhm Han and Eleazar Eskin Hap-seq: an Optimal Algorithm for Haplotype Phasing with Imputation Using Sequencing Data . . . . . . . . . . . . 80--92 Sebastien Roch and Sagi Snir Recovering the Treelike Trend of Evolution Despite Extensive Lateral Genetic Transfer: a Probabilistic Analysis . . . . . . . . . . . . . . . . 93--112 Armin Töpfer and Osvaldo Zagordi and Sandhya Prabhakaran and Volker Roth and Eran Halperin and Niko Beerenwinkel Probabilistic Inference of Viral Quasispecies Subject to Recombination 113--123 Nurcan Tuncbag and Alfredo Braunstein and Andrea Pagnani and Shao-Shan Carol Huang and Jennifer Chayes and Christian Borgs and Riccardo Zecchina and Ernest Fraenkel Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem 124--136 Lu He and Fabio Vandin and Gopal Pandurangan and Chris Bailey-Kellogg Ballast: a Ball-based Algorithm for Structural Motifs . . . . . . . . . . . 137--151 Andrew S. Parker and Yoonjoo Choi and Karl E. Griswold and Chris Bailey-Kellogg Structure-Guided Deimmunization of Therapeutic Proteins . . . . . . . . . . 152--165
Yan Huang and Yin Hu and Corbin D. Jones and James N. MacLeod and Derek Y. Chiang and Yufeng Liu and Jan F. Prins and Jinze Liu A Robust Method for Transcript Quantification with RNA-Seq Data . . . . 167--187 Stefan Canzar and Mohammed El-Kebir and René Pool and Khaled Elbassioni and Alpeshkumar K. Malde and Alan E. Mark and Daan P. Geerke and Leen Stougie and Gunnar W. Klau Charge Group Partitioning in Biomolecular Simulation . . . . . . . . 188--198 Jesse M. Rodriguez and Sivan Bercovici and Megan Elmore and Serafim Batzoglou Ancestry Inference in Complex Admixtures via Variable-length Markov Chain Linkage Models . . . . . . . . . . . . . . . . . 199--211 Daniel Holtby and Shuai Cheng Li and Ming Li LoopWeaver: Loop Modeling by the Weighted Scaling of Verified Proteins 212--223 Zhanyong Wang and Farhad Hormozdiari and Wen-Yun Yang and Eran Halperin and Eleazar Eskin CNVeM: Copy Number Variation Detection Using Uncertainty of Read Mapping . . . 224--236 ZhiZhuo Zhang and Cheng Wei Chang and Willy Hugo and Edwin Cheung and Wing-Kin Sung Simultaneously Learning DNA Motif Along with Its Position and Sequence Rank Preferences Through Expectation Maximization Algorithm . . . . . . . . . 237--248 Roded Sharan and Richard M. Karp Reconstructing Boolean Models of Signaling . . . . . . . . . . . . . . . 249--257
John Kececioglu and Dan DeBlasio Accuracy Estimation and Parameter Advising for Protein Multiple Sequence Alignment . . . . . . . . . . . . . . . 259--279 Patrick Holloway and Krister Swenson and David Ardell and Nadia El-Mabrouk Ancestral Genome Organization: an Alignment Approach . . . . . . . . . . . 280--295 Babak Alipanahi and Nathan Krislock and Ali Ghodsi and Henry Wolkowicz and Logan Donaldson and Ming Li Determining Protein Structures from NOESY Distance Constraints by Semidefinite Programming . . . . . . . . 296--310 Imran Rauf and Florian Rasche and François Nicolas and Sebastian Böcker Finding Maximum Colorful Subtrees in Practice . . . . . . . . . . . . . . . . 311--321 Hua Wang and Heng Huang and Chris Ding Function--Function Correlated Multi-label Protein Function Prediction over Interaction Networks . . . . . . . 322--343 Hua Wang and Heng Huang and Chris Ding and Feiping Nie Predicting Protein--Protein Interactions from Multimodal Biological Data Sources via Nonnegative Matrix Tri-Factorization 344--358 Son K. Pham and Dmitry Antipov and Alexander Sirotkin and Glenn Tesler and Pavel A. Pevzner and Max A. Alekseyev Pathset Graphs: a Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly . . . . . . . . 359--371
Andrea Califano and Manolis Kellis and Gustavo Stolovitzky Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2012 Special Issue . . . . . . . . . . . . . 373--374 Yaron Orenstein and Eran Mick and Ron Shamir RAP: Accurate and Fast Motif Finding Based on Protein-Binding Microarray Data 375--382 Roberto Pagliarini and Diego di Bernardo A Genome-Scale Modeling Approach to Study Inborn Errors of Liver Metabolism: Toward an In Silico Patient . . . . . . 383--397 Andreas Tjärnberg and Torbjörn E. M. Nordling and Matthew Studham and Erik L. L. Sonnhammer Optimal Sparsity Criteria for Network Inference . . . . . . . . . . . . . . . 398--408 Christopher L. Poirel and Richard R. Rodrigues and Katherine C. Chen and John J. Tyson and T. M. Murali Top-Down Network Analysis to Drive Bottom-Up Modeling of Physiological Processes . . . . . . . . . . . . . . . 409--418
Emmanuel Faure and Isabelle S. Peter and Eric H. Davidson A New Software Package for Predictive Gene Regulatory Network Modeling and Redesign . . . . . . . . . . . . . . . . 419--423 Franco P. Preparata On Contigs and Coverage . . . . . . . . 424--432 Michael Antosh and David Fox and Leon N. Cooper and Nicola Neretti CORaL: Comparison of Ranked Lists for Analysis of Gene Expression Data . . . . 433--443 Cong-Jun Wang and Rong-Hua Xu and Qiong-Ying Yuan and Yong-Kun Wang and Dong-Wei Shen and Xu-Jing Wang and Wei Gao and Hui Zhang and Hua Jiang Bioinformatics Method to Analyze the Mechanism of Pancreatic Cancer Disorder 444--452 Shruthi Prabhakara and Raunaq Malhotra and Raj Acharya and Mary Poss Mutant-Bin: Unsupervised Haplotype Estimation of Viral Population Diversity Without Reference Genome . . . . . . . . 453--463 Huilan Chang and Hung-Lin Fu and ChiH-Huai Shih Threshold Group Testing on Inhibitor Model . . . . . . . . . . . . . . . . . 464--470
Ehsan Behnam and Michael S. Waterman and Andrew D. Smith A Geometric Interpretation for Local Alignment-Free Sequence Comparison . . . 471--485 Hamidreza Chitsaz and Elmirasadat Forouzmand and Gholamreza Haffari An Efficient Algorithm for Upper Bound on the Partition Function of Nucleic Acids . . . . . . . . . . . . . . . . . 486--494 Jing Qin and Christian M. Reidys On Topological RNA Interaction Structures . . . . . . . . . . . . . . . 495--513 Yalu Wen and Ming Li and Wenjiang J. Fu Catching the Genomic Wave in Oligonucleotide Single-Nucleotide Polymorphism Arrays by Modeling Sequence Binding . . . . . . . . . . . . . . . . 514--523 Jaejik Kim and Jiaxu Li and Srirangapatnam G. Venkatesh and Douglas S. Darling and Grzegorz A. Rempala Model Discrimination in Dynamic Molecular Systems: Application to Parotid De-differentiation Network . . . 524--539 Henry C. M. Leung and Siu-Ming Yiu and John Parkinson and Francis Y. L. Chin IDBA-MT: \em De Novo Assembler for Metatranscriptomic Data Generated from Next-Generation Sequencing Technology 540--550
Hoyt Koepke and Elizabeth Thompson Efficient Identification of Equivalences in Dynamic Graphs and Pedigree Structures . . . . . . . . . . . . . . . 551--570 Mitsunori Kayano and Seiya Imoto and Rui Yamaguchi and Satoru Miyano Multi-omics Approach for Estimating Metabolic Networks Using Low-Order Partial Correlations . . . . . . . . . . 571--582 Steven Flygare and Michael Campbell and Robert Mars Ross and Barry Moore and Mark Yandell ImagePlane: an Automated Image Analysis Pipeline for High-Throughput Screens Using the Planarian \bionameSchmidtea mediterranea . . . . . . . . . . . . . . 583--592 Emanuele Giaquinta and Laura Pozzi An Effective Exact Algorithm and a New Upper Bound for the Number of Contacts in the Hydrophobic-Polar Two-Dimensional Lattice Model . . . . . . . . . . . . . 593--609 Lyamine Hedjazi and Marie-Veronique Le Lann and Tatiana Kempowsky and Florence Dalenc and Joseph Aguilar-Martin and Gilles Favre Symbolic Data Analysis to Defy Low Signal-to-Noise Ratio in Microarray Data for Breast Cancer Prognosis . . . . . . 610--620
Emanuele Giaquinta and Szymon Grabowski and Esko Ukkonen Fast Matching of Transcription Factor Motifs Using Generalized Position Weight Matrix Models . . . . . . . . . . . . . 621--630 Janusz Dutkowski and Jerzy Tiuryn A Probabilistic Model of Neutral and Selective Dynamics of Protein Network Evolution . . . . . . . . . . . . . . . 631--642 Sandro Andreotti and Knut Reinert and Stefan Canzar The Duplication-Loss Small Phylogeny Problem: From Cherries to Trees . . . . 643--659 Hervé Seligmann Triplex DNA:RNA, 3'-to-5' Inverted RNA and Protein Coding in Mitochondrial Genomes . . . . . . . . . . . . . . . . 660--671 Guillaume Chapuis and Olivier Filangi and Jean-Michel Elsen and Dominique Lavenier and Pascale Le Roy Graphics Processing Unit--Accelerated Quantitative Trait Loci Detection . . . 672--686 Carl Nettelblad and Behrang Mahjani and Sverker Holmgren Fast and Accurate Detection of Multiple Quantitative Trait Loci . . . . . . . . 687--702 Xiayu Rao and Dejian Lai and Xuelin Huang A New Method for Quantitative Real-Time Polymerase Chain Reaction Data Analysis 703--711
Fengzhu Sun Preface: Research in Computational Molecular Biology (RECOMB 2013) . . . . 713--713 Sergey Nurk and Anton Bankevich and Dmitry Antipov and Alexey A. Gurevich and Anton Korobeynikov and Alla Lapidus and Andrey D. Prjibelski and Alexey Pyshkin and Alexander Sirotkin and Yakov Sirotkin and Ramunas Stepanauskas and Scott R. Clingenpeel and Tanja Woyke and Jeffrey S. Mclean and Roger Lasken and Glenn Tesler and Max A. Alekseyev and Pavel A. Pevzner Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products . . . . . . . . . . . . . . . . 714--737 Mukul S. Bansal and Eric J. Alm and Manolis Kellis Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss . . . . 738--754 William A. Bryant and Ali A. Faruqi and John W. Pinney Analysis of Metabolic Evolution in Bacteria Using Whole-Genome Metabolic Models . . . . . . . . . . . . . . . . . 755--764 Fei Guo and Shuai Cheng Li and Wenji Ma and Lusheng Wang Detecting Protein Conformational Changes in Interactions via Scaling Known Structures . . . . . . . . . . . . . . . 765--779 Dan He and Zhanyong Wang and Buhm Han and Laxmi Parida and Eleazar Eskin IPED: Inheritance Path-based Pedigree Reconstruction Algorithm Using Genotype Data . . . . . . . . . . . . . . . . . . 780--791 Yufeng Wu An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees . . . . . . 792--804 Dong Xu and Hua Li and Yang Zhang Protein Depth Calculation and the Use for Improving Accuracy of Protein Fold Recognition . . . . . . . . . . . . . . 805--816 Emrah Kostem and Eleazar Eskin Efficiently Identifying Significant Associations in Genome-wide Association Studies . . . . . . . . . . . . . . . . 817--830
ZhiZhuo Zhang and Guoliang Li and Kim-Chuan Toh and Wing-Kin Sung $3$D Chromosome Modeling with Semi-Definite Programming and Hi-C Data 831--846 Shijian Chen and Anqi Wang and Lei M. Li SEME: a Fast Mapper of Illumina Sequencing Reads with Statistical Evaluation . . . . . . . . . . . . . . . 847--860 Itamar Eskin and Farhad Hormozdiari and Lucia Conde and Jacques Riby and Christine F. Skibola and Eleazar Eskin and Eran Halperin eALPS: Estimating Abundance Levels in Pooled Sequencing Using Available Genotyping Data . . . . . . . . . . . . 861--877 Lei Deng and Jihong Guan and Xiaoming Wei and Yuan Yi and Qiangfeng Cliff Zhang and Shuigeng Zhou Boosting Prediction Performance of Protein--Protein Interaction Hot Spots by Using Structural Neighborhood Properties . . . . . . . . . . . . . . . 878--891 Kriti Puniyani and Eric P. Xing NP-MuScL: Unsupervised Global Prediction of Interaction Networks from Multiple Data Sources . . . . . . . . . . . . . . 892--904 Vladimir Reinharz and Yann Ponty and Jérôme Waldispühl Using Structural and Evolutionary Information to Detect and Correct Pyrosequencing Errors in Noncoding RNAs 905--919 Mohammad J. Sadeh and Giusi Moffa and Rainer Spang Considering Unknown Unknowns: Reconstruction of Nonconfoundable Causal Relations in Biological Networks . . . . 920--932 Raheleh Salari and Syed Shayon Saleh and Dorna Kashef-Haghighi and David Khavari and Daniel E. Newburger and Robert B. West and Arend Sidow and Serafim Batzoglou Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery . . 933--944
Dima Blokh and Danny Segev and Roded Sharan The Approximability of Shortest Path-Based Graph Orientations of Protein--Protein Interaction Networks 945--957 Avraham A. Melkman and Tatsuya Akutsu An Improved Satisfiability Algorithm for Nested Canalyzing Functions and its Application to Determining a Singleton Attractor of a Boolean Network . . . . . 958--969 Steven N. Hart and Terry M. Therneau and Yuji Zhang and Gregory A. Poland and Jean-Pierre Kocher Calculating Sample Size Estimates for RNA Sequencing Data . . . . . . . . . . 970--978 Paul Kirk and Aviva Witkover and Charles R. M. Bangham and Sylvia Richardson and Alexandra M. Lewin and Michael P. H. Stumpf Balancing the Robustness and Predictive Performance of Biomarkers . . . . . . . 979--989 Yuval Nov and Alexander Fulton and Karl-Erich Jaeger Optimal Scanning of All Single-Point Mutants of a Protein . . . . . . . . . . 990--997
Jakub Ková\vc On the Complexity of Rearrangement Problems under the Breakpoint Distance 1--15 Stefano Beretta and Paola Bonizzoni and Gianluca Della Vedova and Yuri Pirola and Raffaella Rizzi Modeling Alternative Splicing Variants from RNA-Seq Data with Isoform Graphs 16--40 Conrad J. Burden and Paul Leopardi and Sylvain Forêt The Distribution of Word Matches Between Markovian Sequences with Periodic Boundary Conditions . . . . . . . . . . 41--63 A\"\ida Ouangraoua and Mathieu Raffinot On the Identification of Conflicting Contiguities in Ancestral Genome Reconstruction . . . . . . . . . . . . . 64--79 Chuan-Xi Li and Ru-Jing Wang and Peng Chen and He Huang and Ya-Ru Su Interaction Relation Ontology Learning 80--88 Pawe\l Górecki and Oliver Eulenstein DrML: Probabilistic Modeling of Gene Duplications . . . . . . . . . . . . . . 89--98
Francesco Bartolucci and Silvia Pandolfi A New Constant Memory Recursion for Hidden Markov Models . . . . . . . . . . 99--117 David J. Galas and Nikita A. Sakhanenko and Alexander Skupin and Tomasz Ignac Describing the Complexity of Systems: Multivariable ``Set Complexity'' and the Information Basis of Systems Biology . . 118--140 Junshan Wang and Ajay Jasra and Maria De Iorio Computational Methods for a Class of Network Models . . . . . . . . . . . . . 141--161 Wajdi Dhifli and Rabie Saidi and Engelbert Mephu Nguifo Smoothing $3$D Protein Structure Motifs Through Graph Mining and Amino Acid Similarities . . . . . . . . . . . . . . 162--172 Nissan Levtov and Sandeep Amberkar and Zakharia M. Frenkel and Lars Kaderali and Zeev Volkovich Detecting Non-Uniform Clusters in Large-Scale Interaction Graphs . . . . . 173--183
Chaozhi Zheng and Mary K. Kuhner and Elizabeth A. Thompson Joint Inference of Identity by Descent Along Multiple Chromosomes from Population Samples . . . . . . . . . . . 185--200 Yang Ding and William A. Lorenz and Ivan Dotu and Evan Senter and Peter Clote Computing the Probability of RNA Hairpin and Multiloop Formation . . . . . . . . 201--218 Heewook Lee and Ellen Popodi and Patricia L. Foster and Haixu Tang Detection of Structural Variants Involving Repetitive Regions in the Reference Genome . . . . . . . . . . . . 219--233 Mu-Fen Hsieh and Sing-Hoi Sze Finding Alignments of Conserved Graphlets in Protein Interaction Networks . . . . . . . . . . . . . . . . 234--246 Dariusz Plewczynski and Anna Philips and Marcin Von Grotthuss and Leszek Rychlewski and Krzysztof Ginalski HarmonyDOCK: The Structural Analysis of Poses in Protein-Ligand Docking . . . . 247--256 Guillermo Peris and Andrés Marzal Statistical Significance of Normalized Global Alignment . . . . . . . . . . . . 257--268 Andrew F. Neuwald A Bayesian Sampler for Optimization of Protein Domain Hierarchies . . . . . . . 269--286
Andrew F. Neuwald Evaluating, Comparing, and Interpreting Protein Domain Hierarchies . . . . . . . 287--302 Lavanya Kannan and Ward C. Wheeler Exactly Computing the Parsimony Scores on Phylogenetic Networks Using Dynamic Programming . . . . . . . . . . . . . . 303--319 Xun Wang and Ying Miao and Minquan Cheng Finding Motifs in DNA Sequences Using Low-Dispersion Sequences . . . . . . . . 320--329 Matteo Comin and Montse Farreras Parallel Continuous Flow: a Parallel Suffix Tree Construction Tool for Whole Genomes . . . . . . . . . . . . . . . . 330--344 Seyoung Kim and Eric P. Xing Exploiting Genome Structure in Association Analysis . . . . . . . . . . 345--360 Robert Hochberg and Treena Larrew Milam Data Structures for Parsimony Correlation and Biosequence Co-Evolution 361--369
Andrea Califano and Manolis Kellis and Gustavo Stolovitzky RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2013 Special Issue 371--372 Patrick K. O'Neill and Robert Forder and Ivan Erill Informational Requirements for Transcriptional Regulation . . . . . . . 373--384 Zhiyong Wang and Jinbo Xu and Xinghua Shi Finding Alternative Expression Quantitative Trait Loci by Exploring Sparse Model Space . . . . . . . . . . . 385--393 Arnon Mazza and Irit Gat-Viks and Roded Sharan Elucidating Influenza Inhibition Pathways via Network Reconstruction . . 394--404
John G. Cleary and Ross Braithwaite and Kurt Gaastra and Brian S. Hilbush and Stuart Inglis and Sean A. Irvine and Alan Jackson and Richard Littin and Sahar Nohzadeh-Malakshah and Mehul Rathod and David Ware and Len Trigg and Francisco M. De La Vega Joint Variant and \em De Novo Mutation Identification on Pedigrees from High-Throughput Sequencing Data . . . . 405--419 Wei Hu and John Hu Prediction of siRNA Potency Using Sparse Logistic Regression . . . . . . . . . . 420--427 Sebastian Klie and Zoran Nikoloski and Joachim Selbig Biological Cluster Evaluation for Gene Function Prediction . . . . . . . . . . 428--445 Vamsi Kundeti and Sanguthevar Rajasekaran and Hieu Dinh Border Length Minimization Problem on a Square Array . . . . . . . . . . . . . . 446--455 Nivit Gill and Shailendra Singh and Trilok C. Aseri Computational Disease Gene Prioritization: An Appraisal . . . . . . 456--465 Abdul Arif Khan \em In Silico Prediction of \bionameEscherichia coli Proteins Targeting the Host Cell Nucleus, with Special Reference to Their Role in Colon Cancer Etiology . . . . . . . . . . . . 466--475 Anonymous Correction: \booktitleJournal of Computational Biology: 2014; \bf 21/4:303--319 . . . . . . . . . . . . . 476--476
Jérôme Waldispühl and Charles W. O'Donnell and Sebastian Will and Srinivas Devadas and Rolf Backofen and Bonnie Berger Simultaneous Alignment and Folding of Protein Sequences . . . . . . . . . . . 477--491 M. Muksitul Haque and Michael K. Skinner and Lawrence B. Holder Imbalanced Class Learning in Epigenetics 492--507 Daniel Gamermann and Arnaud Montagud and J. Alberto Conejero and Javier F. Urchueguía and Pedro Fernández de Córdoba New Approach for Phylogenetic Tree Recovery Based on Genome-Scale Metabolic Networks . . . . . . . . . . . . . . . . 508--519 Fabien de Montgolfier and Mathieu Raffinot and Irena Rusu Easy Identification of Generalized Common and Conserved Nested Intervals 520--533 Anna Zhukova and David James Sherman Knowledge-based Generalization of Metabolic Models . . . . . . . . . . . . 534--547 Wen-Shyong Tzou and Ying-Tsang Lo and Tun-Wen Pai and Chin-Hwa Hu and Chung-Hao Li Stochastic Simulation of Notch Signaling Reveals Novel Factors That Mediate the Differentiation of Neural Stem Cells . . 548--567
Alexei A. Sharov and Akira Nishiyama and Yong Qian and Dawood B. Dudekula and Dan L. Longo and David Schlessinger and Minoru S. H. Ko Chromatin Properties of Regulatory DNA Probed by Manipulation of Transcription Factors . . . . . . . . . . . . . . . . 569--577 Yu Zheng and Louxin Zhang Are the Duplication Cost and Robinson--Foulds Distance Equivalent? 578--590 Hillary S. W. Han and Thomas J. X. Li and Christian M. Reidys Combinatorics of $ \gamma $-Structures 591--608 Cuncong Zhong and Shaojie Zhang Simultaneous Folding of Alternative RNA Structures with Mutual Constraints: an Application to Next-Generation Sequencing-based RNA Structure Probing 609--621 Nikita Alexeev and Peter Zograf Random Matrix Approach to the Distribution of Genomic Distance . . . . 622--631 Ponne Saravanaraman and Raj Kumar Chinnadurai and Rathanam Boopathy A New Role for the Nonpathogenic Nonsynonymous Single-Nucleotide Polymorphisms of Acetylcholinesterase in the Treatment of Alzheimer's Disease: a Computational Study . . . . . . . . . . 632--647
