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 PROTEIN EVOLUTION AND STRUCTURAL GENOMICS Session Introduction 3(3) D. Frishman R. A. Goldstein D. D. Pollock Enzyme Evolution Explained (Sort Of) 6(12) A. M. Dean G. B. Golding Modeling Evolution at the Protein Level Using an Adjustable Amino Acid Fitness Model 18(12) M. W. Dimmic D. P. Mindell R. A. Goldstein Protein Folds in the Worm Genome 30(12) M. Gerstein J. Lin H. Hegyi Sensitive Sequence Comparison as Protein Function Predictor 42(12) K. Pawlowski L. Jaroszewski L. Rychlewski A. Godzik High-Throughput Functional Annotation of Novel Gene Products Using Document Clustering 54(15) A. Renner A. Aszodi The Evolution of Duplicated Genes Considering Protein Stability Constraints 69(12) D. M. Taverna R. M. Goldstein Relating Physicochemmical Properties of Amino Acids to Variable Nucleotide Substitution Patterns Among Sites 81(12) Z. Yang PROTEIN STRUCTURE PREDICTION IN BIOLOGY AND MEDICINE Session Introduction 93(2) R. L. Dunbrack Jr. K. Dunker A. Godzik Algorithmic Approach to Quantifying the Hydrophobic Force Contribution in Protein Folding 95(12) R. Backofen S. Will P. Clote Eliminating Superfluous Neighbor Pairs While Threading Fold Models 107(12) J. R. Bienkowska R. G. Rogers Jr. T. F. Smith Hybrid Fold Recognition: Combining Sequence Derived Properties with Evolutionary Information 119(12) D. Fischer Folding Nuclei in 3D Protein Structures 131(12) O. V. Galzitskaya A. V. Skoogarev D. N. Ivankov A. V. Finkelstein How Universal Are Fold Recognition Parameters. A Comprehensive Study of Alignment and Scoring Function Parameters Influence on Recognition of Distant Folds 143(12) K. A. Olszewski Pinpointing the Putative Heparin/Sialic Acid-Binding Residues in the `Sushi Domain 7 of Factor H: A Molecular Modeling Study 155(13) S. Ranganathan D. A. Male R. J. Ormsby E. Giannakis D. L. Gordon Recognition of Protein Structure: Determining the Relative Energetic Contributions of β-strands, α-helices and Loops 168(11) B. Reva S. Topiol Probing Structure-Function Relationships of the DNA Polymerase Alpha-Associated Zinc-Finger Protein Using Computational Approaches 179(12) R. Samudrala Y. Xia M. Levitt N. J. Cotton E. S. Huang R. Davis Flexibility and Critical Hydrogen Bonds in Cytochrome C 191(12) M. F. Thorpe B. M. Hespenheide Y. Yang L. A. Kuhn MOLECULES TO MAPS: TOOLS FOR VISUALIZATION AND INTERACTION IN COMPUTATIONAL BIOLOGY Session Introduction 203(3) E. T. Kraemer T. E. Ferrin MappetShow: Non-Linear Visualization for Genome Data 206(12) F. Guyon G. Vaysseix E. Barillot ProFeel: Low Cost Visual-Haptic Perceptualization of Protein Structure-Structure Alignments 218(12) M. D. Hansen S. Lodha A. Pang Integrated Tools for Structural and Sequence Alignment and Analysis 230(12) C. C. Huang W. R. Novak P. C. Babbitt A. I. Jewett T. E. Ferrin T. E. Klein In Vest: Interactive and Visual Edge Selection Tool for Constructing Evolutionary Trees 242(12) P. Kearney A. Secord H. Zhang The Ensemble/Legacy Chimera Extension: Standardized User and Programmer Interface to Molecular Ensemble Data and Legacy Modeling Programs 254(12) D. E. Konerding Generating Interactive Molecular Documentaries Using a Library of Graphical Actions 266(12) P. Pulavarthi R. Chiang R. B. Altman Visual Management of Large Scale Data Mining Projects 278(13) I. Shah L. Hunter MOLECULAR NETWORK MODELING AND DATA ANALYSIS Session Introduction 291(2) R. Somogyi H. Kitano S. Miyano Q. Zheng Algorithms for Inferring Qualitative Models of Biological Networks 293(12) T. Akutsu S. Miyano S. Kuhara Discovery of Regulatory Interactions Through Perturbation: Inference and Experimental Design 305(12) T. E. Ideker V. Thorsson R. M. Karp Construction of a Generalized Simulator for Multi-Cellular Organisms and its Application to SMAD Signal Transduction 317(12) K. M. Kyoda M. Muraki H. Kitano Delta-Notch Lateral Inhibitory Patterning in the Emergence of Ciliated Cells in Xenopus: Experimental Observations and a Gene Network Model 329(12) G. Marnellos G. A. Deblandre E. Mjolsness C. Kinter Hybrid Petri Net Representation of Gene Regulatory Network 341(12) H. Matsuno A. Doi