The Pacific Symposium on Biocomputing brings together key researchers from the international biocomputing community. It is designed to be maximally responsive to the need for critical mass in subdisciplines within biocomputing. This book contains peer-reviewed articles in computational biology.
Preface v HUMAN GENOME VARIATION: LINKING GENOTYPES TO CLINICAL PHENOTYPES Session Introduction 3(3) F. M. De la Vega M. Kreitman I. S. Kohane Determining Significant Fold Differences in Gene Expression Analysis 6(12) A. J. Butte J. Ye H. U. Haring M. Stumvoll M. F. White I. S. Kohane Assessment and Management of Single Nucleotide Polymorphism Genotype Errors in Genetic Association Analysis 18(12) D. Gordon J. Ott Unsupervised Learning from Complex Data: The Matrix Incision Tree Algorithm 30(12) J. H. Kim L. Ohno-Machado I. S. Kohane Mutual Information Analysis as a Tool to Assess the Role of Aneuploidy in the Generation of Cancer-Associated Differential Gene Expression Patterns 42(10) G. T. Klus A. Song A. Schick M. Wahde Z. Szallasi A Nonparametric Scoring Algorithm for Identifying Informative Genes from Microarray Data 52(15) P. J. Park M. Pagano M. Bonetti DISORDER AND FLEXIBILITY IN PROTEIN STRUCTURE AND FUNCTION Session Introduction 64(3) C. Bracken M. M. Young K. Dunker An NMR-Based Quenched Hydrogen Exchange Investigation of Model Amyloid Fibrils Formed by Cold Shock Protein A 67(12) A. T. Alexandrescu Collective Reorientational Motion and Nuclear Spin Relaxation in Proteins 79(10) J. J. Prompers S. F. Lienin R. Bruschweiler The Protein Non-Folding Problem: Amino Acid Determinants of Intrinsic Order and Disorder 89(14) R. M. Williams Z. Obradovic V. Mathura W. Braun E. C. Garner J. Young S. Takayama C. J. Brown A. K. Dunker DNA STRUCTURE, PROTEIN-DNA INTERACTIONS, AND DNA-PROTEIN EXPRESSION Session Introduction 101(2) P. F. Baldi R. H. Lathrop Stress-Induced DNA Duplex Destabilization in Transcriptional Initiation 103(12) C. J. Benham SAMIE: Statistical Algorithm for Modeling Interaction Energies 115(12) P. V. Benos A. S. Lapedes D. S. Fields G. D. Stormo BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes 127(12) X. Liu D. L. Brutlag J. S. Liu A Structure-Based Approach for Prediction of Protein Binding Sites in Gene-Upstream Regions 139(12) Y. Mandel-Gutfreund A. Baron H. Margalit Promoter Region-Based Classification of Genes 151(16) P. Pavlidis T. S. Furey M. Liberto D. Haussler W. N. Grundy STRUCTURES, PHYLOGENIES, AND GENOMES: THE INTEGRATED STUDY OF PROTEIN EVOLUTION Session Introduction 164(3) R. A. Goldstein D. D. Pollock J. L. Thorne Nucleotide Substitutions and the Evolution of Duplicate Genes 167(12) J. S. Conery M. Lynch An Algorithm for Statistical Alignment of Sequences Related by a Binary Tree 179(12) J. Hein Analyzing Site Heterogeneity During Protein Evolution 191(12) J. M. Koshi R. A. Goldstein Markov Chain Monte Carlo Computation of Confidence Intervals for Substitution-Rate Variation in Proteins 203(12) A. Rzhetsky P. Morozov A Model for Phylogenetic Inference Using Structural and Chemical Covariates 215(11) S. Tavare D. C. Adams O. Fedrigo G. J. P. Naylor Maximum Likelihood Analysis of Adaptive Evolution in HIV-1 GP120 ENV Gene 226(14) Z. Yang HIGH PERFORMANCE COMPUTING FOR COMPUTATIONAL BIOLOGY Session Introduction 238(2) T. Ferrin B. A. Foster R. Hughey View Feature: Integrated Feature Analysis and Visualization 240(11) D. R. Banatao C. C. Huang P. C. Babbitt R. B. Altman T. E. Klein Analyzing Sensory Systems with the Information Distortion Function 251(12) A. G. Dimitrov J. P. Miller Sequence Analysis With the Kestrel SIMD Parallel Processor 263(12) L. Grate M. Diekhans D. Dahle R. Hughey A New Algorithm for the Alignment of Multiple Protein Structures Using Monte