Benjamin M. M. Fu and Christian M. Reidys Shapes of Interacting RNA Complexes . . 649--664 Maria Brigida Ferraro and Marco Savarese and Giuseppina Di Fruscio and Vincenzo Nigro and Mario Rosario Guarracino Prediction of Rare Single-Nucleotide Causative Mutations for Muscular Diseases in Pooled Next-Generation Sequencing Experiments . . . . . . . . . 665--675 Jan Irvahn and Vladimir N. Minin Phylogenetic Stochastic Mapping Without Matrix Exponentiation . . . . . . . . . 676--690 Yunzhang Huo and Ping Ji Continuous-Time Markov Chain--Based Flux Analysis in Metabolism . . . . . . . . . 691--698 Alexandru Agapie and Anca Andreica and Marius Giuclea Probabilistic Cellular Automata . . . . 699--708 Albert Vexler and Xiwei Chen and Jihnhee Yu Evaluations and Comparisons of Treatment Effects Based on Best Combinations of Biomarkers with Applications to Biomedical Studies . . . . . . . . . . . 709--721
Josh Voorkamp Maximal Acyclic Agreement Forests . . . 723--731 Loni Philip Tabb and Wei Zhao and Jingyu Huang and Gail L. Rosen Characterizing the Empirical Distribution of Prokaryotic Genome $n$-mers in the Presence of Nullomers 732--740 \vZiva Stepan\vci\vc Enhancing Gibbs Sampling Method for Motif Finding in DNA with Initial Graph Representation of Sequences . . . . . . 741--752 Hari Ram and Alok Kumar and Lebin Thomas and Ved Pal Singh \em In silico Approach to Study Adaptive Divergence in Nucleotide Composition of the 16S rRNA Gene Among Bacteria Thriving Under Different Temperature Regimes . . . . . . . . . . . . . . . . 753--759 Alex Radu and Michael Charleston Node Fingerprinting: an Efficient Heuristic for Aligning Biological Networks . . . . . . . . . . . . . . . . 760--770 Peican Zhu and Jie Han Asynchronous Stochastic Boolean Networks as Gene Network Models . . . . . . . . . 771--783
Takanori Hasegawa and Tomoya Mori and Rui Yamaguchi and Seiya Imoto and Satoru Miyano and Tatsuya Akutsu An Efficient Data Assimilation Schema for Restoration and Extension of Gene Regulatory Networks Using Time-Course Observation Data . . . . . . . . . . . . 785--798 Amir Carmel and Noa Musa-Lempel and Dekel Tsur and Michal Ziv-Ukelson The Worst Case Complexity of Maximum Parsimony . . . . . . . . . . . . . . . 799--808 Bogumil M. Konopka and Tomasz Golda and Ma\lgorzata Kotulska Evaluating the Significance of Protein Functional Similarity Based on Gene Ontology . . . . . . . . . . . . . . . . 809--822 José Santos and Pablo Villot and Martin Diéguez Emergent Protein Folding Modeled with Evolved Neural Cellular Automata Using the $3$D HP Model . . . . . . . . . . . 823--845 Nha Nguyen and An Vo and Kyoung-Jae Won A Wavelet Approach to Detect Enriched Regions and Explore Epigenomic Landscapes . . . . . . . . . . . . . . . 846--854 Katrin Illner and Christiane Fuchs and Fabian J. Theis Bayesian Blind Source Separation for Data with Network Structure . . . . . . 855--865
Changchuan Yin and Xuemeng E. Yin and Jiasong Wang A Novel Method for Comparative Analysis of DNA Sequences by Ramanujan-Fourier Transform . . . . . . . . . . . . . . . 867--879 Eman Badr and Lenwood S. Heath Identifying Splicing Regulatory Elements with de Bruijn Graphs . . . . . . . . . 880--897 Alexia Kakourou and Werner Vach and Bart Mertens Combination Approaches Improve Predictive Performance of Diagnostic Rules for Mass-Spectrometry Proteomic Data . . . . . . . . . . . . . . . . . . 898--914 William Y. C. Chen and Qiang-Hui Guo and Lisa H. Sun and Jian Wang Zigzag Stacks and $m$-Regular Linear Stacks . . . . . . . . . . . . . . . . . 915--935 Huda A. Maghawry and Mostafa G. M. Mostafa and Tarek F. Gharib A New Protein Structure Representation for Efficient Protein Function Prediction . . . . . . . . . . . . . . . 936--946 Laurent Noé and Donald E. K. Martin A Coverage Criterion for Spaced Seeds and Its Applications to Support Vector Machine String Kernels and $k$-Mer Distances . . . . . . . . . . . . . . . 947--963 Lizhen Liu and Xuemin Dai and Hanshi Wang and Wei Song and Jingli Lu A Weighted Multipath Measurement Based on Gene Ontology for Estimating Gene Products Similarity . . . . . . . . . . 964--974
Sunita Yadav and D. Swati and Hariharan Chandrasekharan Thiamine Pyrophosphate Riboswitch in Some Representative Plant Species: a Bioinformatics Study . . . . . . . . . . 1--9 Adam Persing and Ajay Jasra and Alexandros Beskos and David Balding and Maria De Iorio A Simulation Approach for Change-Points on Phylogenetic Trees . . . . . . . . . 10--24 Frederic Y. Bois and Ghislaine Gayraud Probabilistic Generation of Random Networks Taking into Account Information on Motifs Occurrence . . . . . . . . . . 25--36 Derek E. Chen and Darryl L. Willick and Joseph B. Ruckel and Wely B. Floriano Principal Component Analysis of Binding Energies for Single-Point Mutants of hT2R16 Bound to an Agonist Correlate with Experimental Mutant Cell Response 37--53 Dhammika Amaratunga and Javier Cabrera and Yung-Seop Lee Resampling-Based Similarity Measures for High-Dimensional Data . . . . . . . . . 54--62 Tuantuan Gui and Xiao Dong and Rudong Li and Yixue Li and Zhen Wang Identification of Hepatocellular Carcinoma--Related Genes with a Machine Learning and Network Analysis . . . . . 63--71
Heewon Park and Atushi Niida and Satoru Miyano and Seiya Imoto Sparse Overlapping Group Lasso for Integrative Multi-Omics Analysis . . . . 73--84 Wei Lu and Takeyuki Tamura and Jiangning Song and Tatsuya Akutsu Computing Smallest Intervention Strategies for Multiple Metabolic Networks in a Boolean Model . . . . . . 85--110 Quan Chen and Xianghong J. Zhou and Fengzhu Sun Finding Genetic Overlaps Among Diseases Based on Ranked Gene Lists . . . . . . . 111--123 Evan Senter and Peter Clote Fast, Approximate Kinetics of RNA Folding . . . . . . . . . . . . . . . . 124--144 Aditya Rao and Deepthi P. and C. H. Renumadhavi and M. Girish Chandra and Rajgopal Srinivasan Compressed Sensing Methods for DNA Microarrays, RNA Interference, and Metagenomics . . . . . . . . . . . . . . 145--158 Xuan Guo and Ning Yu and Xiaojun Ding and Jianxin Wang and Yi Pan DIME: a Novel Framework for \em De Novo Metagenomic Sequence Assembly . . . . . 159--177 Fatemeh Zamanzad Ghavidel and Jürgen Claesen and Tomasz Burzykowski A Nonhomogeneous Hidden Markov Model for Gene Mapping Based on Next-Generation Sequencing Data . . . . . . . . . . . . 178--188
Fabrice Jossinet and Yann Ponty and Jérôme Waldispühl Preface . . . . . . . . . . . . . . . . 189--189 Azadeh Saffarian and Mathieu Giraud and Hél\`ene Touzet Modeling Alternate RNA Structures in Genomic Sequences . . . . . . . . . . . 190--204 Laetitia Bourgeade and Cédric Chauve and Julien Allali Chaining Sequence/Structure Seeds for Computing RNA Similarity . . . . . . . . 205--217 Mattia Petroni and Nikolaj Zimic and Miha Mraz and Miha Mo\vskon Stochastic Simulation Algorithm for Gene Regulatory Networks with Multiple Binding Sites . . . . . . . . . . . . . 218--226 Meltem Gölgeli Matur and Johannes Müller and Christina Kuttler and Burkhard A. Hense An Approximative Approach for Single Cell Spatial Modeling of Quorum Sensing 227--235 Nha Nguyen and An Vo and Inchan Choi and Kyoung-Jae Won A Stationary Wavelet Entropy-Based Clustering Approach Accurately Predicts Gene Expression . . . . . . . . . . . . 236--249
AnDrea Califano and Manolis Kellis and Gustavo Stolovitzky Preface: RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2014 Special Issue . . . . . . . . . . . . . 251--252 Anagha Joshi and Yvonne Beck and Tom Michoel Multi-Species Network Inference Improves Gene Regulatory Network Reconstruction for Early Embryonic Development in \bionameDrosophila . . . . . . . . . . . 253--265 Edison Ong and Anthony Szedlak and Yunyi Kang and Peyton Smith and Nicholas Smith and Madison McBride and Darren Finlay and Kristiina Vuori and James Mason and Edward D. Ball and Carlo Piermarocchi and Giovanni Paternostro A Scalable Method for Molecular Network Reconstruction Identifies Properties of Targets and Mutations in Acute Myeloid Leukemia . . . . . . . . . . . . . . . . 266--288 Brittany Baur and Serdar Bozdag A Canonical Correlation Analysis-Based Dynamic Bayesian Network Prior to Infer Gene Regulatory Networks from Multiple Types of Biological Data . . . . . . . . 289--299 Xueling Li and Min Zhu and Allan R. Brasier and Andrzej S. Kudlicki Inferring Genome-Wide Functional Modulatory Network: a Case Study on NF-$ \kappa $B/RelA Transcription Factor . . 300--312 Bingqing Xie and Gady Agam and Sandhya Balasubramanian and Jinbo Xu and T. Conrad Gilliam and Natalia Maltsev and Daniela Börnigen Disease Gene Prioritization Using Network and Feature . . . . . . . . . . 313--323 Aaron Wise and Ziv Bar-Joseph cDREM: Inferring Dynamic Combinatorial Gene Regulation . . . . . . . . . . . . 324--333
Roded Sharan Preface . . . . . . . . . . . . . . . . 335--335 Rayan Chikhi and Antoine Limasset and Shaun Jackman and Jared T. Simpson and Paul Medvedev On the Representation of de Bruijn Graphs . . . . . . . . . . . . . . . . . 336--352 Adrian Guthals and Christina Boucher and Nuno Bandeira The Generating Function Approach for Peptide Identification in Spectral Networks . . . . . . . . . . . . . . . . 353--366 Henry C. M. Leung and Siu-Ming Yiu and Francis Y. L. Chin IDBA-MTP: a Hybrid Metatranscriptomic Assembler Based on Protein Information 367--376 Siavash Mirarab and Nam Nguyen and Sheng Guo and Li-San Wang and Junhyong Kim and Tandy Warnow PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences . . . . . . . . . . . . . . . 377--386 Ngan Nguyen and Glenn Hickey and Daniel R. Zerbino and Brian Raney and Dent Earl and Joel Armstrong and W. James Kent and David Haussler and Benedict Paten Building a Pan-Genome Reference for a Population . . . . . . . . . . . . . . . 387--401 Keith Noto and Saeed Majidi and Andrea G. Edlow and Heather C. Wick and Diana W. Bianchi and Donna K. Slonim CSAX: Characterizing Systematic Anomalies in eXpression Data . . . . . . 402--413 Arne C. Reimers and Frank J. Bruggeman and Brett G. Olivier and Leen Stougie Fast Flux Module Detection Using Matroid Theory . . . . . . . . . . . . . . . . . 414--424 Mingfu Shao and Yu Lin and Bernard M. E. Moret An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes . . . . . . . . . . 425--435 Shutan Xu and Shuxue Zou and Lincong Wang A Geometric Clustering Algorithm with Applications to Structural Data . . . . 436--450 Wen-Yun Yang and Farhad Hormozdiari and Eleazar Eskin and Bogdan Pasaniuc A Spatial Haplotype Copying Model with Applications to Genotype Imputation . . 451--462
Hamidreza Chitsaz and Mohammad Aminisharifabad Exact Learning of RNA Energy Parameters From Structure . . . . . . . . . . . . . 463--473 Hetunandan Kamisetty and Bornika Ghosh and Christopher James Langmead and Chris Bailey-Kellogg Learning Sequence Determinants of Protein:Protein Interaction Specificity with Sparse Graphical Models . . . . . . 474--486 Arun S. Konagurthu and Parthan Kasarapu and Lloyd Allison and James H. Collier and Arthur M. Lesk On Sufficient Statistics of Least-Squares Superposition of Vector Sets . . . . . . . . . . . . . . . . . . 487--497 Murray Patterson and Tobias Marschall and Nadia Pisanti and Leo van Iersel and Leen Stougie and Gunnar W. Klau and Alexander Schönhuth WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads 498--509 Benjamin J. Raphael and Fabio Vandin Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data . . . . . 510--527 Yana Safonova and Anton Bankevich and Pavel A. Pevzner dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes . . . . . . 528--545 Hua Wang and Heng Huang and Chris Ding Correlated Protein Function Prediction via Maximization of Data-Knowledge Consistency . . . . . . . . . . . . . . 546--562 Zhanyong Wang and Jae Hoon Sul and Sagi Snir and Jose A. Lozano and Eleazar Eskin Gene--Gene Interactions Detection Using a Two-stage Model . . . . . . . . . . . 563--576 Shay Zakov and Vineet Bafna Reconstructing Breakage Fusion Bridge Architectures Using Noisy Copy Numbers 577--594 Marinka \vZitnik and Bla\vz Zupan Data Imputation in Epistatic MAPs by Network-Guided Matrix Completion . . . . 595--608
Yuzhen Guo The Noncompacted Folding of Proteins by Modified Elastic Net Algorithm . . . . . 609--618 Robert Müller and Markus E. Nebel Combinatorics of RNA Secondary Structures with Base Triples . . . . . . 619--648 Jose M. J. Costa and Helcio R. B. Orlande and Haroldo F. Campos Velho and Suani T. R. de Pinho and George S. Dulikravich and Renato M. Cotta and Silvio H. da Cunha Neto Estimation of Tumor Size Evolution Using Particle Filters . . . . . . . . . . . . 649--665 Zhexue Wei and Daming Zhu and Lusheng Wang A Dynamic Programming Algorithm For (1,2)-Exemplar Breakpoint Distance . . . 666--676 Huilan Chang and Yi-Chang Chiu and Yi-Lin Tsai A Variation of Cover-Free Families and Its Applications . . . . . . . . . . . . 677--686 Alex Radu and Michael Charleston Node Handprinting: a Scalable and Accurate Algorithm for Aligning Multiple Biological Networks . . . . . . . . . . 687--697 Florian Kaiser and Alexander Eisold and Dirk Labudde A Novel Algorithm for Enhanced Structural Motif Matching in Proteins 698--713
Sean Simmons and Jian Peng and Jadwiga Bienkowska and Bonnie Berger Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data . . . . . . . . . . . . . . . . . . 715--728 Peter Zörnig Reduced-Size Integer Linear Programming Models for String Selection Problems: Application to the Farthest String Problem . . . . . . . . . . . . . . . . 729--742 Kaisa Koskinen and Petri Auvinen and K. Johanna Björkroth and Jenni Hultman Inconsistent Denoising and Clustering Algorithms for Amplicon Sequence Data 743--751 Chia-Hui Huang Medical Reasoning with Rough-Set Influence Diagrams . . . . . . . . . . . 752--764 Miao Sun and Dejian Lai and Li Zhang and Xuelin Huang Modified SuperCurve Method for Analysis of Reverse-Phase Protein Array Data . . 765--769 Oliver Serang A Fast Numerical Method for Max-Convolution and the Application to Efficient Max-Product Inference in Bayesian Networks . . . . . . . . . . . 770--783
Jing He and Amarda Shehu and Nurit Haspel and Brian Chen The 7th Computational Structural Bioinformatics Workshop . . . . . . . . 785--786 Hui Dong and Jin Seob Kim and Gregory S. Chirikjian Computational Analysis of SAXS Data Acquisition . . . . . . . . . . . . . . 787--805 Irina Hashmi and Amarda Shehu idDock+: Integrating Machine Learning in Probabilistic Search for Protein--Protein Docking . . . . . . . . 806--822 Hsin-Yi (Cindy) Yeh and Aaron Lindsey and Chih-Peng Wu and Shawna Thomas and Nancy M. Amato Decoy Database Improvement for Protein Folding . . . . . . . . . . . . . . . . 823--836 Abhishek Biswas and Desh Ranjan and Mohammad Zubair and Jing He A Dynamic Programming Algorithm for Finding the Optimal Placement of a Secondary Structure Topology in Cryo-EM Data . . . . . . . . . . . . . . . . . . 837--843 Rudy Clausen and Amarda Shehu A Data-Driven Evolutionary Algorithm for Mapping Multibasin Protein Energy Landscapes . . . . . . . . . . . . . . . 844--860 Ziyi Guo and Brian Yuan Chen Conformational Sampling Reveals Amino Acids with a Steric Influence on Specificity . . . . . . . . . . . . . . 861--875 Ping Zhou and Ning Zhang and Ruth Nussinov and Buyong Ma Defining the Domain Arrangement of the Mammalian Target of Rapamycin Complex Component Rictor Protein . . . . . . . . 876--886 Kelin Xia and Zhixiong Zhao and Guo-Wei Wei Multiresolution Topological Simplification . . . . . . . . . . . . . 887--891 Bahar Akbal-Delibas and Marc Pomplun and Nurit Haspel Accurate Prediction of Docked Protein Structure Similarity . . . . . . . . . . 892--904
Yael Baran and Eran Halperin A Note on the Relations Between Spatio-Genetic Models . . . . . . . . . 905--917 Filippo Disanto and Noah A. Rosenberg Coalescent Histories for Lodgepole Species Trees . . . . . . . . . . . . . 918--929 Alexa Pragman and Richard Issacson and Christine Wendt and Cavan Reilly A Method for Determining Taxonomical Contributions to Group Differences in Microbiomic Investigations . . . . . . . 930--939 Tim Wallace and Ali Sekmen and Xiaofei Wang Application of Subspace Clustering in DNA Sequence Analysis . . . . . . . . . 940--952 Alexandre Wagner Chagas Faria and Alisson Marques da Silva and Thiago de Souza Rodrigues and Marcelo Azevedo Costa and Antonio Padua Braga A Ranking Approach for Probe Selection and Classification of Microarray Data with Artificial Neural Networks . . . . 953--961 Bo Li and Xianfang Zheng and Chuancui Hu and Yunxia Cao Human Papillomavirus Genome-Wide Identification of T-Cell Epitopes for Peptide Vaccine Development Against Cervical Cancer: an Integration of Computational Analysis and Experimental Assay . . . . . . . . . . . . . . . . . 962--974
Chin Lung Lu An Efficient Algorithm for the Contig Ordering Problem under Algebraic Rearrangement Distance . . . . . . . . . 975--987 Ping Chen and Xuelin Huang Comparison of Analytic Methods for Quantitative Real-Time Polymerase Chain Reaction Data . . . . . . . . . . . . . 988--996 Anthony O'Hare Inference in High-Dimensional Parameter Space . . . . . . . . . . . . . . . . . 997--1004 Nikita A. Sakhanenko and David J. Galas Biological Data Analysis as an Information Theory Problem: Multivariable Dependence Measures and the Shadows Algorithm . . . . . . . . . 1005--1024 Ajay Jasra and Adam Persing and Alexandros Beskos and Kari Heine and Maria De Iorio Bayesian Inference for Duplication--Mutation with Complementarity Network Models . . . . . 1025--1033 Sera Kim and Kyeongjun Lee and Hokeun Sun Statistical Selection Strategy for Risk and Protective Rare Variants Associated with Complex Traits . . . . . . . . . . 1034--1043 Luís Felipe I. Cunha and Luis Antonio B. Kowada and Rodrigo de A. Hausen and Celina M. H. de Figueiredo A Faster 1.375-Approximation Algorithm for Sorting by Transpositions* . . . . . 1044--1056
Marco Frasca and Alberto Bertoni and Giorgio Valentini UNIPred: Unbalance-Aware Network Integration and Prediction of Protein Functions . . . . . . . . . . . . . . . 1057--1074 Ahmed T. Soliman and Tao Meng and Shu-Ching Chen and S. S. Iyengar and Puneeth Iyengar and John Yordy and Mei-Ling Shyu Driver Missense Mutation Identification Using Feature Selection and Model Fusion 1075--1085 Tuan-Anh Tran and Nam Tri Vo and Hoang Duc Nguyen and Bao The Pham A Novel Method to Predict Highly Expressed Genes Based on Radius Clustering and Relative Synonymous Codon Usage . . . . . . . . . . . . . . . . . 1086--1096 Kyoung-Tak Kang and Sung-Hwan Kim and Juhyun Son and Young Han Lee and Heoung-Jae Chun Probabilistic Approach for Determining the Material Properties of Meniscal Attachments \em In Vivo Using Magnetic Resonance Imaging and a Finite Element Model . . . . . . . . . . . . . . . . . 1097--1107 Shu-Yuan Niu and Ming-Yuan Xin and Jian Luo and Ming-Yao Liu and Zhen-Ran Jiang DSEP: a Tool Implementing Novel Method to Predict Side Effects of Drugs . . . . 1108--1117 Anas Al-Okaily Error Tree: a Tree Structure for Hamming and Edit Distances and Wildcards Matching . . . . . . . . . . . . . . . . 1118--1128 Olga Chernomor and Bui Quang Minh and Arndt von Haeseler Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference . . . . . . . . . 1129--1142
Feilong Deng and Shi-Yi Chen dbHT-Trans: an Efficient Tool for Filtering the Protein-Encoding Transcripts Assembled by RNA-Seq According to Search for Homologous Proteins . . . . . . . . . . . . . . . . 1--9 Sabeur Aridhi and Ha\"\itham Sghaier and Manel Zoghlami and Mondher Maddouri and Engelbert Mephu Nguifo Prediction of Ionizing Radiation Resistance in Bacteria Using a Multiple Instance Learning Model . . . . . . . . 10--20 Christopher Girdlestone and Steven Hayward The DynDom3D Webserver for the Analysis of Domain Movements in Multimeric Proteins . . . . . . . . . . . . . . . . 21--26 Cesar M. Camilo and Gustavo M. A. Lima and Fernando V. Maluf and Rafael V. C. Guido and Igor Polikarpov HTP-OligoDesigner: an Online Primer Design Tool for High-Throughput Gene Cloning and Site-Directed Mutagenesis 27--29 Fabio Vandin and Benjamin J. Raphael and Eli Upfal On the Sample Complexity of Cancer Pathways Identification . . . . . . . . 30--41 Ya-Chun Hsiao and Li-Yu Daisy Liu A Stepwise Approach of Finding Dependent Variables via Coefficient of Intrinsic Dependence . . . . . . . . . . . . . . . 42--55 Yucheng Hu and John S. Lowengrub Collective Properties of a Transcription Initiation Model Under Varying Environment . . . . . . . . . . . . . . 56--66