M. Nagasaki S. Miyano The Effect of Dynamic Receptor Clustering on the Sensitivity of Biochemical Signaling 353(12) C. Zhang S. H. Kim DATA MINING AND KNOWLEDGE DISCOVERY IN MOLECULAR DATABASES Session Introduction 365(2) J. Glasgow I. Jurisica R. Ng Mining the Quantitative Trait Loci Associated with Oral Glucose Tolerance in the Oletf Rat 367(13) A. Nakaya H. Hishigaki S. Morishita Stochastic Segment Models of Eukaryotic Promoter Regions 380(12) U. Ohler G. Stemmer S. Harbeck H. Niemann Stochastic Heuristic Algorithms for Target Motif Identification (Extended Abstract) 392(12) H. T. Wareham T. Jiang X. Zhang C. G. Trendall Identifying Amino Acid Residues in Medium Resolution Critical Point Graphs Using Instance Based Query Generation 404(12) K. Whelan J. Glasgow IDENTIFICATION OF COORDINATED GENE EXPRESSION AND REGULATORY SEQUENCES Session Introduction 416(2) Gary Stormo Mutual Information Relevance Networks: Functional Genomic Clustering Using Pairwise Entropy Measurements 418(12) A. J. Butte I. S. Kohane EST Databases as Multi-Conditional Gene Expression Datasets 430(13) R. M. Ewing J-M. Claverie In Silico Analysis of Gene Expression Patterns During Early Development of Xenopus laevis 443(12) N. Pollet H. A. Schmidt V. Gawantka C. Niehrs M. Vingrom Principal Components Analysis to Summarize Microarray Experiments: Application to Sporulation Time Series 455(12) S. Raychaudhuri J. M. Stuart R. B. Altman ANN-Spec: A Method for Discovering Transcription Factor Binding Sites with Improved Specificity 467(12) C. T. Workman G. D. Stormo Cluster, Function and Promoter:Analysis of Yeast Expression Array 479(12) J. Zhu M. Q. Zhang NATURAL LANGUAGE PROCESSING FOR BIOLOGY Session Introduction 491(2) T. Tsunoda L. Wong Knowledge Representation and Indexing Using the Unified Medical Language System 493(12) K. Baclawski J. Cigna M. M. Kokar P. Mager B. Indurkhya Two Applications of Information Extraction to Biological Science Journal Articles: Enzyme Interactions and Protein Structures 505(12) K. Humphreys G. Demetriou R. Gaizauskas EDGAR: Extraction of Drugs, Genes and Relations from the Biomedical Literature 517(12) T. C. Rindflesch L. Tanabe J. N. Weinstein L. Hunter Biobibliometrics: Information Retrieval and Visualization from Co-Occurrences of Gene Names in Medline Abstracts 529(12) B. J. Stapley G. Benoit Automatic Extraction of Protein Interactions from Scientific Abstracts 541(12) J. Thomas D. Milward C. Ouzounis S. Pulman M. Carroll COMPUTER-AIDED COMBINATORIAL CHEMISTRY AND CHEMINFORMATICS Session Introduction 553(2) A. Tropsha R. S. Pearlman Compound Acquisition Strategies 555(11) J. B. Dunbar Jr. Searching for Molecules with Similar Biological Activity: Analysis by Fingerprint Profiling 566(10) J. W. Godden L. Xue F. L. Stahura J. Bajorath Library Design and Virtual Screening Using Multiple 4-Point Pharmacophore Fingerprints 576(12) J. S. Mason D. L. Cheney Piccolo: A Tool for Combinatorial Library Design Via Multicriterion Optimization 588(12) W. Zheng S. T. Hung J. T. Saunders G. L. Seibel APPLICATIONS OF INFORMATION THEORY TO BIOLOGY Session Introduction 600(2) T. G. Dewey H. Herzel Information Dynamics of In Vitro Selection-Amplification Systems 602(12) T. G. Dewey Average Mutual Information of Coding and Noncoding DNA 614(10) I. Grosse S. V. Buldyrev H. E. Stanley D. Holste H. Herzel Finite-Temperature Sequence Alignment 624(12) M. Kschischo M. Lassing HUMAN GENOME VARIATION: ANALYSIS, MANAGEMENT AND APPLICATION OF SNP DATA Session Introduction 636(3) F. M. De la Vega M. Kreitman ALFRED: A Web-Accessible Allele Frequency Database 639(12) K-H. Cheung P. L. Miller J. R. Kidd K. K. Kidd M. V. Osier A. J. Paksits Linkage Disequilibrium Mapping Using Single Nucleotide Polymorphisms-Which Population? 651(12) A. Collins An Analytic Solution to Single Nucleotide Polymorphism Error-Detection Rates in Nuclear Families: Implications for Study Design 663(12) D. Gordon S. M. Leal S. C. Heath J. Ott The Haplotype Linkage Disequilibrium Test for Genome-Wide Screens: Its Power and Study Design 675 M. Xiong J. Akey L. Jin
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