Carlo Optimization 275(12) C. Guda E. D. Scheeff P. E. Bourne I. N. Shindyalov Gene Verification and Discovery by Walking Tree Method 287(12) T. Hsu P. Cull Predicting Gene Function from Gene Expressions and Ontologies 299(12) T. R. Hvidsten J. Komorowski A. K. Sandvik A. Laegreid A Multithreaded Parallel Implementation of a Dynamic Programming Algorithm for Sequence Comparison 311(12) W. S. Martins J. B. Del Cuvillo F. J. Useche K. B. Theobald G. R. Gao Molecular Fingerprinting on the SIMD Parallel Processor Kestrel 323(12) E. Rice R. Hughey Percolation Clustering: A Novel Approach to the Clustering of Gene Expression Patterns in Dictyostelium Development 335(13) R. Sasik T. Hwa N. Iranfar W. F. Loomis Quality Control in Manufacturing Oligo Arrays: A Combinatorial Design Approach 348(12) R. Sengupta M. Tompa Using Metacomputing Tools to Facilitate Large Scale Analyses of Biological Databases 360(14) A. Waugh G. A. Williams L. Wei R. B. Altman NATURAL LANGUAGE PROCESSING AND INFORMATION EXTRACTION IN BIOLOGY Session Introduction 372(2) J.-I. Tsujii L. Wong Including Biological Literature Improves Homology Search 374(10) J. T. Chang S. Raychaudhuri R. B. Altman Textquest: Document Clustering of Medline Abstracts For Concept Discovery In Molecular Biology 384(12) I. Iliopoulos A. J. Enright C. A. Ouzounis Bidirectional Incremental Parsing for Automatic Pathway Identification with Combinatory Categorial Grammar 396(12) J. C. Park H. S. Kim J. J. Kim Event Extraction from Biomedical Papers Using a Full Parser 408(14) A. Yakushiji Y. Tateisi Y. Miyao J.-I. Tsujii GENOME, PATHWAY, AND INTERACTION BIOINFORMATICS Session Introduction 420(2) P. Karp E. Neumann P. Romero Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks 422(12) A. J. Hartemink D. K. Gifford T. S. Jaakkola R. A. Young Reverse Engineering of Metabolic Pathways from Observed Data Using Genetic Programming 434(12) J. R. Koza W. Mydlowec G. Lanza J. Yu M. A. Keane Development of a System for the Inference of Large Scale Genetic Networks 446(13) Y. Maki D. Tominaga M. Okamoto S. Watanabe Y. Eguchi Representation and Simulation of Biochemical Processes Using the π-Calculus Process Algebra 459(12) A. Regev W. Silverman E. Shapiro Nutrient-Related Analysis of Pathway/Genome Databases 471(12) P. R. Romero P. Karp Detecting Gene Relations from Medline Abstracts 483(13) M. Stephens M. Palakal S. Mukhopadhyay R. Raje J. Mostafa On Reporting Fold Differences 496(12) C. L. Tsien T. A. Libermann X. Gu I. S. Kohane A Comparison of Genetic Network Models 508(12) L. F. A. Wessels E. P. Van Someren M. J. T. Reinders PIES, A Protein Interaction Extraction System 520(12) L. Wong Simulating the Growth of Viruses 532(15) L. You J. Yin PHYLOGENETICS IN THE POST-GENOMIC ERA Session Introduction 544(3) J. E. Steinbachs P. Kearney Scaling of Accuracy in Extremely Large Phylogenetic Trees 547(12) O. R. P. Bininda-Emonds S. G. Brady J. Kim M. J. Sanderson Exact Algorithms for Computing Pairwise Alignments and 3-Medians From Structure-Annotated Sequences (Extended Abstract) 559(12) P. A. Evans H. T. Wareham A Tree Obscured By Vines: Horizontal Gene Transfer and the Median Tree Method of Estimating Species Phylogeny 571(12) J. Kim B. A. Salisbury A New Implementation and Detailed Study of Breakpoint Analysis 583(12) B. M. E. Moret S. Wyman D. A. Bader T. Warnow M. Yan A New Algorithm for Analysis of Within-Host HIV-1 Evolution 595(11) F. Ren S. Ogishima H. Tanaka Efficiencies of Genes and Accuracy of Tree-Building Methods in Recovering a Known Drosophila Genealogy 606 J. E. Steinbachs N. V. Schizas W. O. Ballard BIOETHICS, FICTION SCIENCE, AND THE FUTURE OF MANKIND Session Introduction 618 P. Baldi S. Brunak
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