Yaron Orenstein and Bonnie Berger Efficient Design of Compact Unstructured RNA Libraries Covering All $k$-mers . . 67--79 Leyla Rohani and Derrick J. Morton and Xiao-Qian Wang and Jaideep Chaudhary Relative Stability of Wild-Type and Mutant p53 Core Domain: a Molecular Dynamic Study . . . . . . . . . . . . . 80--89 Daniele Pepe and Jin Hwan Do Comparison of Perturbed Pathways in Two Different Cell Models for Parkinson's Disease with Structural Equation Model 90--101 Xiaoling Peng and Gang Li and Zhenqiu Liu Zero-Inflated Beta Regression for Differential Abundance Analysis with Metagenomics Data . . . . . . . . . . . 102--110 Xiujun (Sylvia) Zhu and Monnie McGee Metagenomic Classification Using an Abstraction Augmented Markov Model . . . 111--122 Haiou Li and Lu Sun and Sheng Luo and Xiaoyan Xia and Qiang Lyu Modeling Protein Loop Structure by Cyclic Coordinate Descent-based Approach 123--136
Paola Bonizzoni and Gianluca Della Vedova and Yuri Pirola and Marco Previtali and Raffaella Rizzi LSG: an External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly . . . . . . . . 137--149 Pavel Avdeyev and Shuai Jiang and Sergey Aganezov and Fei Hu and Max A. Alekseyev Reconstruction of Ancestral Genomes in Presence of Gene Gain and Loss . . . . . 150--164 Ilan Smoly and Amir Carmel and Yonat Shemer-Avni and Esti Yeger-Lotem and Michal Ziv-Ukelson Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human--viral Infection Patterns 165--179 Deeparnab Chakrabarty and Sampath Kannan and Kevin Tian Detecting Character Dependencies in Stochastic Models of Evolution . . . . . 180--191 Zhenqiu Liu and Shili Lin and Nan Deng and Dermot P. B. McGovern and Steven Piantadosi Sparse Inverse Covariance Estimation with $L$$_0$ Penalty for Network Construction with Omics Data . . . . . . 192--202 Stefan Canzar and Khaled Elbassioni and Mitchell Jones and Julián Mestre Resolving Conflicting Predictions from Multimapping Reads . . . . . . . . . . . 203--217 Benjamin Drinkwater and Michael A. Charleston RASCAL: a Randomized Approach for Coevolutionary Analysis . . . . . . . . 218--227
Shi-Yi Chen and Feilong Deng and Ying Huang and Xianbo Jia and Yi-Ping Liu and Song-Jia Lai bioOTU: an Improved Method for Simultaneous Taxonomic Assignments and Operational Taxonomic Units Clustering of 16s rRNA Gene Sequences . . . . . . . 229--238 Arfa Anjum and Seema Jaggi and Eldho Varghese and Shwetank Lall and Arpan Bhowmik and Anil Rai Identification of Differentially Expressed Genes in RNA-seq Data of \bionameArabidopsis thaliana: a Compound Distribution Approach . . . . . . . . . 239--247 Nelson Pérez and Miguel Gutierrez and Nelson Vera Computational Performance Assessment of $k$-mer Counting Algorithms . . . . . . 248--255 Abdoulaye Sarr and Anya Désilles and Alexandra Fronville and Vincent Rodin A Viability Approach for Robustness Measurement, Organizational Autopoiesis, and Cell Turnover in a Multicellular System . . . . . . . . . . . . . . . . . 256--269 Pablo Mier and Miguel A. Andrade-Navarro FastaHerder2: Four Ways to Research Protein Function and Evolution with Clustering and Clustered Databases . . . 270--278 Michael Laimighofer and Jan Krumsiek and Florian Buettner and Fabian J. Theis Unbiased Prediction and Feature Selection in High-Dimensional Survival Regression . . . . . . . . . . . . . . . 279--290 Daniel Lobo and Jennifer Hammelman and Michael Levin MoCha: Molecular Characterization of Unknown Pathways . . . . . . . . . . . . 291--297
Teresa Przytycka Preface . . . . . . . . . . . . . . . . 299--299 Huichao Gong and Sai Zhang and Jiangdian Wang and Haipeng Gong and Jianyang Zeng Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data . . . . . . . . . . 300--310 Mark A. Hallen and Bruce R. Donald comets (Constrained Optimization of Multistate Energies by Tree Search): a Provable and Efficient Protein Design Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence 311--321 Yifeng Li and Chih-Yu Chen and Wyeth W. Wasserman Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters . . . . . . . . . . . . . . . 322--336 Mingfu Shao and Bernard M. E. Moret A Fast and Exact Algorithm for the Exemplar Breakpoint Distance . . . . . . 337--346 Leena Salmela and Kristoffer Sahlin and Veli Mäkinen and Alexandru I. Tomescu Gap Filling as Exact Path Length Problem 347--361 Rasmus Fonseca and Henry van den Bedem and Julie Bernauer Probing RNA Native Conformational Ensembles with Structural Constraints 362--371 Seunghak Lee and Aurélie Lozano and Prabhanjan Kambadur and Eric P. Xing An Efficient Nonlinear Regression Approach for Genome-wide Detection of Marginal and Interacting Genetic Variations . . . . . . . . . . . . . . . 372--389 Arnon Mazza and Allon Wagner and Eytan Ruppin and Roded Sharan Functional Alignment of Metabolic Networks . . . . . . . . . . . . . . . . 390--399 Sumudu P. Leelananda and Robert L. Jernigan and Andrzej Kloczkowski Predicting Designability of Small Proteins from Graph Features of Contact Maps . . . . . . . . . . . . . . . . . . 400--411
Jonathan D. Jou and Swati Jain and Ivelin S. Georgiev and Bruce R. Donald BWM*: a Novel, Provable, Ensemble-based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design . . . . . . . . . . . . . . . . . 413--424 Emre Sefer and Geet Duggal and Carl Kingsford Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent Mixing Structures in Cell Subpopulations 425--438 Yichao Zhou and Yuexin Wu and Jianyang Zeng Computational Protein Design Using AND/OR Branch-and-Bound Search . . . . . 439--451 Sharma V. Thankachan and Sriram P. Chockalingam and Yongchao Liu and Alberto Apostolico and Srinivas Aluru ALFRED: a Practical Method for Alignment-Free Distance Computation . . 452--460 Ilan Ben-Bassat and Benny Chor CRISPR Detection From Short Reads Using Partial Overlap Graphs . . . . . . . . . 461--471 Sharma V. Thankachan and Alberto Apostolico and Srinivas Aluru A Provably Efficient Algorithm for the $k$-Mismatch Average Common Substring Problem . . . . . . . . . . . . . . . . 472--482 Stefano R. Bonissone and Pavel A. Pevzner Immunoglobulin Classification Using the Colored Antibody Graph . . . . . . . . . 483--494 Shuo Yang and Shai Carmi and Itsik Pe'er Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs 495--507 David Manescu and Uri Keich A Symmetric Length-Aware Enrichment Test 508--525 Surojit Biswas and Meredith Mcdonald and Derek S. Lundberg and Jeffery L. Dangl and Vladimir Jojic Learning Microbial Interaction Networks from Metagenomic Count Data . . . . . . 526--535
Zhi-Zhong Chen and Fei Deng and Chao Shen and Yiji Wang and Lusheng Wang Better ILP-Based Approaches to Haplotype Assembly . . . . . . . . . . . . . . . . 537--552 Louxin Zhang On Tree-Based Phylogenetic Networks . . 553--565 Jiawen Chen and Zhong-Ru Xie and Yinghao Wu Elucidating the Functional Roles of Spatial Organization in Cross-Membrane Signal Transduction by a Hybrid Simulation Method . . . . . . . . . . . 566--584 Boxin Guan and Changsheng Zhang and Jiaxu Ning EDGA: a Population Evolution Direction-Guided Genetic Algorithm for Protein--Ligand Docking . . . . . . . . 585--596 Yi Wang and Shuangshuang Wang and Dongjie Zhou and Shuai Yang and Yongchao Xu and Chao Yang and Long Yang CsSNP: a Web-Based Tool for the Detecting of Comparative Segments SNPs 597--602 Fabrizio Serra and Chiara Romualdi and Federico Fogolari Similarity Measures Based on the Overlap of Ranked Genes Are Effective for Comparison and Classification of Microarray Data . . . . . . . . . . . . 603--614 Anas Al-Okaily and Chun-Hsi Huang ET-Motif: Solving the Exact $ (l, d)$-Planted Motif Problem Using Error Tree Structure . . . . . . . . . . . . . 615--623
Jira Jindalertudomdee and Morihiro Hayashida and Tatsuya Akutsu Enumeration Method for Structural Isomers Containing User-Defined Structures Based on Breadth-First Search Approach . . . . . . . . . . . . . . . . 625--640 Eli Goz and Tamir Tuller Evidence of a Direct Evolutionary Selection for Strong Folding and Mutational Robustness Within HIV Coding Regions . . . . . . . . . . . . . . . . 641--650 Ravi P. More and Hemant J. Purohit The Identification of Discriminating Patterns from 16S rRNA Gene to Generate Signature for Bacillus Genus . . . . . . 651--661 Metodi Traykov and Slav Angelov and Nicola Yanev A New Heuristic Algorithm for Protein Folding in the HP Model . . . . . . . . 662--668 Duo Chen and Jiasong Wang and Ming Yan and Forrest Sheng Bao A Complex Prime Numerical Representation of Amino Acids for Protein Function Comparison . . . . . . . . . . . . . . . 669--677 Enrique J. deAndrés-Galiana and Juan Luis Fernández-Martínez and Stephen T. Sonis Design of Biomedical Robots for Phenotype Prediction Problems . . . . . 678--692 Yuandi Wang and Jinyu Cong An Improved Model of Nonuniform Coleochaete Cell Division . . . . . . . 693--709
Sergey Pirogov and Alexander Rybko and Anastasia Kalinina and Mikhail Gelfand Recombination Processes and Nonlinear Markov Chains . . . . . . . . . . . . . 711--717 Paola Bonizzoni and Riccardo Dondi and Gunnar W. Klau and Yuri Pirola and Nadia Pisanti and Simone Zaccaria On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes . . . . . . . . . . . 718--736 Yuchao Pan and Yuxi Dong and Jingtian Zhou and Mark Hallen and Bruce R. Donald and Jianyang Zeng and Wei Xu cOSPREY: a Cloud-Based Distributed Algorithm for Large-Scale Computational Protein Design . . . . . . . . . . . . . 737--749 Andy S. Alic and Ignacio Blanquer MuffinInfo: HTML5-Based Statistics Extractor from Next-Generation Sequencing Data . . . . . . . . . . . . 750--755 Kerstin Gärtner and Andreas Futschik Improved Versions of Common Estimators of the Recombination Rate . . . . . . . 756--768 Eduard Fomin A Simple Approach to the Reconstruction of a Set of Points from the Multiset of $ n^2 $ Pairwise Distances in $ n^2 $ Steps for the Sequencing Problem: I. Theory . . . . . . . . . . . . . . . . . 769--775 Martin McGrane and Michael A. Charleston Biological Network Edit Distance . . . . 776--788
Eliza O'Reilly and François Baccelli and Gustavo De Veciana and Haris Vikalo End-to-End Optimization of High-Throughput DNA Sequencing . . . . . 789--800 Sergio Gálvez and Adis Ferusic and Francisco J. Esteban and Pilar Hernández and Juan A. Caballero and Gabriel Dorado Speeding-up Bioinformatics Algorithms with Heterogeneous Architectures: Highly Heterogeneous Smith-Waterman (HHeterSW) 801--809 Troy Hernandez and Jie Yang Descriptive Statistics of the Genome: Phylogenetic Classification of Viruses 810--820 Shufang Zhao and Yichao He and Xinlu Zhang and Wen Xu and Weili Wu and Suogang Gao Group Testing with Multiple Inhibitor Sets and Error-Tolerant and Its Decoding Algorithms . . . . . . . . . . . . . . . 821--829 Yucheng Hu and Gongrong Yang Sequence Evolution Under Constraints: Lessons Learned from Sudoku . . . . . . 830--840 Morgan Madec and François Pecheux and Yves Gendrault and Elise Rosati and Christophe Lallement and Jacques Haiech GeNeDA: an Open-Source Workflow for Design Automation of Gene Regulatory Networks Inspired from Microelectronics 841--855
Christopher L. Barrett and Thomas J. X. Li and Christian M. Reidys RNA Secondary Structures Having a Compatible Sequence of Certain Nucleotide Ratios . . . . . . . . . . . 857--873 Strahil Ristov A Fast and Simple Pattern Matching with Hamming Distance on Large Alphabets . . 874--876 Wenchuan Guo and Zhenqiu Liu and Shujie Ma Nonparametric Regularized Regression for Phenotype-Associated Taxa Selection and Network Construction with Metagenomic Count Data . . . . . . . . . . . . . . . 877--890 Mariana Buongermino Pereira and Mikael Wallroth and Erik Kristiansson and Marina Axelson-Fisk HattCI: Fast and Accurate \bionameattC site Identification Using Hidden Markov Models . . . . . . . . . . . . . . . . . 891--902 Somaye Hashemifar and Qixing Huang and Jinbo Xu Joint Alignment of Multiple Protein--Protein Interaction Networks via Convex Optimization . . . . . . . . 903--911 Lamiaa A. Amar and Nahla A. Belal and Shaheera Rashwan Comparing Unlabeled Pedigree Graphs via Covering with Bipartite and Path . . . . 912--922
Manca Bizjak and Nikolaj Zimic and Miha Mraz and Miha Mo\vskon Computational Framework for Modeling Multiple Noncooperative Transcription Factor Binding and Its Application to the Analysis of Nuclear Factor Kappa B Oscillatory Response . . . . . . . . . . 923--933 Eduard Fomin A Simple Approach to the Reconstruction of a Set of Points from the Multiset of $ n^2 $ Pairwise Distances in $ n^2 $ Steps for the Sequencing Problem: II. Algorithm . . . . . . . . . . . . . . . 934--942 Qiang-Hui Guo and Lisa H. Sun and Jian Wang Enumeration of Extended $m$-Regular Linear Stacks . . . . . . . . . . . . . 943--956 Enrique J. Deandrés-Galiana and Juan Luis Fernández-Martínez and Leorey N. Saligan and Stephen T. Sonis Impact of Microarray Preprocessing Techniques in Unraveling Biological Pathways . . . . . . . . . . . . . . . . 957--968 Sean B. Johnston and Ronald T. Raines PTENpred: a Designer Protein Impact Predictor for PTEN-related Disorders . . 969--975 Stefano Pirr\`o and Antonella Minutolo and Andrea Galgani and Marina Potest\`a and Vittorio Colizzi and Carla Montesano Bioinformatics Prediction and Experimental Validation of MicroRNAs Involved in Cross-Kingdom Interaction 976--989
Jing He and Nurit Haspel and Brian Chen Preface: Selected Articles from 2015 Computational Structural Bioinformatics Workshop . . . . . . . . . . . . . . . . 1--1 Hu Cao and Yonggang Lu Using Variable-Length Aligned Fragment Pairs and an Improved Transition Function for Flexible Protein Structure Alignment . . . . . . . . . . . . . . . 2--12 Jin Seob Kim and Bijan Afsari and Gregory S. Chirikjian Cross-Validation of Data Compatibility Between Small Angle X-ray Scattering and Cryo-Electron Microscopy . . . . . . . . 13--30 Wen Cheng and Changhui Yan A Graph Approach to Mining Biological Patterns in the Binding Interfaces . . . 31--39 Roshanak Farhoodi and Bahar Akbal-Delibas and Nurit Haspel Machine Learning Approaches for Predicting Protein Complex Similarity 40--51 Stephanie Zeil and Julio Kovacs and Willy Wriggers and Jing He Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix . . . . . . . . . . . . . . . . 52--67 Bridget E. Nolan and Emily Levenson and Brian Y. Chen Influential Mutations in the SMAD4 Trimer Complex Can Be Detected from Disruptions of Electrostatic Complementarity . . . . . . . . . . . . 68--78 Anastasia Novinskaya and Didier Devaurs and Mark Moll and Lydia E. Kavraki Defining Low-Dimensional Projections to Guide Protein Conformational Sampling 79--89
Adrian-Horia Dediu and Carlos Martín-Vide Preface: Selected Articles of the Second International Conference on Algorithms for Computational Biology (AlCoB 2015) 91--92 Nikita Alexeev and Anna Pologova and Max A. Alekseyev Generalized Hultman Numbers and Cycle Structures of Breakpoint Graphs . . . . 93--105 Jesper Jansson and Ramesh Rajaby A More Practical Algorithm for the Rooted Triplet Distance . . . . . . . . 106--126 Ron Zeira and Ron Shamir Sorting by Cuts, Joins, and Whole Chromosome Duplications . . . . . . . . 127--137 Heewon Park and Atsushi Niida and Seiya Imoto and Satoru Miyano Interaction-Based Feature Selection for Uncovering Cancer Driver Genes Through Copy Number-Driven Expression Level . . 138--152 Elizabeth S. Allman and John A. Rhodes and Seth Sullivant Statistically Consistent $k$-mer Methods for Phylogenetic Tree Reconstruction . . 153--171 Xin Tian and Mingyuan Xin and Jian Luo and Mingyao Liu and Zhenran Jiang Identification of Genes Involved in Breast Cancer Metastasis by Integrating Protein--Protein Interaction Information with Expression Data . . . . . . . . . . 172--182 Jie Zhou Effect of Protein Repetitiveness on Protein--Protein Interaction Prediction Results Using Support Vector Machines 183--192
Bartek Wilczynski and Jerzy Tiuryn FastBill: an Improved Tool for Prediction of \em Cis-Regulatory Modules 193--199 Celine Prakash and Arndt Von Haeseler An Enumerative Combinatorics Model for Fragmentation Patterns in RNA Sequencing Provides Insights into Nonuniformity of the Expected Fragment Starting-Point and Coverage Profile . . . . . . . . . . . . 200--212 David Budden and Mitchell Jones Cautionary Tales of Inapproximability 213--216 Li Zhang and Han Wang and Lun Yan and Lingtao Su and Dong Xu OMPcontact: an Outer Membrane Protein Inter-Barrel Residue Contact Prediction Method . . . . . . . . . . . . . . . . . 217--228 Marc Cole and Steffen Eikenberry and Takahide Kato and Roman A. Sandler and Stanley M. Yamashiro and Vasilis Z. Marmarelis Nonparametric Model of Smooth Muscle Force Production During Electrical Stimulation . . . . . . . . . . . . . . 229--237 James Gigrich and Shahryar Sarkani and Thomas Holzer A New Approach in Applying Systems Engineering Tools and Analysis to Determine Hepatocyte Toxicogenomics Risk Levels to Human Health . . . . . . . . . 238--254 Bruno Borguesan and Mario Inostroza-Ponta and Márcio Dorn NIAS-Server: Neighbors Influence of Amino acids and Secondary Structures in Proteins . . . . . . . . . . . . . . . . 255--265
Serge Sverdlov and Elizabeth Thompson Combinatorial Methods for Epistasis and Dominance . . . . . . . . . . . . . . . 267--279 Anas Al-Okaily and Badar Almarri and Sultan Al Yami and Chun-Hsi Huang Toward a Better Compression for DNA Sequences Using Huffman Encoding . . . . 280--288 Doo Yang and Ilya Ioshikhes \bionameDrosophila H2A and H2A.Z Nucleosome Sequences Reveal Different Nucleosome Positioning Sequence Patterns 289--298 Lianping Yang and Weilin Zhang A Multiresolution Graphical Representation for Similarity Relationship and Multiresolution Clustering for Biological Sequences . . 299--310 Viktor Jonsson and Tobias Österlund and Olle Nerman and Erik Kristiansson Variability in Metagenomic Count Data and Its Influence on the Identification of Differentially Abundant Genes . . . . 311--326 Priya S. Venkat and Krishna R. Narayanan and Aniruddha Datta A Bayesian Network-Based Approach to Selection of Intervention Points in the Mitogen-Activated Protein Kinase Plant Defense Response Pathway . . . . . . . . 327--339 Grigoriy Gogoshin and Eric Boerwinkle and Andrei S. Rodin New Algorithm and Software (BNOmics) for Inferring and Visualizing Bayesian Networks from Heterogeneous Big Biological and Genetic Data . . . . . . 340--356 Audrone Jakaitiene and Mariano Avino and Mario Rosario Guarracino Beta-Binomial Model for the Detection of Rare Mutations in Pooled Next-Generation Sequencing Experiments . . . . . . . . . 357--367 Ying Wang and Haiyan Hu and Xiaoman Li rRNAFilter: a Fast Approach for Ribosomal RNA Read Removal Without a Reference Database . . . . . . . . . . . 368--375
Amrit Dhar and Vladimir N. Minin Calculating Higher-Order Moments of Phylogenetic Stochastic Mapping Summaries in Linear Time . . . . . . . . 377--399 Gira Lee and Hokeun Sun Selection Probability for Rare Variant Association Studies . . . . . . . . . . 400--411 Nicola Yanev and Metodi Traykov and Peter Milanov and Borislav Yurukov Protein Folding Prediction in a Cubic Lattice in Hydrophobic-Polar Model . . . 412--421 Damian Bogdanowicz and Krzysztof Giaro Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions . . . . . . . . . . . 422--435 Sihai Yang and Xianhua Han and Yukako Tohsato and Koji Kyoda and Shuichi Onami and Ikuko Nishikawa and Yenwei Chen Phenotype Analysis Method for Identification of Gene Functions Involved in Asymmetric Division of \bionameCaenorhabditis elegans . . . . . 436--446 David Barrios and Carlos Prieto D3GB: an Interactive Genome Browser for R, Python, and WordPress . . . . . . . . 447--449 Ngoc Tam L. Tran and Chun-Hsi Huang Cloud-based MOTIFSIM: Detecting Similarity in Large DNA Motif Data Sets 450--459 Rajat Anand and Samrat Chatterjee Extracting Genes Involved in Disease from a Connected Network of Perturbed Biological Processes . . . . . . . . . . 460--469
Anonymous Preface: Selected Papers from RECOMB 2016 . . . . . . . . . . . . . . . . . . 471--471 Chandler Zuo and Kailei Chen and Sündüz Kele\cs A MAD-Bayes Algorithm for State-Space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets . . . 472--485 Hao Wang and Joel McManus and Carl Kingsford Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast . . . . . 486--500 Meghana Kshirsagar and Keerthiram Murugesan and Jaime G. Carbonell and Judith Klein-Seetharaman Multitask Matrix Completion for Learning Protein Interactions Across Diseases . . 501--514 Nilgun Donmez and Salem Malikic and Alexander W. Wyatt and Martin E. Gleave and Colin C. Collins and S. Cenk Sahinalp Clonality Inference from Single Tumor Samples Using Low-Coverage Sequence Data 515--523 Nicolo Fusi and Jennifer Listgarten Flexible Modeling of Genetic Effects on Function-Valued Traits . . . . . . . . . 524--535 Mark A. Hallen and Jonathan D. Jou and Bruce R. Donald LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid Rotamer-Like Efficiency . . . . . 536--546 David Pellow and Darya Filippova and Carl Kingsford Improving Bloom Filter Performance on Sequence Data Using $k$-mer Bloom Filters . . . . . . . . . . . . . . . . 547--557 Alexander Artyomenko and Nicholas C. Wu and Serghei Mangul and Eleazar Eskin and Ren Sun and Alex Zelikovsky Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants . . . . . . . . . . . . . . . . 558--570 Mingfu Shao and Bernard M. E. Moret On Computing Breakpoint Distances for Genomes with Duplicate Genes . . . . . . 571--580 Kristoffer Sahlin and Mattias Frånberg and Lars Arvestad Structural Variation Detection with Read Pair Information: an Improved Null Hypothesis Reduces Bias . . . . . . . . 581--589 Alexandru I. Tomescu and Paul Medvedev Safe and Complete Contig Assembly Through Omnitigs . . . . . . . . . . . . 590--602 Simona Cristea and Jack Kuipers and Niko Beerenwinkel pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Progression Dynamics . . . . . . . . . . 603--615 Daniel Doerr and Luis Antonio B. Kowada and Eloi Araujo and Shachi Deshpande and Simone Dantas and Bernard M. E. Moret and Jens Stoye New Genome Similarity Measures based on Conserved Gene Adjacencies . . . . . . . 616--634
Haiyan Huang and Hua Tang and Jing Huang and Bin Chen and Ruixiao Liu and Rui (Sammi) Tang and Ying Lu and Peng Yang Special Issue: Selected Papers of the Inaugural DahShu Data Science Symposium: Computational Precision Health (CPH 2017) . . . . . . . . . . . . . . . . . 635--636 Yangyang Hao and Xiaoling Xuei and Lang Li and Harikrishna Nakshatri and Howard J. Edenberg and Yunlong Liu RareVar: a Framework for Detecting Low-Frequency Single-Nucleotide Variants 637--646 Tianzhou Ma and Faming Liang and Steffi Oesterreich and George C. Tseng A Joint Bayesian Model for Integrating Microarray and RNA Sequencing Transcriptomic Data . . . . . . . . . . 647--662 Funan Shi and Haiyan Huang Identifying Cell Subpopulations and Their Genetic Drivers from Single-Cell RNA-Seq Data Using a Biclustering Approach . . . . . . . . . . . . . . . . 663--674 Sara M. Clifton and Chaeryon Kang and Jingyi Jessica Li and Qi Long and Nirmish Shah and Daniel M. Abrams Hybrid Statistical and Mechanistic Mathematical Model Guides Mobile Health Intervention for Chronic Pain . . . . . 675--688 Hu Yang and Xiaoqin Liu Studies on the Clustering Algorithm for Analyzing Gene Expression Data with a Bidirectional Penalty . . . . . . . . . 689--698 Huaying Fang and Chengcheng Huang and Hongyu Zhao and Minghua Deng gCoda: Conditional Dependence Network Inference for Compositional Data . . . . 699--708 Minhyeok Lee and Junhee Seok and Donghyun Tae and Hua Zhong and Sung Won Han A Comparison of Two-Stage Approaches Based on Penalized Regression for Estimating Gene Networks . . . . . . . . 709--720 Yoonha Choi and Marc Coram and Jie Peng and Hua Tang A Poisson Log-Normal Model for Constructing Gene Covariation Network Using RNA-seq Data . . . . . . . . . . . 721--731
Abdoulaye Baniré Diallo and Engelbert Mephu Nguifo and Mohammed J. Zaki Preface: Selected Papers from the Workshop Bioinformatics and Artificial Intelligence Joined with the International Joint Conference on Artificial Intelligence . . . . . . . . 733--733 Vincent Picard and Anne Siegel and Jérémie Bourdon A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks . . . . . . . . . . . . . . . . 734--745 Abedalrhman Alkhateeb and Luis Rueda Zseq: an Approach for Preprocessing Next-Generation Sequencing Data . . . . 746--755 Forough Firoozbakht and Iman Rezaeian and Michele D'agnillo and Lisa Porter and Luis Rueda and Alioune Ngom An Integrative Approach for Identifying Network Biomarkers of Breast Cancer Subtypes Using Genomic, Interactomic, and Transcriptomic Data . . . . . . . . 756--766 Ieva Vasiljeva and Ognjen Arandjelovi\'c Diagnosis Prediction from Electronic Health Records Using the Binary Diagnosis History Vector Representation 767--786 Ham Ching Lam and Xuan Bi and Srinand Sreevatsan and Daniel Boley Evolution and Vaccination of Influenza Virus . . . . . . . . . . . . . . . . . 787--798 Ahmed Halioui and Petko Valtchev and Abdoulaye Baniré Diallo T-GOWler: Discovering Generalized Process Models Within Texts . . . . . . 799--808 Ricardo De Souza Jacomini and David Correa Martins, Jr. and Felipe Leno Da Silva and Anna Helena Reali Costa GeNICE: a Novel Framework for Gene Network Inference by Clustering, Exhaustive Search, and Multivariate Analysis . . . . . . . . . . . . . . . . 809--830
Filippo Disanto and Noah A. Rosenberg Enumeration of Ancestral Configurations for Matching Gene Trees and Species Trees . . . . . . . . . . . . . . . . . 831--850 Zheng Dai and David Becerra and Jérôme Waldispühl On Stable States in a Topologically Driven Protein Folding Model . . . . . . 851--862 Doaa Altarawy and Fatma-Elzahraa Eid and Lenwood S. Heath PEAK: Integrating Curated and Noisy Prior Knowledge in Gene Regulatory Network Inference . . . . . . . . . . . 863--873 Daniel J. White and Jing Wang and Richard J. Hall Assessing the Impact of Assemblers on Virus Detection in a De Novo Metagenomic Analysis Pipeline . . . . . . . . . . . 874--881 Radhika Khanna and Sangeeta Mittal and Sujata Mohanty Development of Computer Algorithm for Editing of Next Generation Sequencing Metagenome Data . . . . . . . . . . . . 882--894 Ngoc Tam L. Tran and Chun-Hsi Huang MOTIFSIM 2.1: an Enhanced Software Platform for Detecting Similarity in Multiple DNA Motif Data Sets . . . . . . 895--905 Noa Godin and Jerry Eichler The Mitochondrial Protein Atlas: a Database of Experimentally Verified Information on the Human Mitochondrial Proteome . . . . . . . . . . . . . . . . 906--916 Byeonghyeok Park and Min-Jeong Baek and Byoungnam Min and In-Geol Choi Prokaryotic Contig Annotation Pipeline Server: Web Application for a Prokaryotic Genome Annotation Pipeline Based on the \pkgShiny App Package . . . 917--922 Xiuli Ma and Guangyu Zhou and Jingbo Shang and Jingjing Wang and Jian Peng and Jiawei Han Detection of Complexes in Biological Networks Through Diversified Dense Subgraph Mining . . . . . . . . . . . . 923--941 Yu Zheng and Xiaoyang Li and Lydia C. Manor and Hongbao Cao and Qiusheng Chen An Integrative Computational Approach to Evaluate Genetic Markers for Chronic Lymphocytic Leukemia . . . . . . . . . . 942--952
Paola Bonizzoni and Gianluca Della Vedova and Yuri Pirola and Marco Previtali and Raffaella Rizzi FSG: Fast String Graph Construction for De Novo Assembly . . . . . . . . . . . . 953--968 Irina Balaur and Mansoor Saqi and Ana Barat and Artem Lysenko and Alexander Mazein and Christopher J. Rawlings and Heather J. Ruskin and Charles Auffray EpiGeNet: a Graph Database of Interdependencies Between Genetic and Epigenetic Events in Colorectal Cancer 969--980 Cheng-Hong Yang and Yu-Shiun Lin and Li-Yeh Chuang and Hsueh-Wei Chang A Particle Swarm Optimization-Based Approach with Local Search for Predicting Protein Folding . . . . . . . 981--994 Pedro P. González-Pérez and Daniel J. Orta and Irving Peña and Eduardo C. Flores and José U. Ramírez and Hiram I. Beltrán and Salomón J. Alas A Computational Approach to Studying Protein Folding Problems Considering the Crucial Role of the Intracellular Environment . . . . . . . . . . . . . . 995--1013 Marek C. Milewski and Karol Kamel and Anna Kurzynska-Kokorniak and Marcin K. Chmielewski and Marek Figlerowicz EvOligo: a Novel Software to Design and Group Libraries of Oligonucleotides Applicable for Nucleic Acid-Based Experiments . . . . . . . . . . . . . . 1014--1028 Lebin Thomas and Hari Ram and Ved Pal Singh Evolutionary Relationships and Taxa-Specific Conserved Signature Indels Among Cellulases of Archaea, Bacteria, and Eukarya . . . . . . . . . . . . . . 1029--1042 Rajashekar Varma Kadumuri and Ramakrishna Vadrevu LoopX: a Graphical User Interface-Based Database for Comprehensive Analysis and Comparative Evaluation of Loops from Protein Structures . . . . . . . . . . . 1043--1049 Haixin Ai and Runlin Wu and Li Zhang and Xuewei Wu and Junchao Ma and Huan Hu and Liangchao Huang and Wen Chen and Jian Zhao and Hongsheng Liu pSuc-PseRat: Predicting Lysine Succinylation in Proteins by Exploiting the Ratios of Sequence Coupling and Properties . . . . . . . . . . . . . . . 1050--1059 Feilong Deng and Shi-Yi Chen and Zhou-Lin Wu and Yongsong Hu and Xianbo Jia and Song-Jia Lai GFFview: a Web Server for Parsing and Visualizing Annotation Information of Eukaryotic Genome . . . . . . . . . . . 1060--1064 Aldona Krupska Influence of Oscillatory Enzyme Activity on the Reaction Kinetics: Mathematical Model . . . . . . . . . . . . . . . . . 1065--1070
Christina J. Castro and Terry Fei Fan Ng U$_{50}$: a New Metric for Measuring Assembly Output Based on Non-Overlapping, Target-Specific Contigs 1071--1080 Mahmut \cSam\.il Sa\ugiro\uglu and M. O\uguzhan Külekc\.i A System Architecture for Efficient Transmission of Massive DNA Sequencing Data . . . . . . . . . . . . . . . . . . 1081--1088 Pawe\l B\la\.zej and Ma\lgorzata Wn\ketrzak and Ma\lgorzata Grabi\'nska and Pawe\l Mackiewicz Representations of Search Spaces in the Problem of Mutational Pressure Optimization According to Protein-Coding Sequences . . . . . . . . . . . . . . . 1089--1098 Yan Zhou and Baoxue Zhang and Gaorong Li and Tiejun Tong and Xiang Wan GD-RDA: a New Regularized Discriminant Analysis for High-Dimensional Data . . . 1099--1111 Shengqing Lv and Yimin Chen and Zeyu Li and Jiahui Lu and Mingke Gao and Rongrong Lu Application of Time-Frequency Domain Transform to Three-Dimensional Interpolation of Medical Images . . . . 1112--1124 Gesiele Almeida Barros-Carvalho and Marie-Anne Van Sluys and Fabricio Martins Lopes An Efficient Approach to Explore and Discriminate Anomalous Regions in Bacterial Genomes Based on Maximum Entropy . . . . . . . . . . . . . . . . 1125--1133 Natacha Cerisier and Leslie Regad and Dhoha Triki and Anne-Claude Camproux and Michel Petitjean Cavity Versus Ligand Shape Descriptors: Application to Urokinase Binding Pockets 1134--1137 Andrey Kechin and Uljana Boyarskikh and Alexander Kel and Maxim Filipenko cutPrimers: a New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing . . 1138--1143 Álvaro Rubio-Largo and Leonardo Vanneschi and Mauro Castelli and Miguel A. Vega-Rodríguez Reducing Alignment Time Complexity of Ultra-Large Sets of Sequences . . . . . 1144--1152
Nikita A. Sakhanenko and James Kunert-Graf and David J. Galas The Information Content of Discrete Functions and Their Application in Genetic Data Analysis . . . . . . . . . 1153--1178 Ron Zeira and Meirav Zehavi and Ron Shamir A Linear-Time Algorithm for the Copy Number Transformation Problem . . . . . 1179--1194 Wenbin Chen and William Hendrix and Nagiza F. Samatova The Application of the Weighted $k$-Partite Graph Problem to the Multiple Alignment for Metabolic Pathways . . . . . . . . . . . . . . . . 1195--1211 Cheng-Hong Yang and Yu-Da Lin and Li-Yeh Chuang and Jin-Bor Chen and Hsueh-Wei Chang Joint Analysis of SNP--SNP-Environment Interactions for Chronic Dialysis by an Improved Branch and Bound Algorithm . . 1212--1225 Haitham Elmarakeby and Mostafa Arefiyan and Elijah Myers and Song Li and Ruth Grene and Lenwood S. Heath Beacon Editor: Capturing Signal Transduction Pathways Using the Systems Biology Graphical Notation Activity Flow Language . . . . . . . . . . . . . . . . 1226--1229 Wenhe Su and Xiangke Liao and Yutong Lu and Quan Zou and Shaoliang Peng Multiple Sequence Alignment Based on a Suffix Tree and Center-Star Strategy: a Linear Method for Multiple Nucleotide Sequence Alignment on Spark Parallel Framework . . . . . . . . . . . . . . . 1230--1242 Chao Pei and Shu-Lin Wang and Jianwen Fang and Wei Zhang GSMC: Combining Parallel Gibbs Sampling with Maximal Cliques for Hunting DNA Motif . . . . . . . . . . . . . . . . . 1243--1253 Shin-Fu Tsai and Chih-Wei Tung and Chen-An Tsai and Chen-Tuo Liao An Exhaustive Scan Method for SNP Main Effects and SNP $ \times $ SNP Interactions Over Highly Homozygous Genomes . . . . . . . . . . . . . . . . 1254--1264 Samana Shrestha and Adam Vanasse and Leon N. Cooper and Michael P. Antosh Gene Expression as a Dosimeter in Irradiated \bionameDrosophila melanogaster . . . . . . . . . . . . . . 1265--1274 Md Shahinuzzaman and Dipak Barua A Multiscale Algorithm for Spatiotemporal Modeling of Multivalent Protein--Protein Interaction . . . . . . 1275--1283
Jing He and Kamal Al Nasr and Weitao Sun and Yonggang Lu \em Special Issue Preface: The 9th Computational Structural Bioinformatics Workshop . . . . . . . . . . . . . . . . 1--2 Jayvee R. Abella and Mark Moll and Lydia E. Kavraki Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods . . . . . . . 3--20 Kamal Al Nasr and Christopher Jones and Feras Yousef and Ruba Jebril PEM-fitter: a Coarse-Grained Method to Validate Protein Candidate Models . . . 21--32 Tatiana Maximova and Zijing Zhang and Daniel B. Carr and Erion Plaku and Amarda Shehu Sample-Based Models of Protein Energy Landscapes and Slow Structural Rearrangements . . . . . . . . . . . . . 33--50 Nathan Clement and Muhibur Rasheed and Chandrajit Lal Bajaj Viral Capsid Assembly: a Quantified Uncertainty Approach . . . . . . . . . . 51--71 Jin Seob Kim and Gregory S. Chirikjian Symmetrical Parameterization of Rigid Body Transformations for Biomolecular Structures . . . . . . . . . . . . . . . 72--88 Michael Siderius and Filip Jagodzinski Mutation Sensitivity Maps: Identifying Residue Substitutions That Impact Protein Structure Via a Rigidity Analysis In Silico Mutation Approach . . 89--102 Weitao Sun The Relationship Between Low-Frequency Motions and Community Structure of Residue Network in Protein Molecules . . 103--113 Tunazzina Islam and Michael Poteat and Jing He Quantification of Twist from the Central Lines of $ \beta $-Strands . . . . . . . 114--120
Stephen F. Altschul and Andrew F. Neuwald Initial Cluster Analysis . . . . . . . . 121--129 Heewon Park and Teppei Shimamura and Seiya Imoto and Satoru Miyano Adaptive NetworkProfiler for Identifying Cancer Characteristic-Specific Gene Regulatory Networks . . . . . . . . . . 130--145 Jin-Hua He and Ze-Ping Han and Mao-Xian Zou and Li Wang and Yu Bing Lv and Jia Bin Zhou and Ming-Rong Cao and Yu-Guang Li Analyzing the LncRNA, miRNA, and mRNA Regulatory Network in Prostate Cancer with Bioinformatics Software . . . . . . 146--157 Cheng-Hong Yang and Yi-Cheng Chiang and Li-Yeh Chuang and Yu-Da Lin A CpGCluster-Teaching--Learning-Based Optimization for Prediction of CpG Islands in the Human Genome . . . . . . 158--169 Fatima A. Morad and Omran M. Rashidi and Saida S. Sadath and Faisal A. Al-Allaf and Mohammad Athar and Mohamed N. Alama and Sherif E. Edris and Nabeel S. Bondagji and Noor A. Shaik and Babajan Banaganapalli and Zuhier Awan In Silico Approach to Investigate the Structural and Functional Attributes of Familial Hypercholesterolemia Variants Reported in the Saudi Population . . . . 170--181 Mohammad S. Rahman and Ann E. Nicholson and Gholamreza Haffari HetFHMM: a Novel Approach to Infer Tumor Heterogeneity Using Factorial Hidden Markov Models . . . . . . . . . . . . . 182--193 Evaldo Bezerra Costa MELC Genomics: a Framework for De Novo Genome Assembly . . . . . . . . . . . . 194--199 Jordi Vilaplana and Rui Alves and Francesc Solsona and Jordi Mateo and Ivan Teixidó and Marc Pifarré MetReS, an Efficient Database for Genomic Applications . . . . . . . . . . 200--213 Arnon Benshahar and Vered Chalifa-Caspi and Danny Hermelin and Michal Ziv-Ukelson A Biclique Approach to Reference-Anchored Gene Blocks and Its Applications to Genomic Islands . . . . 214--235 Sawsan Kanj and Thomas Brüls and Stéphane Gazut Shared Nearest Neighbor Clustering in a Locality Sensitive Hashing Framework . . 236--250
Zhipeng Cai and Pavel Skums and Alexander Zelikovsky \em Special Issue Preface: 13th International Symposium on Bioinformatics Research and Applications (ISBRA 2017) . . . . . . . . . . . . . . 251--252 Kuang-Yu Chang and Yun Cui and Siu-Ming Yiu and Wing-Kai Hon Reconstructing One-Articulated Networks with Distance Matrices . . . . . . . . . 253--269 Zihao Wang and Yu Chen and Jingrong Zhang and Lun Li and Xiaohua Wan and Zhiyong Liu and Fei Sun and Fa Zhang ICON-MIC: Implementing a CPU/MIC Collaboration Parallel Framework for ICON on Tianhe-2 Supercomputer . . . . . 270--281 Micha\l Aleksander Ciach and Mateusz Krzysztof \L\kacki and B\la\.zej Miasojedow and Frederik Lermyte and Dirk Valkenborg and Frank Sobott and Anna Gambin Estimation of Rates of Reactions Triggered by Electron Transfer in Top-Down Mass Spectrometry . . . . . . . 282--301 Ruofan Xia and Yu Lin and Jun Zhou and Bing Feng and Jijun Tang A Median Solver and Phylogenetic Inference Based on Double-Cut-and-Join Sorting . . . . . . . . . . . . . . . . 302--312 Rashika Mishra and Ovidiu Daescu and Patrick Leavey and Dinesh Rakheja and Anita Sengupta Convolutional Neural Network for Histopathological Analysis of Osteosarcoma . . . . . . . . . . . . . . 313--325 Albert Ng and Dong Si Beta-Barrel Detection for Medium Resolution Cryo-Electron Microscopy Density Maps Using Genetic Algorithms and Ray Tracing . . . . . . . . . . . . 326--336 Xiuchun Xiao and Bing Liu and Jing Zhang and Xueli Xiao and Yi Pan An Optimized Method for Bayesian Connectivity Change Point Model . . . . 337--347 Bruno Fosso and Graziano Pesole and Francesc Rosselló and Gabriel Valiente Unbiased Taxonomic Annotation of Metagenomic Samples . . . . . . . . . . 348--360 Lei Wang and Zhu-Hong You and Xing Chen and Shi-Xiong Xia and Feng Liu and Xin Yan and Yong Zhou and Ke-Jian Song A Computational-Based Method for Predicting Drug-Target Interactions by Using Stacked Autoencoder Deep Neural Network . . . . . . . . . . . . . . . . 361--373
Ana M. Jelovic and Nenad S. Mitic and Samira Eshafah and Milos V. Beljanski Finding Statistically Significant Repeats in Nucleic Acids and Proteins 375--387 Hong Wang and Xiaolin Chen and Gang Li Survival Forests with $R$-Squared Splitting Rules . . . . . . . . . . . . 388--395 Lingling Li and Tianhai Tian and Xinan Zhang Mutation Mechanisms of Human Breast Cancer . . . . . . . . . . . . . . . . . 396--404 Hsin-Hsiung Huang and Senthil B. Girimurugan A Novel Real-Time Genome Comparison Method Using Discrete Wavelet Transform 405--416 Jaeil Ahn and Brian Conkright and Simina M. Boca and Subha Madhavan POPSTR: Inference of Admixed Population Structure Based on Single-Nucleotide Polymorphisms and Copy Number Variations 417--429 Andreas M. Kist and Angelika Lampert and Andrias O. O'Reilly DIsulfide Mapping PLanner Software Tool 430--434 Jun Fan and Jing Yang and Zhenran Jiang Prediction of Central Nervous System Side Effects Through Drug Permeability to Blood--Brain Barrier and Recommendation Algorithm . . . . . . . . 435--443 Andrey Minarsky and Nadya Morozova and Robert Penner and Christophe Soulé Theory of Morphogenesis . . . . . . . . 444--450 Rodrigo Ligabue-Braun and Bruno Borguesan and Hugo Verli and Mathias J. Krause and Márcio Dorn Everyone Is a Protagonist: Residue Conformational Preferences in High-Resolution Protein Structures . . . 451--465
Chen Sun and Robert S. Harris and Rayan Chikhi and Paul Medvedev AllSome Sequence Bloom Trees . . . . . . 467--479 Néli J. Fonseca-Júnior and Marcelo Q. L. Afonso and Lucas C. Oliveira and Lucas Bleicher PFstats: a Network-Based Open Tool for Protein Family Analysis . . . . . . . . 480--486 Qianghui Guo and Jian Wang and Zhao Xu Approximation Algorithms for Protein Folding in the Hydrophobic-Polar Model on $3$D Hexagonal Prism Lattice . . . . 487--498 Yang Xu and Xiao-Chun Luo PyPathway: Python Package for Biological Network Analysis and Visualization . . . 499--504 Miha Mo\vskon and Nikolaj Zimic and Miha Mraz Grohar: Automated Visualization of Genome-Scale Metabolic Models and Their Pathways . . . . . . . . . . . . . . . . 505--508 Shuangyang Wu and Wanfei Liu and Hasan Awad Aljohi and Sarah A. Alromaih and Ibrahim O. Alanazi and Qiang Lin and Jun Yu and Songnian Hu REDO: RNA Editing Detection in Plant Organelles Based on Variant Calling Results . . . . . . . . . . . . . . . . 509--516 Carlos N. Fischer and Victor De A.Campos and Victor H. Barella On the Search for Retrotransposons: Alternative Protocols to Obtain Sequences to Learn Profile Hidden Markov Models . . . . . . . . . . . . . . . . . 517--527
Yongan Zhao and Xiaofeng Wang and Haixu Tang A Secure Alignment Algorithm for Mapping Short Reads to Human Genome . . . . . . 529--540 Albert Vexler and Jihnhee Yu To $t$-Test or Not to $t$-Test? A $p$-Values-Based Point of View in the Receiver Operating Characteristic Curve Framework . . . . . . . . . . . . . . . 541--550 Lu Zeng and Stephen M. Pederson and Danfeng Cao and Zhipeng Qu and Zhiqiang Hu and David L. Adelson and Chaochun Wei Genome-Wide Analysis of the Association of Transposable Elements with Gene Regulation Suggests that \bionameAlu Elements Have the Largest Overall Regulatory Impact . . . . . . . . . . . 551--562 Xiaodong Wang and Lei Wang A Simple Linear Space Algorithm for Computing Nonoverlapping Inversion and Transposition Distance in Quadratic Average Time . . . . . . . . . . . . . . 563--575 Yan Dong and Hongbao Cao and Zhigang Liang A Curated Target Gene Pool Assisting Early Disease Prediction and Patient-Specific Treatment for Small Cell Lung Cancer . . . . . . . . . . . . 576--585 Lizhen Liu and Xiaowu Sun and Wei Song and Chao Du A Method for Predicting Protein Complexes from Dynamic Weighted Protein--Protein Interaction Networks 586--605 Chelsea M. Lawhorn and Rachel Schomaker and Jonathan T. Rowell and Olav Rueppell Simple Comparative Analyses of Differentially Expressed Gene Lists May Overestimate Gene Overlap . . . . . . . 606--612 Markus Boenn ShRangeSim: Simulation of Single Nucleotide Polymorphism Clusters in Next-Generation Sequencing Data . . . . 613--622
Cenk Sahinalp Preface: Selected Articles from RECOMB 2017 . . . . . . . . . . . . . . . . . . 623--623 Ashok Rajaraman and Jian Ma Toward Recovering Allele-specific Cancer Genome Graphs . . . . . . . . . . . . . 624--636 Soyeon Ahn and Haris Vikalo aBayesQR: a Bayesian Method for Reconstruction of Viral Populations Characterized by Low Diversity . . . . . 637--648 Benedict Paten and Jordan M. Eizenga and Yohei M. Rosen and Adam M. Novak and Erik Garrison and Glenn Hickey Superbubbles, Ultrabubbles, and Cacti 649--663 David Haussler and Maciej Smuga-Otto and Jordan M. Eizenga and Benedict Paten and Adam M. Novak and Sergei Nikitin and Maria Zueva and Dmitrii Miagkov A Flow Procedure for Linearization of Genome Sequence Graphs . . . . . . . . . 664--676 Victoria Popic and Volodymyr Kuleshov and Michael Snyder and Serafim Batzoglou Fast Metagenomic Binning via Hashing and Bayesian Clustering . . . . . . . . . . 677--688 Simone Zaccaria and Mohammed El-Kebir and Gunnar W. Klau and Benjamin J. Raphael Phylogenetic Copy-Number Factorization of Multiple Tumor Samples . . . . . . . 689--708 Robert O. Ness and Karen Sachs and Parag Mallick and Olga Vitek A Bayesian Active Learning Experimental Design for Inferring Signaling Networks 709--725 Adegoke A. Ojewole and Jonathan D. Jou and Vance G. Fowler and Bruce R. Donald \em BBK* (Branch and Bound Over K*): a Provable and Efficient Ensemble-Based Protein Design Algorithm to Optimize Stability and Binding Affinity Over Large Sequence Spaces . . . . . . . . . 726--739 Jesper Jansson and Andrzej Lingas and Ramesh Rajaby and Wing-Kin Sung Determining the Consistency of Resolved Triplets and Fan Triplets . . . . . . . 740--754 Brad Solomon and Carl Kingsford Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees . . . . . . . . . . 755--765 Chirag Jain and Alexander Dilthey and Sergey Koren and Srinivas Aluru and Adam M. Phillippy A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases 766--779 Dan DeBlasio and John Kececioglu Adaptive Local Realignment of Protein Sequences . . . . . . . . . . . . . . . 780--793 Regev Schweiger and Eyal Fisher and Elior Rahmani and Liat Shenhav and Saharon Rosset and Eran Halperin Using Stochastic Approximation Techniques to Efficiently Construct Confidence Intervals for Heritability 794--808 Xiaoqian Wang and Jingwen Yan and Xiaohui Yao and Sungeun Kim and Kwangsik Nho and Shannon L. Risacher and Andrew J. Saykin and Li Shen and Heng Huang Longitudinal Genotype--Phenotype Association Study through Temporal Structure Auto-Learning Predictive Model 809--824 Guillaume Holley and Roland Wittler and Jens Stoye and Faraz Hach Dynamic Alignment-Free and Reference-Free Read Compression . . . . 825--836
Miguel A. Vega-Rodríguez and José M. Granado-Criado \em Preface to the Special Issue: Parallel Computing in Computational Biology: a Technological Point of View 837--840 Esteban Pérez-Wohlfeil and Oswaldo Trelles Precise and Parallel Pairwise Metagenomic Comparisons . . . . . . . . 841--849 Andreia Sofia Teixeira and Pedro T. Monteiro and João A. Carriço and Francisco C. Santos and Alexandre P. Francisco Large-Scale Simulations of Bacterial Populations Over Complex Networks . . . 850--861 Héctor Martínez and Sergio Barrachina and Maribel Castillo and Enrique S. Quintana-Ortí and Jordi Rambla de Argila and Xavier Farré and Arcadi Navarro FaST-LMM for Two-Way Epistasis Tests on High-Performance Clusters . . . . . . . 862--870 Marek Nowicki and Davit Bzhalava and Piotr Ba\la Massively Parallel Implementation of Sequence Alignment with Basic Local Alignment Search Tool Using Parallel Computing in Java Library . . . . . . . 871--881 Juan José Escobar and Julio Ortega and Antonio Francisco Díaz and Jesús González and Miguel Damas A Power--Performance Perspective to Multiobjective Electroencephalogram Feature Selection on Heterogeneous Parallel Platforms . . . . . . . . . . . 882--893 Jordi Lladós and Fernando Cores and Fernando Guirado Scalable Consistency in T-Coffee Through Apache Spark and Cassandra Database . . 894--906 Jian-Xin Wen and Xiao-Qin Li and Yu Chang Signature Gene Identification of Cancer Occurrence and Pattern Recognition . . . 907--916 Elise Rosati and Morgan Madec and Jean-Baptiste Kammerer and Luc Hébrard and Christophe Lallement and Jacques Haiech Efficient Modeling and Simulation of Space-Dependent Biological Systems . . . 917--933 Fengqian Pang and Heng Li and Yonggang Shi and Zhiwen Liu Computational Analysis of Cell Dynamics in Videos with Hierarchical-Pooled Deep-Convolutional Features . . . . . . 934--953 Tatsuhiko Naito Human Splice-Site Prediction with Deep Neural Networks . . . . . . . . . . . . 954--961
Jian Zhao and Jiasong Wang and Hongmei Jiang Detecting Periodicities in Eukaryotic Genomes by Ramanujan Fourier Transform 963--975 Tsukasa Fukunaga and Michiaki Hamada A Novel Method for Assessing the Statistical Significance of RNA-RNA Interactions Between Two Long RNAs . . . 976--986 Yoonji Kim and Jaejik Kim Estimation of Dynamic Systems for Gene Regulatory Networks from Dependent Time-Course Data . . . . . . . . . . . . 987--996 Bandana Kumari and Ravindra Kumar and Manish Kumar Prediction of Rare Palmitoylation Events in Proteins . . . . . . . . . . . . . . 997--1008 Álvaro Rubio-Largo and Mauro Castelli and Leonardo Vanneschi and Miguel A. Vega-Rodríguez A Parallel Multiobjective Metaheuristic for Multiple Sequence Alignment . . . . 1009--1022 Komlan Atitey and Pavel Loskot and Paul Rees Determining the Transcription Rates Yielding Steady-State Production of mRNA in the \bionameLac Genetic Switch of \bionameEscherichia coli . . . . . . . . 1023--1039 Nicholas B. Larson and Chen Wang and Jie Na and Ross A. Rowsey and William Edward Highsmith and Nicole L. Hoppman and Jean-Pierre Kocher and Eric W. Klee Improving Single-Nucleotide Polymorphism-Based Fetal Fraction Estimation of Maternal Plasma Circulating Cell-Free DNA Using Bayesian Hierarchical Models . . . . . . . . . . 1040--1049 Xinrui Huang and Sha Li and Song Gao Applying a Modified Wavelet Shrinkage Filter to Improve Cryo-Electron Microscopy Imaging . . . . . . . . . . . 1050--1058 Joonyeon Park and Myeongji Cho and Hyeon S. Son Simulation Model of Bacterial Resistance to Antibiotics Using Individual-Based Modeling . . . . . . . . . . . . . . . . 1059--1070
Yu Bao and Morihiro Hayashida and Pengyu Liu and Masayuki Ishitsuka and Jose C. Nacher and Tatsuya Akutsu Analysis of Critical and Redundant Vertices in Controlling Directed Complex Networks Using Feedback Vertex Sets . . 1071--1090 Stefano Beretta and Mauro Castelli and Ivo Gonçalves and Ivan Kel and Valentina Giansanti and Ivan Merelli Improving eQTL Analysis Using a Machine Learning Approach for Data Integration: a Logistic Model Tree Solution . . . . . 1091--1105 Marek Palkowski and Wlodzimierz Bielecki Parallel Tiled Codes Implementing the Smith--Waterman Alignment Algorithm for Two and Three Sequences . . . . . . . . 1106--1119 \.Irfan Kösesoy and Murat Gök and Cemil Öz PROSES: a Web Server for Sequence-Based Protein Encoding . . . . . . . . . . . . 1120--1122 Shisheng Wang and Wen Zheng and Liqiang Hu and Meng Gong and Hao Yang MixProTool: a Powerful and Comprehensive Web Tool for Analyzing and Visualizing Multigroup Proteomics Data . . . . . . . 1123--1127 Jie Chen and Shirong Deng Detection of Copy Number Variation Regions Using the DNA-Sequencing Data from Multiple Profiles with Correlated Structure . . . . . . . . . . . . . . . 1128--1140 Jan Voges and Ali Fotouhi and Jörn Ostermann and Muhammed O\uguzhan Külekci A Two-Level Scheme for Quality Score Compression . . . . . . . . . . . . . . 1141--1151 Qie Liu and Min Liu and Wenfa Wu Strong/Weak Feature Recognition of Promoters Based on Position Weight Matrix and Ensemble Set-Valued Models 1152--1160 Xuedong Wang and Wenhui Shang and Yu Chang and Xiaoqin Li Methylation Signature Genes Identification of the Lung Squamous Cell Carcinoma Occurrence and Recognition Research . . . . . . . . . . . . . . . . 1161--1169
Yaron Orenstein and Yun William Yu and Bonnie Berger Joker de Bruijn: Covering $k$-Mers Using Joker Characters . . . . . . . . . . . . 1171--1178 Christopher Barrett and Qijun He and Fenix W. Huang and Christian M. Reidys An Efficient Dual Sampling Algorithm with Hamming Distance Filtration . . . . 1179--1192 Xinrui Zhou and Amihood Amir and Concettina Guerra and Gadi Landau and Jarek Rossignac EDoP Distance Between Sets of Incomplete Permutations: Application to Bacteria Classification Based on Gene Order . . . 1193--1202 Nikita Alexeev and Max A. Alekseyev Combinatorial Scoring of Phylogenetic Trees and Networks Based on Homoplasy-Free Characters . . . . . . . 1203--1219 Theodore Alexandrov and Nina Golyandina and David Holloway and Alex Shlemov and Alexander Spirov Two-Exponential Models of Gene Expression Patterns for Noisy Experimental Data . . . . . . . . . . . 1220--1230 Siamak K. Sorooshyari and Matthew P. Taylor and H. Vincent Poor Probabilistic Modeling of Pseudorabies Virus Infection in a Neural Circuit . . 1231--1246 Ali Yousefian-Jazi and Jinwook Choi Sequential Integration of Fuzzy Clustering and Expectation Maximization for Transcription Factor Binding Site Identification . . . . . . . . . . . . . 1247--1256 Tiago Tambonis and Marcelo Boareto and Vitor B. P. Leite Differential Expression Analysis in RNA-seq Data Using a Geometric Approach 1257--1265 Hui Yang and Hao Lv and Hui Ding and Wei Chen and Hao Lin iRNA-2OM: a Sequence-Based Predictor for Identifying 2'-O-Methylation Sites in \bionameHomo sapiens . . . . . . . . . . 1266--1277 Dinko Osmankovic and Semir Doric and Naris Pojskic and Lada Lukic Bilela New Approach to Detect Coiled Coil and Leucine Zipper Motifs in Protein Sequences . . . . . . . . . . . . . . . 1278--1283
José M. J. Costa and Helcio R. B. Orlande and Viviane O. F. Lione and Antonio G. F. Lima and Tayná C. S. Cardoso and Leonardo A. B. Varón Simultaneous Model Selection and Model Calibration for the Proliferation of Tumor and Normal Cells During In Vitro Chemotherapy Experiments . . . . . . . . 1285--1300 Vijaya Raghavan Rangamaran and Bharathram Uppili and Dharani Gopal and Kirubagaran Ramalingam EasyQC: Tool with Interactive User Interface for Efficient Next-Generation Sequencing Data Quality Control . . . . 1301--1311 Xiaoping Yan and Yu Huang and Jiabin Wu Identify Cross Talk Between Circadian Rhythm and Coronary Heart Disease by Multiple Correlation Analysis . . . . . 1312--1327 Caio Santiago and Vivian Pereira and Luciano Digiampietri Homology Detection Using Multilayer Maximum Clustering Coefficient . . . . . 1328--1338 Matthias Werner and Pascal Fieth and Alexander Hartmann Large-Deviation Properties of Sequence Alignment of Correlated Sequences . . . 1339--1346 Hsin-Yao Wang and Shih-Cheng Chang and Wan-Ying Lin and Chun-Hsien Chen and Szu-Hsien Chiang and Kai-Yao Huang and Bo-Yu Chu and Jang-Jih Lu and Tzong-Yi Lee Machine Learning-Based Method for Obesity Risk Evaluation Using Single-Nucleotide Polymorphisms Derived from Next-Generation Sequencing . . . . 1347--1360 Ming Yang and Louis Z. Yang Determining a Reasonable Range of Relative Numerical Tolerance Values for Simulating Deterministic Models of Biochemical Reactions . . . . . . . . . 1361--1364 Snehalika Lall and Debajyoti Sinha and Sanghamitra Bandyopadhyay and Debarka Sengupta Structure-Aware Principal Component Analysis for Single-Cell RNA-seq Data 1365--1373 Jeonifer M. Garren and Jaejik Kim Bootstrapping Time-Course Gene Expression Data for Gene Networks: Application to Gene Relevance Networks 1374--1384 Yue Liu and Shu-Lin Wang and Jun-Feng Zhang Prediction of Microbe--Disease Associations by Graph Regularized Non-Negative Matrix Factorization . . . 1385--1394
Yanshen Yang and Jeffrey A. Robertson and Zhen Guo and Jake Martinez and Christy Coghlan and Lenwood S. Heath MCAT: Motif Combining and Association Tool . . . . . . . . . . . . . . . . . . 1--15 Defne Surujon and Yann Ponty and Peter Clote Small-World Networks and RNA Secondary Structures . . . . . . . . . . . . . . . 16--26 Eliran Avni and Sagi Snir A New Quartet-Based Statistical Method for Comparing Sets of Gene Trees Is Developed Using a Generalized Hoeffding Inequality . . . . . . . . . . . . . . . 27--37 Dat Duong and Wasi Uddin Ahmad and Eleazar Eskin and Kai-Wei Chang and Jingyi Jessica Li Word and Sentence Embedding Tools to Measure Semantic Similarity of Gene Ontology Terms by Their Definitions . . 38--52 Vaddadi Naga Sai Kavya and Kshitij Tayal and Rajgopal Srinivasan and Naveen Sivadasan Sequence Alignment on Directed Graphs 53--67 Eduard Fomin A Simple Approach to the Reconstruction of a Set of Points from the Multiset of Pairwise Distances in $ n^2 $ Steps for the Sequencing Problem: III. Noise Inputs for the Beltway Case . . . . . . 68--75 Daniel Mellem and Frank Fischer and Sören Jaspers and Horst Wenck and Michael Rübhausen Mitochondrial Morphologies Driven by Energy-Consuming Cell Sites in a Spatially and Time-Resolved Quality Model . . . . . . . . . . . . . . . . . 76--85 Shih-Chiang Lo and Feng-You Liu and Wun-Sin Jhang and Che-Chi Shu The Insight into Protein-Ligand Interactions, a Novel Way of Buffering Protein Noise in Gene Expression . . . . 86--95 Michael Ta and Changchuan Yin and Gary Lee Smith and Wenbo Xu A Workflow to Improve Variant Calling Accuracy in Molecular Barcoded Sequencing Reads . . . . . . . . . . . . 96--103
Gopinath Samykannu and Princy Vijayababu and Christian Bharathi Antonyraj and Perumal Perumal and Sundarabaalaji Narayanan and Syed Ibrahim Basheer Ahamed and Jeyakumar Natarajan In Silico Characterization of B Cell and T Cell Epitopes for Subunit Vaccine Design of \bionameSalmonella typhi PgtE: a Molecular Dynamics Simulation Approach 105--116 Filip Zavadil Koká\vs and Véronique Bergougnoux and Mária Majeská \vCudejková SATrans: New Free Available Software for Annotation of Transcriptome and Functional Analysis of Differentially Expressed Genes . . . . . . . . . . . . 117--123 Vasily Ershov and Artem Tarasov and Alla Lapidus and Anton Korobeynikov IonHammer: Homopolymer-Space Hamming Clustering for IonTorrent Read Error Correction . . . . . . . . . . . . . . . 124--127 Sihai Yang and Xianhua Han and Yenwei Chen Three-Dimensional Embryonic Image Segmentation and Registration Based on Shape Index and Ellipsoid-Fitting Method 128--142 Changchuan Yin Encoding and Decoding DNA Sequences by Integer Chaos Game Representation . . . 143--151 Lisa Uechi and David J. Galas and Nikita A. Sakhanenko Multivariate Analysis of Data Sets with Missing Values: an Information Theory-Based Reliability Function . . . 152--171
Christopher Barrett and Qijun He and Fenix W. Huang and Christian M. Reidys A Boltzmann Sampler for $1$-Pairs with Double Filtration . . . . . . . . . . . 173--192 Xiaodong Wang and Lei Wang Computing Nonoverlapping Inversion Distance Between Two Strings in Linear Average Time . . . . . . . . . . . . . . 193--201 Heewon Park and Makoto Yamada and Seiya Imoto and Satoru Miyano Robust Sample-Specific Stability Selection with Effective Error Control 202--217 Xiaodan Mao and Yichen Xu and Zhenran Jiang HColonDB: a Database for Human Colon Cancer Research . . . . . . . . . . . . 218--224 bBiju Viswanath and Naren P. Rao and Janardhanan C. Narayanaswamy and Palanimuthu T. Sivakumar and Arunkandaswamy and Muralidharankesavan and Urvakhsh-Meherwan Mehta and Ganesanvenkatasubramanian and John P. John and Odity Mukherjee and Meerapurushottam and Ramakrishnankannan and Bhupesh Mehta and Thennarasukandavel and B. Binukumar and Jitendersaini and Deepak Jayarajan and A. Shyamsundar and Sydney Moirangthem and Kumar G. Vijay and Jagadishathirthalli and Prabha S. Chandra and Bangalore N. Gangadhar and Pratima Murthy and Mitradas M. Panicker and Upinder S. Bhalla and Sumantrachattarji and Vivekbenegal and Mathew Varghese and Janardhan Y. C. Reddy and Padinjat Raghu and Mahendrarao and Sanjeev Jain INDEX-db: The Indian Exome Reference Database (Phase I) . . . . . . . . . . . 225--234 Monika Piwowar and Tomasz Ku\laga Directional Association Measurement in Contingency Tables: Genomic Case . . . . 235--240 Yuandi Wang and Qingmei Wen and Zhigang Zhou and Nanjun Yan Cell Modeling Based on Bubbles with Weighted Membranes . . . . . . . . . . . 241--265 Roberto Solar and Victor Sepulveda and Alonso Inostrosa-Psijas and Oscar Rojas and Veronica Gil-Costa and Mauricio Marin A Service-Oriented Platform for Approximate Bayesian Computation in Population Genetics . . . . . . . . . . 266--279 Baekdoo Kim and Thahmina Ali and Changsu Dong and Carlos Lijeron and Raja Mazumder and Claudia Wultsch and Konstantinos Krampis \em miCloud: a Plug-n-Play, Extensible, On-Premises Bioinformatics Cloud for Seamless Execution of Complex Next-Generation Sequencing Data Analysis Pipelines . . . . . . . . . . . . . . . 280--284 Andreas D. M. Gunawan and Hongwei Yan and Louxin Zhang Compression of Phylogenetic Networks and Algorithm for the Tree Containment Problem . . . . . . . . . . . . . . . . 285--294
Soonweng Cho and Hyun-Seok Kim and Martha A. Zeiger and Christopher B. Umbricht and Leslie M. Cope Measuring DNA Copy Number Variation Using High-Density Methylation Microarrays . . . . . . . . . . . . . . 295--304 Rafa\l Zaborowski and Bartek Wilczy\'nski BPscore: an Effective Metric for Meaningful Comparisons of Structural Chromosome Segmentations . . . . . . . . 305--314 Yi Wang and Kun Tian and Stephen S.-T. Yau Protein Sequence Classification Using Natural Vector and Convex Hull Method 315--321 Paulina Urban and Vahid Rezaei and Grzegorz Bokota and Micha\l Denkiewicz and Subhadip Basu and Dariusz Plewczy\'nski Dendritic Spines Taxonomy: The Functional and Structural Classification $ \bullet $ Time-Dependent Probabilistic Model of Neuronal Activation . . . . . . 322--335 Kyu Min Lee and Minhyeok Lee and Junhee Seok and Sung Won Han Regression-Based Network Estimation for High-Dimensional Genetic Data . . . . . 336--349 Yusong Ye and Zhuoqin Yang and Jinzhi Lei Stochastic Telomere Shortening and the Route to Limitless Replicative Potential 350--363 Yuewen Qi and Haowen Qi and Zeyuan Liu and Peiyuan He and Bingqing Li Bioinformatics Analysis of Key Genes and Pathways in Colorectal Cancer . . . . . 364--375 Bruno César Feltes and Eduardo Bassani Chandelier and Bruno Iochins Grisci and Márcio Dorn CuMiDa: an Extensively Curated Microarray Database for Benchmarking and Testing of Machine Learning Approaches in Cancer Research . . . . . . . . . . . 376--386 Huan Liu and Li Liu and Hong Zhu The Role of Significantly Deregulated MicroRNAs in Recurrent Cervical Cancer Based on Bioinformatic Analysis of the Cancer Genome Atlas Data . . . . . . . . 387--395 Luigi Marongiu and Heike Allgayer Mingle: a Command Line Utility for Merging Multi-fasta Files . . . . . . . 396--404
Prachi Kothiyal and Wendy S. W. Wong and Dale L. Bodian and John E. Niederhuber Mendelian Inconsistent Signatures from 1314 Ancestrally Diverse Family Trios Distinguish Biological Variation from Sequencing Error . . . . . . . . . . . . 405--419 Andre Rodrigues Oliveira and Klairton Lima Brito and Zanoni Dias and Ulisses Dias Sorting by Weighted Reversals and Transpositions . . . . . . . . . . . . . 420--431 Jaegyoon Ahn and Junhyeok Choi and Harrim Kim and Jibum Kim RN$^+$: a Novel Biclustering Algorithm for Analysis of Gene Expression Data Using Protein--Protein Interaction Network . . . . . . . . . . . . . . . . 432--441 Guilherme Torres Castro and Luis Enrique Zárate and Cristiane Neri Nobre and Henrique Cota Freitas A Fast Parallel $K$-Modes Algorithm for Clustering Nucleotide Sequences to Predict Translation Initiation Sites . . 442--456 Guru Raj Rao Ravi and Jayashree Biswal and Sureka Kanagarajan and Jeyaraman Jeyakanthan Exploration of N5-CAIR Mutase Novel Inhibitors from \bionamePyrococcus horikoshii OT3: a Computational Study 457--472 Xi Hu and Wenling Yi and Ling Jiang and Sijia Wu and Yan Zhang and Jianqiang Du and Tianyou Ma and Tong Wang and Xiaoming Wu Classification of Metaphase Chromosomes Using Deep Convolutional Neural Network 473--484 Zide Chen and Jiehua Chen and Xuan Huang and Yi Wu and Kuiyuan Huang and Weikang Xu and Linqing Xie and Xiaoyong Zhang and Hongyan Liu Identification of Potential Key Genes for Hepatitis B Virus-Associated Hepatocellular Carcinoma by Bioinformatics Analysis . . . . . . . . 485--494 Wei Liang and Yuxiao Yang and Yusi Fang and Zhongying Zhao and Jie Hu Bayesian Detection of Abnormal Asynchrony of Division Between Sister Cells in Mutant \bionameCaenorhabditis elegans Embryos . . . . . . . . . . . . 495--505
Abdoulaye Baniré Diallo and Engelbert Mephu Nguifo and Wajdi Dhifli and Elham Azizi and Sandhya Prabhakaran and Wesley Tansey Selected Papers from the Workshop on Computational Biology: Joint with the International Joint Conference on Artificial Intelligence and the International Conference on Machine Learning, 2018 . . . . . . . . . . . . . 507--508 Romain Menegaux and Jean-Philippe Vert Continuous Embeddings of DNA Sequencing Reads and Application to Metagenomics 509--518 Dylan Lebatteux and Amine M. Remita and Abdoulaye Baniré Diallo Toward an Alignment-Free Method for Feature Extraction and Accurate Classification of Viral Sequences . . . 519--535 Andreea Deac and Petar Veli\vckovi\'c and Pietro Sormanni Attentive Cross-Modal Paratope Prediction . . . . . . . . . . . . . . . 536--545 Antonio Moretti and Andrew Stirn and Gabriel Marks and Itsik Pe'er Autoencoding Topographic Factors . . . . 546--560 Rabie Saidi and Wajdi Dhifli and Mondher Maddouri and Engelbert Mephu Nguifo Efficiently Mining Recurrent Substructures from Protein Three-Dimensional Structure Graphs . . . 561--571 Hamid Eghbal-Zadeh and Lukas Fischer and Niko Popitsch and Florian Kromp and Sabine Taschner-Mandl and Teresa Gerber and Eva Bozsaky and Peter F. Ambros and Inge M. Ambros and Gerhard Widmer and Bernhard A. Moser DeepSNP: an End-to-End Deep Neural Network with Attention-Based Localization for Breakpoint Detection in Single-Nucleotide Polymorphism Array Genomic Data . . . . . . . . . . . . . . 572--596 Brenden K. Petersen and Jiachen Yang and Will S. Grathwohl and Chase Cockrell and Claudio Santiago and Gary An and Daniel M. Faissol Deep Reinforcement Learning and Simulation as a Path Toward Precision Medicine . . . . . . . . . . . . . . . . 597--604 Qingyu Chen and Xiuzhen Zhang and Yu Wan and Justin Zobel and Karin Verspoor Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions . . . . . . . . . . . . . . . 605--617 Alexandre Bazin and Didier Debroas and Engelbert Mephu Nguifo A De Novo Robust Clustering Approach for Amplicon-Based Sequence Data . . . . . . 618--624
Guest Editor Ute Deichmann \em Special Issue: Genomic Regulation: Experiments, Computational Modeling, and Philosophy . . . . . . . . . . . . . . . 625--628 Michel Morange A Time to Model and a Time to Experiment 629--636 Ute Deichmann From Gregor Mendel to Eric Davidson: Mathematical Models and Basic Principles in Biology . . . . . . . . . . . . . . . 637--652 Sorin Istrail Eric Davidson's Regulatory Genome for Computer Science: Causality, Logic, and Proof Principles of the Genomic \em cis-Regulatory Code . . . . . . . . . . 653--684 Sorin Istrail and Isabelle S. Peter How Does the Regulatory Genome Work? . . 685--695 James Briscoe Understanding Pattern Formation in Embryos: Experiment, Theory, and Simulation . . . . . . . . . . . . . . . 696--702 Ellen V. Rothenberg Causal Gene Regulatory Network Modeling and Genomics: Second-Generation Challenges . . . . . . . . . . . . . . . 703--718 Aldo Ciau-Uitz and Roger Patient Gene Regulatory Networks Governing the Generation and Regeneration of Blood . . 719--725 Anthony S. Travis Chemical Modeling: From Paul Ehrlich's Dyes to $ \beta $-Blockers --- A Brief History . . . . . . . . . . . . . . . . 726--734 Douglas H. Erwin Prospects for a General Theory of Evolutionary Novelty . . . . . . . . . . 735--744 Jonathan Engel and Isana Veksler-Lublinsky and Michal Ziv-Ukelson Constrained Gene Block Discovery and Its Application to Prokaryotic Genomes . . . 745--766
Zhipeng Cai and Pavel Skums and Alexander Zelikovsky Preface: 14th International Symposium on Bioinformatics Research and Applications (ISBRA 2018) . . . . . . . . . . . . . . 767--768 Huiyu Li and Sheng-Jun Li and Junliang Shang and Jin-Xing Liu and Chun-Hou Zheng A Dynamic Scale-Free Network Particle Swarm Optimization for Extracting Features on Multi-Omics Data . . . . . . 769--781 Krzysztof Gogolewski and Maciej Sykulski and Neo Christopher Chung and Anna Gambin Truncated Robust Principal Component Analysis and Noise Reduction for Single Cell RNA Sequencing Data . . . . . . . . 782--793 Ben Yohay and Sagi Snir Extending the Evolvability Model to the Prokaryotic World: Simulations and Results on Real Data . . . . . . . . . . 794--805 Sagi Snir Bounds on Identification of Genome Evolution Pacemakers . . . . . . . . . . 806--821 Marmar Moussa and Ion I. M\uandoiu Locality Sensitive Imputation for Single Cell RNA-Seq Data . . . . . . . . . . . 822--835 Qingfeng Chen and Canshang Deng and Wei Lan and Zhixian Liu and Ruiqing Zheng and Jin Liu and Jianxin Wang Identifying Interactions Between Kinases and Substrates Based on Protein--Protein Interaction Network . . . . . . . . . . 836--845 Wolfgang Kopp and Martin Vingron DNA Motif Match Statistics Without Poisson Approximation . . . . . . . . . 846--865 Juan Pablo Acosta and Silvia Restrepo and Juan David Henao and Liliana López-Kleine Multivariate Method for Inferential Identification of Differentially Expressed Genes in Gene Expression Experiments . . . . . . . . . . . . . . 866--874 Dahye Chung and Kaiyuan Zhang and Jihoon Yang Method for Identifying Cancer-Related Genes Using Gene Similarity-Based Collaborative Filtering . . . . . . . . 875--881 Shahid Hussain and Javed Ferzund and Raza Ul-Haq Prediction of Drug Target Sensitivity in Cancer Cell Lines Using Apache Spark . . 882--889
Carlos Martín-Vide and Miguel A. Vega-Rodríguez Preface . . . . . . . . . . . . . . . . 891--892 Jesper Jansson and Ramesh Rajaby and Wing-Kin Sung An Efficient Algorithm for the Rooted Triplet Distance Between Galled Trees 893--907 Gabriel H. G. Silva and Edans F. O. Sandes and George Teodoro and Alba C. M. A. Melo Using Multiple Fickett Bands to Accelerate Biological Sequence Comparisons . . . . . . . . . . . . . . 908--922 Shuto Hayashi and Takuya Moriyama and Rui Yamaguchi and Shinichi Mizuno and Mitsuhiro Komura and Satoru Miyano and Hidewaki Nakagawa and Seiya Imoto ALPHLARD-NT: Bayesian Method for Human Leukocyte Antigen Genotyping and Mutation Calling through Simultaneous Analysis of Normal and Tumor Whole-Genome Sequence Data . . . . . . . 923--937 Xiaodong Wang and Lei Wang and Daxin Zhu Efficient Computation of Longest Common Subsequences with Multiple Substring Inclusive Constraints . . . . . . . . . 938--947 Paola Bonizzoni and Gianluca Della Vedova and Yuri Pirola and Marco Previtali and Raffaella Rizzi Multithread Multistring Burrows--Wheeler Transform and Longest Common Prefix Array . . . . . . . . . . . . . . . . . 948--961 Muslum Yildiz and Abdulkadir Kocak Molecular Dynamics Studies of Histo-Blood Group Antigen Blocking Human Immunoglobulin A Antibody and Escape Mechanism in Noroviruses Upon Mutation 962--974 Yushuang Yang and Wei Yang and Ling Jin The Role of Long Non-coding RNA Prostate Cancer-Associated Transcript 1 in Prostate Cancer . . . . . . . . . . . . 975--984 Mohammad S. Rahman and Gholamreza Haffari Analyzing Tumor Heterogeneity by Incorporating Long-Range Mutational Influences and Multiple Sample Data into Heterogeneity Factorial Hidden Markov Model . . . . . . . . . . . . . . . . . 985--1002 Jacques Demongeot and Hervé Seligmann Bias for 3$^\prime $-Dominant Codon Directional Asymmetry in Theoretical Minimal RNA Rings . . . . . . . . . . . 1003--1012 Fangfang Ge and Yi Wang and Huayang Li and Rui Zhang and Xiaotong Wang and Qingyun Li and Zhenchang Liang and Long Yang Plant-GQ: an Integrative Database of G-Quadruplex in Plant . . . . . . . . . 1013--1019 Zhicheng Li and Shijian Li and Xian Wei and Qing Zhao Scaled Alternating Steepest Descent Algorithm Applied for Protein Structure Determination from Nuclear Magnetic Resonance Data . . . . . . . . . . . . . 1020--1029 Guo Mao and Shu-Lin Wang and Wei Zhang Prediction of Potential Associations Between MicroRNA and Disease Based on Bayesian Probabilistic Matrix Factorization Model . . . . . . . . . . 1030--1039
Sergey A. Solodskikh and Alexey S. Velikorondy and Vasily N. Popov Predictive Estimates of Risks Associated with Type 2 Diabetes Mellitus on the Basis of Biochemical Biomarkers and Derived Time-Dependent Parameters . . . 1041--1049 Louis Z. Yang and Ming Yang Modeling Biological Oscillations: Integration of Short Reaction Pauses into a Stationary Model of a Negative Feedback Loop Generates Sustained Long Oscillations . . . . . . . . . . . . . . 1050--1066 Yan Ye and Chunde Bao and Wei Fan Overexpression of miR-101 May Target DUSP1 to Promote the Cartilage Degradation in Rheumatoid Arthritis . . 1067--1079 Qi Li and Zhengqiang Luo Identification of Candidate Genes for Skeletal Muscle Injury Prevention in Two Different Types . . . . . . . . . . . . 1080--1089 Qi Li and Zhengqiang Luo Transcriptional Regulatory Network Analysis to Reveal the Key Genes Involved in Skeletal Muscle Injury . . . 1090--1099 Neeraj Budhlakoti and Dwijesh Chandra Mishra and Anil Rai and S. B. Lal and Krishna Kumar Chaturvedi and Rajeev Ranjan Kumar A Comparative Study of Single-Trait and Multi-Trait Genomic Selection . . . . . 1100--1112 Xiao Liang and William Chad Young and Ling-Hong Hung and Adrian E. Raftery and Ka Yee Yeung Integration of Multiple Data Sources for Gene Network Inference Using Genetic Perturbation Data . . . . . . . . . . . 1113--1129 Chao Sun and Yifan Gu and Guoqing Chen and Yibao Du Bioinformatics Analysis of Stromal Molecular Signatures Associated with Breast and Prostate Cancer . . . . . . . 1130--1139 Liang Wang and Yuquan Pei and Shaolei Li and Shanyuan Zhang and Yue Yang Distinct Molecular Mechanisms Analysis of Three Lung Cancer Subtypes Based on Gene Expression Profiles . . . . . . . . 1140--1155 Fatima Ghrifi and Loubna Allam and Lakhlili Wiame and Azeddine Ibrahimi Curcumin-Synthetic Analogs Library Screening by Docking and Quantitative Structure--Activity Relationship Studies for AXL Tyrosine Kinase Inhibition in Cancers . . . . . . . . . . . . . . . . 1156--1167 Yudong Zhang and Wenxiang Wu and Hao Qu Integrated Analysis of the Gene Expression Changes During Colorectal Cancer Progression by Bioinformatic Methods . . . . . . . . . . . . . . . . 1168--1176 Victor Hugo Urrutia-Baca and Ricardo Gomez-Flores and Myriam Angélica De La Garza-Ramos and Patricia Tamez-Guerra and Daniela Guadalupe Lucio-Sauceda and María Cristina Rodríguez-Padilla Immunoinformatics Approach to Design a Novel Epitope-Based Oral Vaccine Against \bionameHelicobacter pylori . . . . . . 1177--1190
Michael Rosenthal and Darshan Bryner and Fred Huffer and Shane Evans and Anuj Srivastava and Nicola Neretti Bayesian Estimation of Three-Dimensional Chromosomal Structure from Single-Cell Hi-C Data . . . . . . . . . . . . . . . 1191--1202 Yue Wu and Farhad Hormozdiari and Jong Wha J. Joo and Eleazar Eskin Improving Imputation Accuracy by Inferring Causal Variants in Genetic Studies . . . . . . . . . . . . . . . . 1203--1213 Luís Felipe I. Cunha and Fábio Protti Genome Rearrangements on Multigenomic Models: Applications of Graph Convexity Problems . . . . . . . . . . . . . . . . 1214--1222 Andre Rodrigues Oliveira and Klairton Lima Brito and Ulisses Dias and Zanoni Dias On the Complexity of Sorting by Reversals and Transpositions Problems 1223--1229 Chao-Kun Yan and Wen-Xiu Wang and Ge Zhang and Jian-Lin Wang and Ashutosh Patel BiRWDDA: a Novel Drug Repositioning Method Based on Multisimilarity Fusion 1230--1242 Chaoxuan Dong and Xiao-Yan Chen and Chao-Yi Dong Discerning Functional Connections in the Pulsed Neural Networks with the Dynamic Bayesian Network Structure Search Method Based on a Genetic Algorithm . . . . . . 1243--1252 Yulia M. Suvorova and Eugene V. Korotkov New Method for Potential Fusions Detection in Protein-Coding Sequences 1253--1261 Bao-Xinzi Liu and Guan-Jiang Huang and Hai-Bo Cheng Comprehensive Analysis of Core Genes and Potential Mechanisms in Rectal Cancer 1262--1277 Feng Li and Peiyuan Guo and Keqin Dong and Peng Guo and Haoyuan Wang and Xianqiang Lv Identification of Key Biomarkers and Potential Molecular Mechanisms in Renal Cell Carcinoma by Bioinformatics Analysis . . . . . . . . . . . . . . . . 1278--1295 Shangjie Ai and Guanfei Lin and Yong Bai and Xiande Liu and Linghua Piao QSAR Classification-Based Virtual Screening Followed by Molecular Docking Identification of Potential COX-2 Inhibitors in a Natural Product Library 1296--1315 Shunxin Zheng and Liuhong Yang and Yisong Dai and Lifang Jiang and Yi Wei and Hongwei Wen and Yingfang Xu Screening and Survival Analysis of Hub Genes in Gastric Cancer Based on Bioinformatics . . . . . . . . . . . . . 1316--1325 Yufang Li and Aoshen Wu and Gang Liu and Lei Liu A Review of Methods to Quantify the Genomic Similarity of Topological Associating Domains . . . . . . . . . . 1326--1338
Denis Kazakiewicz and Jürgen Claesen and Katarzyna Górczak and Dariusz Plewczynski and Tomasz Burzykowski A Multivariate Negative-Binomial Model with Random Effects for Differential Gene-Expression Analysis of Correlated mRNA Sequencing Data . . . . . . . . . . 1339--1348 David Toubiana and Rami Puzis and Avi Sadka and Eduardo Blumwald A Genetic Algorithm to Optimize Weighted Gene Co-Expression Network Analysis . . 1349--1366 Kexin Shen and Shujuan Zhang and Shurong Ma and Haishan Zhang Molecular Markers and Diagnostic Model Specific for Barrett's Esophagus . . . . 1367--1378 Yong Qiu and Ling-bing Meng and Chen-yi Di and Yu-hu Huo and Bo-chen Yao and Teng-jiao Zhang and Zhen Hua Exploration of the Differentially Expressed Long Noncoding RNAs and Genes of Morphine Tolerance via Bioinformatic Analysis . . . . . . . . . . . . . . . . 1379--1393 Jie Wu and Yijian Zhang and Maolan Li Identification of Methylation Markers and Differentially Expressed Genes with Prognostic Value in Breast Cancer . . . 1394--1408 Xi Jia and Qian Zhao and Yuanyuan Zhang and Yiping Dong and Li Lei and Ramone A. Williamson and Yutiantian Lei and Xinyue Tan and Dan Zhang and Jinsong Hu Identification of a Five-CpG Signature with Diagnostic Value in Thyroid Cancer 1409--1417 Hengxi Chen and Shuting Cheng and Chang Liu and Jing Fu and Wei Huang Bioinformatics Analysis of Differentially Expressed Genes, Methylated Genes, and miRNAs in Unexplained Recurrent Spontaneous Abortion . . . . . . . . . . . . . . . . 1418--1426 B. Sharan Sharma and Prabodha K. Swain and Ramtej J. Verma A Systematic Bioinformatics Approach to Motif-Based Analysis of Human Locus Control Regions . . . . . . . . . . . . 1427--1437 Xinxin Liu and Xinqiang Li Key Genes Involved in Diabetic Nephropathy Investigated by Microarray Analysis . . . . . . . . . . . . . . . . 1438--1447 Mingxiang Wen and Xiang Qu and Yanyan Zhu and Lingfang Tian and Zhongqin Shen and Xiulin Yang and Xianqing Shi Exploration of Novel Biomarkers in Vasculitis by Integrated Bioinfomatic Approaches . . . . . . . . . . . . . . . 1448--1457 Wilson Alberto Tárraga and Horacio Alberto Garda and Juan Domingo Toledo and Marina Cecilia Gonzalez Potential Inhibitors of the Activity of the Cholesterol-Ester Transfer Protein 1458--1469 Avinash Mishra and Megan Cross and Andreas Hofmann and Mark J. Coster and Abdul Karim and Abdul Sattar Identification of a Novel Scaffold for Inhibition of Dipeptidyl Peptidase-4 . . 1470--1486
Rupeng Zhang and Leifeng Lv and Wenrui Ban and Xiaoqian Dang and Chen Zhang Identification of Hub Genes in Duchenne Muscular Dystrophy: Evidence from Bioinformatic Analysis . . . . . . . . . 1--8 Yangchun Xu and Yan Mu and Ling Wang and Xuan Zhang Detailed Analysis of Molecular Mechanisms in Primary and Metastatic Melanoma . . . . . . . . . . . . . . . . 9--19 Yaron Ilan Advanced Tailored Randomness: a Novel Approach for Improving the Efficacy of Biological Systems . . . . . . . . . . . 20--29 Jing Zhao and Linlin Yin and Ling He The MicroRNA Landscapes Profiling Reveals Potential Signatures of Necrotizing Enterocolitis in Infants . . 30--39 Bao Yang and Keqin Dong and Peiyuan Guo and Peng Guo and Guo Jie and Guanhua Zhang and Tianke Li Identification of Key Biomarkers and Potential Molecular Mechanisms in Oral Squamous Cell Carcinoma by Bioinformatics Analysis . . . . . . . . 40--54 Yang-fan Zou and Ling-bing Meng and Qing-qing Wang and Zhao-kai He and Chen-hao Hu and Meng-jie Shan and Deng-yuan Wang and Xin Yu Identification and Functional Enrichment Analysis of Potential Diagnostic and Therapeutic Targets in Adamantinomatous Craniopharyngioma . . . . . . . . . . . 55--68 Mengwei Chen and Chengqi Kong and Zhiyuan Zheng and Yin Li Identification of Biomarkers Associated with Septic Cardiomyopathy Based on Bioinformatics Analyses . . . . . . . . 69--80 Guozhang Hu and Rui Wang and Bo Wei and Le Wang and Qi Yang and Daliang Kong and Chao Du Prognostic Markers Identification in Glioma by Gene Expression Profile Analysis . . . . . . . . . . . . . . . . 81--90 Partha Sarathi Mohanty and Sandeep Sharma and Farah Naaz and Dilip Kumar and Archana Raikwar and Shripad A. Patil Inhibition of \bionameMycobacterium tuberculosis tRNA-Ligases Using siRNA-Based Gene Silencing Method: a Computational Approach . . . . . . . . . 91--99 Shanshan Liu and Wenjuan Tian and Burong Li Integrative Bioinformatics Analysis Identifies NEK2 as a Potential Biomarker in Head and Neck Squamous Cell Carcinoma 100--108 Ke Shi and Meng-na Ge and Xiao-qiao Chen Coordinated DNA Methylation and Gene Expression Data for Identification of the Critical Genes Associated with Childhood Atopic Asthma . . . . . . . . 109--120 Zhenan Zhang and Yuqin Liu and Wei Wang and Yue Xing and Nanyang Jiang and Hongrui Zhang and Hanwen Zhang and Lei He and Wei Yue and Lianju Jiang and Kaili Wang Identification of Differentially Expressed Genes Associated with Lymph Node Tuberculosis by the Bioinformatic Analysis Based on a Microarray . . . . . 121--130
Zhipeng Cai and Pavel Skums and Alexander Zelikovsky Preface Special Issue: 15th International Symposium on Bioinformatics Research and Applications (ISBRA 2019) . . . . . . . . . . . . . . 131--132 Ariel Bruner and Roded Sharan A Robustness Analysis of Dynamic Boolean Models of Cellular Circuits . . . . . . 133--143 Filipe Gouveia and Inês Lynce and Pedro T. Monteiro Revision of Boolean Models of Regulatory Networks Using Stable State Observations 144--155 Klairton Lima Brito and Géraldine Jean and Guillaume Fertin and Andre Rodrigues Oliveira and Ulisses Dias and Zanoni Dias Sorting by Genome Rearrangements on Both Gene Order and Intergenic Sizes . . . . 156--174 Zhi-zhong Chen and Shohei Ueta and Jingyu Li and Lusheng Wang Computing a Consensus Phylogeny via Leaf Removal . . . . . . . . . . . . . . . . 175--188 Francesco Delfino and Yuri Porozov and Eugene Stepanov and Gaik Tamazian and Valentina Tozzini Evolutionary Switches Structural Transitions via Coarse-Grained Models 189--199 Lixin Liu and Haitao Jiang and Peiqiang Liu and Binhai Zhu and Daming Zhu Maximum Stacking Base Pairs: Hardness and Approximation by Nonlinear Linear Programming-Rounding . . . . . . . . . . 200--211 Zihao Wang and Jingrong Zhang and Weifang Gao and Zhiyong Liu and Xiaohua Wan and Fa Zhang A Consensus Framework of Distributed Multiple-Tilt Reconstruction in Electron Tomography . . . . . . . . . . . . . . . 212--222 Enrico Petrucci and Laurent Noé and Cinzia Pizzi and Matteo Comin Iterative Spaced Seed Hashing: Closing the Gap Between Spaced Seed Hashing and $k$-mer Hashing . . . . . . . . . . . . 223--233 Jelena Fiosina and Maksims Fiosins and Stefan Bonn Explainable Deep Learning for Augmentation of Small RNA Expression Profiles . . . . . . . . . . . . . . . . 234--247 Heta P. Desai and Anuja P. Parameshwaran and Rajshekhar Sunderraman and Michael Weeks Comparative Study Using Neural Networks for 16S Ribosomal Gene Classification 248--258 Charles E. Wimberley and Steffen Heber PeakPass: Automating ChIP-Seq Blacklist Creation . . . . . . . . . . . . . . . . 259--268 Jakob L. Andersen and Daniel Merkle and Peter S. Rasmussen Combining Graph Transformations and Semigroups for Isotopic Labeling Design 269--287 Ana A. Hernandez-lopez and Claudio Alberti and Marco Mattavelli Toward a Dynamic Threshold for Quality Score Distortion in Reference-Based Alignment . . . . . . . . . . . . . . . 288--300
Sorin Istrail Preface Special Issue: RECOMB 2018 . . . 301 Édouard Bonnet and Pawe\l Rz\ka\.zewski and Florian Sikora Designing RNA Secondary Structures Is Hard . . . . . . . . . . . . . . . . . . 302--316 Ali Ebrahimpour Boroojeny and Akash Shrestha and Ali Sharifi-Zarchi and Suzanne Renick Gallagher and S. Cenk Sahinalp and Hamidreza Chitsaz Graph Traversal Edit Distance and Extensions . . . . . . . . . . . . . . . 317--329 Shounak Chakraborty and Stefan Canzar and Tobias Marschall and Marcel H. Schulz Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data . . . 330--341 Franziska Görtler and Marian Schön and Jakob Simeth and Stefan Solbrig and Tilo Wettig and Peter J. Oefner and Rainer Spang and Michael Altenbuchinger Loss-Function Learning for Digital Tissue Deconvolution . . . . . . . . . . 342--355 Jan Hoinka and Yijie Wang and Teresa M. Przytycka AptaBlocks Online: a Web-Based Toolkit for the In Silico Design of Oligonucleotide Sticky Bridges . . . . . 356--360 Gary Larson and Jeffrey L. Thorne and Scott Schmidler Incorporating Nearest-Neighbor Site Dependence into Protein Evolution Models 361--375 Yaron Orenstein Reverse de Bruijn: Utilizing Reverse Peptide Synthesis to Cover All Amino Acid $k$-mers . . . . . . . . . . . . . 376--385 Marian Schön and Jakob Simeth and Paul Heinrich and Franziska Görtler and Stefan Solbrig and Tilo Wettig and Peter J. Oefner and Michael Altenbuchinger and Rainer Spang DTD: an R Package for Digital Tissue Deconvolution . . . . . . . . . . . . . 386--389 Antoine Soulé and Jean-Marc Steyaert and Jérôme Waldispühl A Nested $2$-Level Cross-Validation Ensemble Learning Pipeline Suggests a Negative Pressure Against Crosstalk snoRNA-mRNA Interactions in \em Saccharomyces cerevisiae . . . . . . . . 390--402 Yuriy Sverchkov and Yi-hsuan Ho and Audrey Gasch and Mark Craven Context-Specific Nested Effects Models 403--417 Yue Wu and Eleazar Eskin and Sriram Sankararaman A Unifying Framework for Imputing Summary Statistics in Genome-Wide Association Studies . . . . . . . . . . 418--428 Naomi Yamada and Prashant Kumar Kuntala and B. Franklin Pugh and Shaun Mahony ChExMix: a Method for Identifying and Classifying Protein--DNA Interaction Subtypes . . . . . . . . . . . . . . . . 429--435 Ali Ebrahimpour Boroojeny and Akash Shrestha and Ali Sharifi-zarchi and Suzanne Renick Gallagher and Süleyman Cenk Sahinalp and Hamidreza Chitsaz PyGTED: Python Application for Computing Graph Traversal Edit Distance . . . . . 436--439
Lenore J. Cowen Preface Special Issue: RECOMB 2019 . . . 441 Philipp Benner and Martin Vingron ModHMM: a Modular Supra-Bayesian Genome Segmentation Method . . . . . . . . . . 442--457 Boying Gong and Elizabeth Purdom MethCP: Differentially Methylated Region Detection with Change Point Models . . . 458--471 Kristoffer Sahlin and Paul Medvedev De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality Value-Based Algorithm . . . . . 472--484 Fatemeh Almodaresi and Prashant Pandey and Michael Ferdman and Rob Johnson and Rob Patro An Efficient, Scalable, and Exact Representation of High-Dimensional Color Information Enabled Using de Bruijn Graph Search . . . . . . . . . . . . . . 485--499 Alan Kuhnle and Taher Mun and Christina Boucher and Travis Gagie and Ben Langmead and Giovanni Manzini Efficient Construction of a Complete Index for Pan-Genomics Read Alignment 500--513 Taher Mun and Alan Kuhnle and Christina Boucher and Travis Gagie and Ben Langmead and Giovanni Manzini Matching Reads to Many Genomes with the $r$-Index . . . . . . . . . . . . . . . 514--518 Weihua Pan and Tao Jiang and Stefano Lonardi OMGS: Optical Map-Based Genome Scaffolding . . . . . . . . . . . . . . 519--533 Leonardo Pellegrina and Cinzia Pizzi and Fabio Vandin Fast Approximation of Frequent $k$-Mers and Applications to Metagenomics . . . . 534--549 Jonathan D. Jou and Graham T. Holt and Anna U. Lowegard and Bruce R. Donald Minimization-Aware Recursive $ K* $: a Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape . . . . . . . . . . . . 550--564 Haoyun Lei and Bochuan Lyu and E. Michael Gertz and Alejandro A. Schäffer and Xulian Shi and Kui Wu and Guibo Li and Liqin Xu and Yong Hou and Michael Dean and Russell Schwartz Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data . . . . . . . . . . . . 565--598 Joel Mefford and Danny Park and Zhili Zheng and Arthur Ko and Mika Ala-Korpela and Markku Laakso and Päivi Pajukanta and Jian Yang and John Witte and Noah Zaitlen Efficient Estimation and Applications of Cross-Validated Genetic Predictions to Polygenic Risk Scores and Linear Mixed Models . . . . . . . . . . . . . . . . . 599--612 Younhun Kim and Frederic Koehler and Ankur Moitra and Elchanan Mossel and Govind Ramnarayan How Many Subpopulations Is Too Many? Exponential Lower Bounds for Inferring Population Histories . . . . . . . . . . 613--625 Mikhail Karasikov and Harun Mustafa and Amir Joudaki and Sara Javadzadeh-no and Gunnar Rätsch and André Kahles Sparse Binary Relation Representations for Genome Graph Annotation . . . . . . 626--639 Chirag Jain and Haowen Zhang and Yu Gao and Srinivas Aluru On the Complexity of Sequence-to-Graph Alignment . . . . . . . . . . . . . . . 640--654 Lodewijk Brand and Xue Yang and Kai Liu and Saad Elbeleidy and Hua Wang and Hao Zhang and Feiping Nie Learning Robust Multilabel Sample Specific Distances for Identifying HIV-1 Drug Resistance . . . . . . . . . . . . 655--672 Anonymous \em Retraction of: Identification of Prognosis Biomarkers of Prostatic Cancer in a Cohort of 498 Patients from TCGA, by Chen Z, Hu H. (J Comput Biol Dec 2019: epub ahead of print; DOI: 10.1089/cmb.2019.0224) . . . . . . . . . 673
Yury Gusev and Svyatoslav Mazilov and Irina Volokhina and Mikhail Chumakov Agrobacterial, Single-Stranded DNA-Binding Protein VirE2 and Its Complexes . . . . . . . . . . . . . . . 675--682 Brenda Ivette Garcia-Maya and Nikolaos Limnios Identification of Words in Biological Sequences Under the Semi-Markov Hypothesis . . . . . . . . . . . . . . . 683--697 Lixia Zhang and Leonardo O. Rodrigues and Niven R. Narain and Viatcheslav R. Akmaev \em bAIcis: a Novel Bayesian Network Structural Learning Algorithm and Its Comprehensive Performance Evaluation Against Open-Source Software . . . . . . 698--708 Zhicheng Li and Shijian Li and Xian Wei and Xubiao Peng and Qing Zhao Recovering the Missing Regions in Crystal Structures from the Nuclear Magnetic Resonance Measurement Data Using Matrix Completion Method . . . . . 709--717 Jingwei Zhao and Le Wang and Daliang Kong and Guozhang Hu and Bo Wei Construction of Novel DNA Methylation-Based Prognostic Model to Predict Survival in Glioblastoma . . . . 718--728 Lei Li and Linhua Jiang and Sihua Peng Protein Network Analysis of the Fifth Chromosome of Zebrafish . . . . . . . . 729--737 Rahul Singh Jasrotia and Sarika Jaiswal and Pramod Kumar Yadav and Mustafa Raza and Mir Asif Iquebal and Anil Rai and Dinesh Kumar Genome-Wide Analysis of HSP70 Family Protein in \bionameVigna radiata and Coexpression Analysis Under Abiotic and Biotic Stress . . . . . . . . . . . . . 738--754 Lopamudra Dey and Anirban Mukhopadhyay A Graph-Based Approach for Finding the Dengue Infection Pathways in Humans Using Protein--Protein Interactions . . 755--768 Ying Lu and Qixiu Lu and Houlin Liu and Jixiang Yu and Chunlei Xin and Yingping Liu and Yanfang Liu and Linlin Fan Time-Series Expression Analysis of Epidermal Stem Cells from High Fat Diet Mice . . . . . . . . . . . . . . . . . . 769--778 Guochang Zhang and Juan Li and Hong Sun and Guanzheng Yang Screening for the Biomarkers Associated with Myocardial Infarction by Bioinformatics Analysis . . . . . . . . 779--785 Hanadi M. Baeissa and Frances M. G. Pearl Identifying the Impact of Inframe Insertions and Deletions on Protein Function in Cancer . . . . . . . . . . . 786--795 Jack Hanson and Kuldip K. Paliwal and Thomas Litfin and Yuedong Yang and Yaoqi Zhou Getting to Know Your Neighbor: Protein Structure Prediction Comes of Age with Contextual Machine Learning . . . . . . 796--814 Yangchun Xu and Ling Wang and Lanxiang Jiang and Xuan Zhang Novel MicroRNA Biomarkers, \em miR-142-5p, \em miR-550a, \em miR-1826, and \em miR-1201, Were Identified for Primary Melanoma . . . . . . . . . . . . 815--824 Xuedong Wang and Xiaoxi Wang and Xiaoqin Li and Yu Chang Identification of Specific Candidate Diagnostic Biomarkers for Lung Squamous Cell Carcinoma Based on Methylation . . 825--833 Xihai Wu and Yunhui Han and Fangmei Liu and Lihong Ruan Downregulations of miR-449a and miR-145-5p Act as Prognostic Biomarkers for Endometrial Cancer . . . . . . . . . 834--844
Sayanti Guha Majumdar and Anil Rai and Dwijesh C. Mishra Integrated Framework for Selection of Additive and Nonadditive Genetic Markers for Genomic Selection . . . . . . . . . 845--855 Tongchuan Zhang and Guodong Hu and Yuedong Yang and Jihua Wang and Yaoqi Zhou All-Atom Knowledge-Based Potential for RNA Structure Discrimination Based on the Distance-Scaled Finite Ideal-Gas Reference State . . . . . . . . . . . . 856--867 Sultan Alyami and Chun-Hsi Huang Nongreedy Unbalanced Huffman Tree Compressor for Single and Multifasta Files . . . . . . . . . . . . . . . . . 868--876 Ye Feng and Chunyu Shi and Dayu Wang and Xuefeng Wang and Zhi Chen Integrated Analysis of DNA Copy Number Changes and Gene Expression Identifies Key Genes in Gastric Cancer . . . . . . 877--887 Fan Yu and Zhong-Sen Le and Li-Hua Chen and Hong Qian and Bo Yu and Wen-Hua Chen Identification of Biomolecular Information in Rotenone-Induced Cellular Model of Parkinson's Disease by Public Microarray Data Analysis . . . . . . . . 888--903 Sha-Sha Ruan and Yi-Chen Xiao and Pei-Cheng He and Yi Wang and Tao Ma Identification of Potential Gene Signatures Related to Sleep Deprivation 904--913 Lujiao Mo and Guanhua Xu and Channi Wu and Kanda Pan and Ping Pan and Lingfeng Yu and Xiaoyuan Shen Key Regulatory Effect of Activated \em HIF-1$ \alpha $ /VEGFA Signaling Pathway in Systemic Capillary Leak Syndrome Confirmed by Bioinformatics Analysis . . . . . . . . . . . . . . . . 914--922 Xihua Dong and Xiaoou Yu and Hua Li and Hui Kang Identification of Marker Genes and Pathways in Patients with Primary Biliary Cholangitis . . . . . . . . . . 923--933 Chian Chen and Hsiuying Wang Logistic Regression Method for Ligand Discovery . . . . . . . . . . . . . . . 934--940 Nermin Jukan and David Zagor\vsek and Julija Lazarevi\vc and Irena Prelo\vznik Zupan and Nata\vsa Debeljak and Miha Mo\vskon ViDis: a Platform for Constructing and Sharing of Medical Algorithms . . . . . 941--947 Teng Zhao and Kun Qian and Yi Zhang High Expression of \em FGF5 Is an Independent Prognostic Factor for Poor Overall Survival and Relapse-Free Survival in Lung Adenocarcinoma . . . . 948--957 Fangping Jiang and Hong Fan and Lian Luo and Yun Li An Integrative Transcriptome Analysis Reveals Consistently Dysregulated Long Noncoding RNAs and Their Transcriptional Regulation Relationships in Heart Failure . . . . . . . . . . . . . . . . 958--964 Lianmei Bai and Yu Ren and Tianqing Cui Overexpression of \em CDCA5, \em KIF4A, \em TPX2, and \em FOXM1 Coregulated Cell Cycle and Promoted Hepatocellular Carcinoma Development . . . . . . . . . 965--974 Krishna Kanhaiya and Dwitiya Tyagi-Tiwari Identification of Drug Targets in Breast Cancer Metabolic Network . . . . . . . . 975--986 Ying Liu and Shenghua Xiong and Shiying Liu and Jie Chen and Hao Yang and Gang Liu and Gengmi Li Analysis of Gene Expression in Bladder Cancer: Possible Involvement of Mitosis and Complement and Coagulation Cascades Signaling Pathway . . . . . . . . . . . 987--998
Icaro Alves Pinto and Nelson José Freitas Da Silveira In Silico Identification of Potential Inhibitors of the Wnt Signaling Pathway in Human Breast Cancer . . . . . . . . . 999--1010 Aanchal Mongia and Debarka Sengupta and Angshul Majumdar deepMc: Deep Matrix Completion for Imputation of Single-Cell RNA-seq Data 1011--1019 Sai H. Sankara Subramanian and Karpaga Raja Sundari Balachandran and Vijaya Raghavan Rangamaran and Dharani Gopal RemeDB: Tool for Rapid Prediction of Enzymes Involved in Bioremediation from High-Throughput Metagenome Data Sets . . 1020--1029 Yifan Gu and Guoqing Chen and Yibao Du Screening of Prognosis-Related Genes in Primary Breast Carcinoma Using Genomic Expression Data . . . . . . . . . . . . 1030--1040 Weiqing Wang and Shaohua Wang and Xiao Chu and Hui Liu and Ming Xiang Predicting the Lung Squamous Cell Carcinoma Diagnosis and Prognosis Markers by Unique DNA Methylation and Gene Expression Profiles . . . . . . . . 1041--1054 Xiaochen Jia and Yehui Shi and Yuehong Zhu and Wenjing Meng and Lihong He and Yongsheng Jia and Zhongsheng Tong Integrated Analysis of mRNA--miRNA--lncRNA ceRNA Network in Human HR+/Her-2- Breast Cancer and Triple Negative Breast Cancer . . . . . 1055--1066 Yingxuan Tian and Min Yu and Li Sun and Linghua Liu and Jun Wang and Ke Hui and Qiaofeng Nan and Xinyu Nie and Yajuan Ren and Xiaoping Ren Distinct Patterns of mRNA and lncRNA Expression Differences Between Lung Squamous Cell Carcinoma and Adenocarcinoma . . . . . . . . . . . . . 1067--1078 Meng Zhang and Chen-Yi Di and Peng Guo and Ling-Bing Meng and Meng-Jie Shan and Yong Qiu and Pei-Yuan Guo and Ke-Qin Dong and Qi Xie and Qiang Wang Screening and Identification of Key Biomarkers in Pancreatic Cancer: Evidence from Bioinformatic Analysis . . 1079--1091 Tian Zeng and Can Chen and Pan Yang and Wenwei Zuo and Xiaoqing Liu and Yanling Zhang A Protective Role for RHOJ in NonSmall Cell Lung Cancer Based on Integrated Bioinformatics Analysis . . . . . . . . 1092--1103 Ruike Wang and Xia Du and Yaqin Zhi Screening of Critical Genes Involved in Metastasis and Prognosis of High-Grade Serous Ovarian Cancer by Gene Expression Profile Data . . . . . . . . . . . . . . 1104--1114 Xiaoguang Niu and Yongtao Xu and Ni Gao and Aiwu Li Weighted Gene Coexpression Network Analysis Reveals the Critical lncRNAs and mRNAs in Development of Hirschsprung's Disease . . . . . . . . . 1115--1129 Chao Deng and Timothy Daley and Peter Calabrese and Jie Ren and Andrew D. Smith Predicting the Number of Bases to Attain Sufficient Coverage in High-Throughput Sequencing Experiments . . . . . . . . . 1130--1143 Kumar Saurabh and Maxim Solovchuk and Tony Wen Hann Sheu Solution of Ion Channel Flow Using Immersed Boundary--Lattice Boltzmann Methods . . . . . . . . . . . . . . . . 1144--1156 Amir Asiaee and Zachary B. Abrams and Samantha Nakayiza and Deepa Sampath and Kevin R. Coombes Explaining Gene Expression Using Twenty-One MicroRNAs . . . . . . . . . . 1157--1170 Vitara Pungpapong and Min Zhang and Dabao Zhang Integrating Biological Knowledge Into Case--Control Analysis Through Iterated Conditional Modes/Medians Algorithm . . 1171--1179
Dan Deblasio and Kwanho Kim and Carl Kingsford More Accurate Transcript Assembly via Parameter Advising . . . . . . . . . . . 1181--1189 Trung Ngo Trong and Juha Mehtonen and Gerardo González and Roger Kramer and Ville Hautamäki and Merja Heinäniemi Semisupervised Generative Autoencoder for Single-Cell Data . . . . . . . . . . 1190--1203 Zhenghao Chen and Ilya Soifer and Hugo Hilton and Leeat Keren and Vladimir Jojic Modeling Multiplexed Images with \em Spatial--LDA Reveals Novel Tissue Microenvironments . . . . . . . . . . . 1204--1218 Brandon Carter and Maxwell Bileschi and Jamie Smith and Theo Sanderson and Drew Bryant and David Belanger and Lucy J. Colwell Critiquing Protein Family Classification Models Using Sufficient Input Subsets 1219--1231 Katarzyna Górczak and Jürgen Claesen and Tomasz Burzykowski A Conceptual Framework for Abundance Estimation of Genomic Targets in the Presence of Ambiguous Short Sequencing Reads . . . . . . . . . . . . . . . . . 1232--1247 Evaldo Bezerra Costa and Gabriel Pereira Silva and Marcello Goulart Teixeira An Approach to Parallel Algorithms for Long DNA Sequences Alignment on Manycore Architecture . . . . . . . . . . . . . . 1248--1252 El\.If Pala and Tuba Denkçeken Evaluation of miRNA Expression Profiles in Schizophrenia Using Principal-Component Analysis-Based Unsupervised Feature Extraction Method 1253--1263 Danni Cui and Yingying Liu and Gang Liu and Lei Liu A Multiple-Instance Learning-Based Convolutional Neural Network Model to Detect the \em IDH1 Mutation in the Histopathology Images of Glioma Tissues 1264--1272 Daniele Pepe and Jin Hwan Do Analyzing Apomorphine-Mediated Effects in a Cell Model for Parkinson's Disease with Partial Least Squares Structure Equation Modeling . . . . . . . . . . . 1273--1282 Stefano Pirr\`o and Filomena Spada and Emanuela Gadaleta and Federica Ferrentino and Graeme J. Thorn and Gianni Cesareni and Claude Chelala HiPPO and PANDA: Two Bioinformatics Tools to Support Analysis of Mass Cytometry Data . . . . . . . . . . . . . 1283--1294 Xin Duan and Kejun Wang and Jia Ke and Ping Lan and Feng Gao and Xiaojian Wu Multiomics-Based Colorectal Cancer Molecular Subtyping Using Local Scaling Network Fusion . . . . . . . . . . . . . 1295--1302 Ruochen Cong and Jushun Yang and Jie Zhou and Jianhua Shi and Yihua Zhu and Jianfeng Zhu and Jing Xiao and Ping Wang and Ying He and Bosheng He The Potential Role of Protein Tyrosine Phosphatase, Receptor Type C (CD45) in the Intestinal Ischemia--Reperfusion Injury . . . . . . . . . . . . . . . . . 1303--1312 A. K. M. Firoj Mahmud and Doo Yang and Per Stenberg and Ilya Ioshikhes and Soumyadeep Nandi Exploring a \bionameDrosophila Transcription Factor Interaction Network to Identify Cis-Regulatory Modules . . . 1313--1328 Chunling Xu and Huayi Lu and Fuqiang Li and Guanfang Su Protein Expression Profile on Differentiation of Bone Marrow Mesenchymal Stem Cells into Retinal Ganglion-Like Cells . . . . . . . . . . 1329--1336
Mehmet Eren Ahsen and Robert Vogel and Gustavo A. Stolovitzky \pkgR/PY-SUMMA: an R/Python Package for Unsupervised Ensemble Learning for Binary Classification Problems in Bioinformatics . . . . . . . . . . . . . 1337--1340 Zongjiang Fan and Wanqiu Zhao and Shengning Fan and Chunxiao Li and Jing Qiao and Yongqing Xu Identification of Potential Biomarkers for Intervertebral Disc Degeneration Using the Genome-Wide Expression Analysis . . . . . . . . . . . . . . . . 1341--1349 Jianye Fan and Shoubin Dong and Bo Wang Variant-Kudu: an Efficient Tool kit Leveraging Distributed Bitmap Index for Analysis of Massive Genetic Variation Datasets . . . . . . . . . . . . . . . . 1350--1360 Amirhossein Karami and Afshin Fayyaz Movaghar and Sabine Mercier and Louis Ferre New Approximate Statistical Significance of Gapped Alignments Based on the Greedy Extension Model . . . . . . . . . . . . 1361--1372 Yue Wang and Andrey Minarsky and Robert Penner and Christophe Soulé and Nadya Morozova Model of Morphogenesis . . . . . . . . . 1373--1383 Haithem Aouabed and Rodrigo SantamaríA and Mourad Elloumi VisBicluster: a Matrix-Based Bicluster Visualization of Expression Data . . . . 1384--1396 Xiaoxia Chen and Hao Li and Lichao Tian and Qinwei Li and Jinxiang Luo and Yongqiang Zhang Analysis of the Physicochemical Properties of Acaricides Based on Lipinski's Rule of Five . . . . . . . . 1397--1406 Fahad Alqahtani and Ion I. M\uandoiu Statistical Mitogenome Assembly with RepeaTs . . . . . . . . . . . . . . . . 1407--1421 Kohei Yamada and Zhi-zhong Chen and Lusheng Wang Improved Practical Algorithms for Rooted Subtree Prune and Regraft (rSPR) Distance and Hybridization Number . . . 1422--1432 Yu Shi and Shan Zhu and Jianxin Yang and Minghai Shao and Wenxiu Ding and Wanrong Jiang and Xinchen Sun and Ninghua Yao Investigation of Potential Mechanisms Associated with Non-small Cell Lung Cancer . . . . . . . . . . . . . . . . . 1433--1442 Feiqi Wang and Tatsuya Akutsu and Tomoya Mori Comparison of Pseudoknotted RNA Secondary Structures by Topological Centroid Identification and Tree Edit Distance . . . . . . . . . . . . . . . . 1443--1451 Shih-Chiang Lo and Chao-Xuan You and Che-Chi Shu A Practicable Method of Tuning the Noise Intensity at Protein Level . . . . . . . 1452--1460 Lloyd T. Elliott Kinship Solutions for Partially Observed Multiphenotype Data . . . . . . . . . . 1461--1470 Paulina Urban and Vahid Rezaei Tabar and Micha\l Denkiewicz and Grzegorz Bokota and Nirmal Das and Subhadip Basu and Dariusz Plewczynski The Mixture of Autoregressive Hidden Markov Models of Morphology for Dentritic Spines During Activation Process . . . . . . . . . . . . . . . . 1471--1485 Weina Zhang and Yilun Zhang Integrated Survival Analysis of mRNA and microRNA Signature of Patients with Breast Cancer Based on Cox Model . . . . 1486--1494
Robert C. Penner Backbone Free Energy Estimator Applied to Viral Glycoproteins . . . . . . . . . 1495--1508 Yier Qiu and Guowen Lu and Yingjie Wu Coexpression of PBX1 and EMP2 as Prognostic Biomarkers in Estrogen Receptor-Negative Breast Cancer via Data Mining . . . . . . . . . . . . . . . . . 1509--1518 Yiyang Tang and Lihuang Zha and Xiaofang Zeng and Zaixin Yu Identification of Biomarkers Related to Systemic Sclerosis With or Without Pulmonary Hypertension Using Co-expression Analysis . . . . . . . . . 1519--1531 Shusen Zhang and Yuanyuan Lu and Zhongxin Liu and Xiaopeng Li and Zhihua Wang and Zhigang Cai Identification Six Metabolic Genes as Potential Biomarkers for Lung Adenocarcinoma . . . . . . . . . . . . . 1532--1543 Pan Zou and Lijin Duan and Shasha Zhang and Xue Bai and Zhenghui Liu and Fengmei Jin and Haibo Sun and Wentao Xu and Rui Chen Target Specificity of the CRISPR-Cas9 System in \bionameArabidopsis thaliana, \bionameOryza sativa, and \bionameGlycine max Genomes . . . . . . 1544--1552 Yongqian Shu and Xiaohong Wu and Jia Shen and Dongdong Luo and Xiang Li and Hailong Wang and Yuanhua Tom Tang Tumor Mutation Burden Computation in Two Pan-Cancer Precision Medicine Next-Generation Sequencing Panels . . . 1553--1560
Roni Zoller and Meirav Zehavi and Michal Ziv-Ukelson A New Paradigm for Identifying Reconciliation-Scenario Altering Mutations Conferring Environmental Adaptation . . . . . . . . . . . . . . . 1561--1580 Xiyuan Liu and Di Gao and Gang Shen Conditional Random Fields with Least Absolute Shrinkage and Selection Operator to Classifying the Barley Genes Based on Expression Level Affected by the Fungal Infection . . . . . . . . . . 1581--1594 Xin Chang and Mei-Feng Yang and Wei Fan and Li-Sheng Wang and Jun Yao and Zhao-Shen Li and De-Feng Li Bioinformatic Analysis Suggests That Three Hub Genes May Be a Vital Prognostic Biomarker in Pancreatic Ductal Adenocarcinoma . . . . . . . . . 1595--1609 Rutvi Prajapati and Isaac Arnold Emerson Gene Prioritization in Parkinson's Disease Using Human Protein--Protein Interaction Network . . . . . . . . . . 1610--1621 Robert C. Penner Conserved High Free Energy Sites in Human Coronavirus Spike Glycoprotein Backbones . . . . . . . . . . . . . . . 1622--1630
Rong Wang and Lei Fu and Jinbin Li and Di Zhao and Yulan Zhao and Ling Yin Microarray Analysis for Differentially Expressed Genes Between Stromal and Epithelial Cells in Development and Metastasis of Invasive Breast Cancer . . 1631--1643 Xiaojie Wang and Yiyi Zhang and Waleed M. Ghareeb and Shuangming Lin and Xingrong Lu and Ying Huang and Shenghui Huang and Zongbin Xu and Pan Chi A Comprehensive Repertoire of Transfer RNA-Derived Fragments and Their Regulatory Networks in Colorectal Cancer 1644--1655 Maolin Hu and Jiangling Xie and Zhifeng Liu and Xuan Wang and Ming Liu and Jianye Wang Comprehensive Analysis Identifying Wnt Ligands Gene Family for Biochemical Recurrence in Prostate Adenocarcinoma and Construction of a Nomogram . . . . . 1656--1667 Yusong Ye and Zhuoqin Yang and Jinzhi Lei DNA Methylation Heterogeneity Induced by Collaborations Between Enhancers . . . . 1668--1677 Baoshan Li and Yi Jiang and Jingxin Chu and Qian Zhou Drug-Target Interaction Network Analysis of Gene-Phenotype Connectivity Maintained by Genistein . . . . . . . . 1678--1687 Nan Sun and Rui Dong and Shaojun Pei and Changchuan Yin and Stephen S.-T. Yau A New Method Based on Coding Sequence Density to Cluster Bacteria . . . . . . 1688--1698
Jael Sanyanda Wekesa and Yushi Luan and Jun Meng Predicting Protein Functions Based on Differential Co-expression and Neighborhood Analysis . . . . . . . . . 1--18 Obiora Cornelius Collins and Kevin Jan Duffy Mathematical Analyses on the Effects of Control Measures for a Waterborne Disease Model with Socioeconomic Conditions . . . . . . . . . . . . . . . 19--32 Buwen Cao and Shuguang Deng and Hua Qin and Jiawei Luo and Guanghui Li and Cheng Liang Inferring MicroRNA-Disease Associations Based on the Identification of a Functional Module . . . . . . . . . . . 33--42 Vishnu Kumar Sharma and Prasad V. Bharatam Identification of Selective Inhibitors of \em Ld DHFR Enzyme Using Pharmacoinformatic Methods . . . . . . . 43--59 Yang Yin and Yang-fan Zou and Yu Xiao and Tian-xi Wang and Ya-ni Wang and Zhi-cheng Dong and Yu-hu Huo and Bo-chen Yao and Ling-bing Meng and Shuang-xia Du Identification of Potential Hub Genes of Atherosclerosis Through Bioinformatic Analysis . . . . . . . . . . . . . . . . 60--78 Enfa Zhao and Hang Xie and Yushun Zhang Identification of Differentially Expressed Genes Associated with Idiopathic Pulmonary Arterial Hypertension by Integrated Bioinformatics Approaches . . . . . . . 79--88 Wan Tang and Degong Mu and Ling Han and Xianmin Guo and Bing Han and Dong Song Screening of Clinical Factors Related to Prognosis of Breast Cancer Based on the Cox Proportional Risk Model . . . . . . 89--98 Yanwei Chen and Keke Wang and Mengyuan Shang and Shuangshuang Zhao and Zheng Zhang and Haizhen Yang and Zheming Chen and Rui Du and Qilong Wang and Baoding Chen Exploration of DNA Methylation-Driven Genes in Papillary Thyroid Carcinoma Based on the Cancer Genome Atlas . . . . 99--114
Ion Mandoiu and T. M. Murali and Giri Narasimhan and Sanguthevar Rajasekaran and Pavel Skums and Alexander Zelikovsky Special Issue: 9th International Computational Advances in Bio and Medical Sciences (ICCABS 2019) . . . . . 115--116 Mohammad Mohebbi and Liang Ding and Russell L. Malmberg and Liming Cai Human MicroRNA Target Prediction via Multi-Hypotheses Learning . . . . . . . 117--132 Shuzhen Kuang and Liangjiang Wang Deep Learning of Sequence Patterns for CCCTC-Binding Factor-Mediated Chromatin Loop Formation . . . . . . . . . . . . . 133--145 Wutao Yin and Sakib Mostafa and Fang-xiang Wu Diagnosis of Autism Spectrum Disorder Based on Functional Brain Networks with Deep Learning . . . . . . . . . . . . . 146--165 Khajamoinuddin Syed and William Sleeman and Payal Soni and Michael Hagan and Jatinder Palta and Rishabh Kapoor and Preetam Ghosh Machine-Learning Models for Multicenter Prostate Cancer Treatment Plans . . . . 166--184 Matthew Hayes and Derrick Mullins and Angela Nguyen Complex Variant Discovery Using Discordant Cluster Normalization . . . . 185--194 Hsin-Hao Chen and Chung-Chin Lu Optimized Fluorescence-Based Detection in Single Molecule Synthesis Process . . 195--208 Ishwor Thapa and Hesham Ali A Multiomics Graph Database System for Biological Data Integration and Cancer Informatics . . . . . . . . . . . . . . 209--219 Chu-Yu Cheng and Chung-Chin Lu The Agility of a Neuron: Phase Shift Between Sinusoidal Current Input and Firing Rate Curve . . . . . . . . . . . 220--234
Alexsandro Oliveira Alexandrino and Andre Rodrigues Oliveira and Ulisses Dias and Zanoni Dias Genome Rearrangement Distance with Reversals, Transpositions, and Indels 235--247 Christopher Barrett and Andrei C. Bura and Qijun He and Fenix W. Huang and Thomas J. X. Li and Michael S. Waterman and Christian M. Reidys Multiscale Feedback Loops in SARS-CoV-2 Viral Evolution . . . . . . . . . . . . 248--256 Gastone Castellani and Leon N. Cooper and Luciana Renata De Oliveira and Brian S. Blais Energy Consumption and Entropy Production in a Stochastic Formulation of BCM Learning . . . . . . . . . . . . 257--268 Jiasong Wang and Changchuan Yin A Fast Algorithm for Computing the Fourier Spectrum of a Fractional Period 269--282 Concettina Guerra and Sarang Joshi and Yinquan Lu and Francesco Palini and Umberto Ferraro Petrillo and Jarek Rossignac Rank-Similarity Measures for Comparing Gene Prioritizations: a Case Study in Autism . . . . . . . . . . . . . . . . . 283--295 Angela M. Taravella Oill and Anagha J. Deshpande and Heini M. Natri and Melissa A. Wilson PopInf: an Approach for Reproducibly Visualizing and Assigning Population Affiliation in Genomic Samples of Uncertain Origin . . . . . . . . . . . . 296--303 Xiao Wang and Dan Hao and Haja N. Kadarmideen \pkgGeneDMRs: an R Package for Gene-Based Differentially Methylated Regions Analysis . . . . . . . . . . . . 304--316 Yijun Xia and Juan Xie and Jun Zhao and Yin Lou and Dongsheng Cao Screening and Identification of Key Biomarkers in Melanoma: Evidence from Bioinformatic Analyses . . . . . . . . . 317--329 Jie Yang and Qing-chun Xu and Zhen-yu Wang and Xun Lu and Liu-kui Pan and Jun Wu and Chen Wang Integrated Analysis of an lncRNA-Associated ceRNA Network Reveals Potential Biomarkers for Hepatocellular Carcinoma . . . . . . . . . . . . . . . 330--344
Russell Schwartz RECOMB 2020 Special Issue . . . . . . . 345 Yuzhi Guo and Jiaxiang Wu and Hehuan Ma and Sheng Wang and Junzhou Huang Comprehensive Study on Enhancing Low-Quality Position-Specific Scoring Matrix with Deep Learning for Accurate Protein Structure Property Prediction: Using Bagging Multiple Sequence Alignment Learning . . . . . . . . . . . 346--361 Yuzhi Guo and Jiaxiang Wu and Hehuan Ma and Sheng Wang and Junzhou Huang EPTool: a New Enhancing PSSM Tool for Protein Secondary Structure Prediction 362--364 Gizem Caylak and Oznur Tastan and A. Ercument Cicek Potpourri: an Epistasis Test Prioritization Algorithm via Diverse SNP Selection . . . . . . . . . . . . . . . 365--377 Gizem Caylak and Oznur Tastan and A. Ercument Cicek A Tool for Detecting Complementary Single Nucleotide Polymorphism Pairs in Genome-Wide Association Studies for Epistasis Testing . . . . . . . . . . . 378--380 Amatur Rahman and Paul Medevedev Representation of $k$-Mer Sets Using Spectrum-Preserving String Sets . . . . 381--394 Hongyu Zheng and Carl Kingsford and Guillaume Marçais Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length . . . . . . . . . 395--409 Leonard Bohnenkämper and Marília D. V. Braga and Daniel Doerr and Jens Stoye Computing the Rearrangement Distance of Natural Genomes . . . . . . . . . . . . 410--431
Russell Schwartz RECOMB 2020 Special Issue . . . . . . . 433--434 Brooks Paige and James Bell and Aurélien Bellet and Adri\`a Gascón and Daphne Ezer Reconstructing Genotypes in Private Genomic Databases from Genetic Risk Scores . . . . . . . . . . . . . . . . . 435--451 Brandon Legried and Erin K. Molloy and Tandy Warnow and Sébastien Roch Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss . . . . . . . . . . . . . . . . 452--468 Matthew A. Reyna and Uthsav Chitra and Rebecca Elyanow and Benjamin J. Raphael NetMix: a Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks . . . . . . . . . . 469--484 Kamran Ghasedi Dizaji and Wei Chen and Heng Huang Deep Large-Scale Multitask Learning Network for Gene Expression Inference 485--500 Songwei Ge and Haohan Wang and Amir Alavi and Eric Xing and Ziv Bar-joseph Supervised Adversarial Alignment of Single-Cell RNA-seq Data . . . . . . . . 501--513 Emre Sefer and Carl Kingsford Metric Labeling and Semimetric Embedding for Protein Annotation Prediction . . . 514--525
David J. Galas and James Kunert-graf and Lisa Uechi and Nikita A. Sakhanenko Toward an Information Theory of Quantitative Genetics . . . . . . . . . 527--559 Philipp Benner Computing Leapfrog Regularization Paths with Applications to Large-Scale $K$-mer Logistic Regression . . . . . . . . . . 560--569 Samaneh Yourdkhani and Elizabeth S. Allman and John A. Rhodes Parameter Identifiability for a Profile Mixture Model of Protein Evolution . . . 570--586 Shijia Wang and Shufei Ge and Caroline Colijn and Priscila Biller and Liangliang Wang and Lloyd T. Elliott Estimating Genetic Similarity Matrices Using Phylogenies . . . . . . . . . . . 587--600 Carlos Soto and Darshan Bryner and Nicola Neretti and Anuj Srivastava Toward a Three-Dimensional Chromosome Shape Alphabet . . . . . . . . . . . . . 601--618 Jinuk Jung and Hyunwhan Joe and Kyungsik Ha and Jin-muk Lim and Hong-gee Kim Biomedical Entity Explorer: a Web Server for Biomedical Entity Exploration . . . 619--628 Sarah E. Innis and Kelsie Reinaltt and Mete Civelek and Warren D. Anderson GSEAplot: a Package for Customizing Gene Set Enrichment Analysis in R . . . . . . 629--631
Anonymous \em JCB Call for Papers for the Special Issue on ``40 Years of Computational Biology: In Honor of Professor Michael Waterman's 80th Birthday'' . . . . . . . 633--635 Zhipeng Cai and Pavel Skums and Yuri Porozov and Alexander Zelikovsky Special Issue: 16th International Symposium on Bioinformatics Research and Applications (ISBRA 2020) . . . . . . . 636 Wei Dai and Bingxi Chen and Wei Peng and Xia Li and Jiancheng Zhong and Jianxin Wang A Novel Multi-Ensemble Method for Identifying Essential Proteins . . . . . 637--649 Lingzhi Zhu and Cheng Yan and Guihua Duan Prediction of Virus--Receptor Interactions Based on Improving Similarities . . . . . . . . . . . . . . 650--659 Gaoyan Wu and Mengyun Yang and Yaohang Li and Jianxin Wang De Novo Prediction of Drug--Target Interactions Using Laplacian Regularized Schatten $p$-Norm Minimization . . . . . 660--673 Chun-cheng Liu and Tao-chuan Shih and Tun-wen Pai and Chin-hwa Hu and Wen-shyong Tzou Enhanced Over-Representation Analysis for the Differential Regulation of Birc5a and HIF2 $ \alpha $-Knockdown Approaches . . . . . . . . . . . . . . . 674--686 Nian Wang and Min Zeng and Yiming Li and Fang-xiang Wu and Min Li Essential Protein Prediction Based on node2vec and XGBoost . . . . . . . . . . 687--700 Nikolai Nòjgaard and Walter Fontana and Marc Hellmuth and Daniel Merkle Cayley Graphs of Semigroups Applied to Atom Tracking in Chemistry . . . . . . . 701--715 Kseniia Cheloshkina and Islam Bzhikhatlov and Maria Poptsova Randomness in Cancer Breakpoint Prediction . . . . . . . . . . . . . . . 716--731 Zhineng Chen and Sai Wang and Caiyan Jia and Kai Hu and Xiongjun Ye and Xuanya Li and Xieping Gao CRDet: Improving Signet Ring Cell Detection by Reinforcing the Classification Branch . . . . . . . . . 732--743 Anonymous \em Retraction of: A Study of Potential SARS-CoV-2 Antiviral Drugs and Preliminary Research of Their Molecular Mechanism, Based on Anti-SARS-CoV Drug Screening and Molecular Dynamics Simulation (doi: 10.1089/cmb.2020.0112) 744
Zhipeng Cai and Pavel Skums and Yuri Porozov and Alexander Zelikovsky Special Issue: 16th International Symposium on Bioinformatics Research and Applications (ISBRA 2020) . . . . . . . 745--746 Ekaterina M. Myasnikova and Marat A. Sabirov and Alexander V. Spirov Quantitative Analysis of the Dynamics of Maternal Gradients in the Early \bionameDrosophila Embryo . . . . . . . 747--757 Jaros\law Paszek and Alexey Markin and Pawe\l Górecki and Oliver Eulenstein Taming the Duplication-Loss-Coalescence Model with Integer Linear Programming 758--773 Wenyan Gu and Aizhong Zhou and Lusheng Wang and Shiwei Sun and Xuefeng Cui and Daming Zhu SVLR: Genome Structural Variant Detection Using Long-Read Sequencing Data . . . . . . . . . . . . . . . . . . 774--788 Wen Yang and Lusheng Wang Fast and Accurate Algorithms for Mapping and Aligning Long Reads . . . . . . . . 789--803 Qiuyue Huang and Jun Wang and Xiangliang Zhang and Maozu Guo and Guoxian Yu IsoDA: Isoform--Disease Association Prediction by Multiomics Data Fusion . . 804--819 Marmar Moussa and Ion I. M\uandoiu SC1: a Tool for Interactive Web-Based Single-Cell RNA-Seq Data Analysis . . . 820--841 Filipp Martin Rondel and Roya Hosseini and Bikram Sahoo and Sergey Knyazev and Igor Mandric and Frank Stewart and Ion I. M\uandoiu and Bogdan Pasaniuc and Yuri Porozov and Alexander Zelikovsky Pipeline for Analyzing Activity of Metabolic Pathways in Planktonic Communities Using Metatranscriptomic Data . . . . . . . . . . . . . . . . . . 842--855