7. PSB 2002: Lihue, Hawaii, USA

• Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein:
  Preface.
  

Human Genome Variation: Disease, Drug Response, and Clinical Phenotypes

• Francisco M. de la Vega, Isaac S. Kohane, J. A. Schneider, J. C. Stephens:
  Human Genome Variation: Disease, Drug Response, and Clinical Phenotypes - Session Introduction. 3-5
  
• Asa Ben-Hur, André Elisseeff, Isabelle Guyon:
  A Stability Based Method for Discovering Structure in Clustered Data. 6-17
  
• Debashis Ghosh:
  Singular Value Decomposition Regression Models for Classification of Tumors from Microarray Experiments. 18-29
  
• J. Heil, S. Glanowski, J. Scott, E. Winn-Deen, I. McMullen, L. Wu, C. Gire, A. Sprague:
  An Automated Computer System to Support Ultra High Throughput SNP Genotyping. 30-40
  
• Bradley Malin, Latanya Sweeney:
  Inferring Genotype from Clinical Phenotype through a Knowledge Based Algorithm. 41-52
  
• Jason H. Moore, Lance W. Hahn:
  A Cellular Automata Approach to Detecting Interactions Among Single-nucleotide Polymorphisms in Complex Multifactorial Diseases. 53-64
  
• Diane E. Oliver, Daniel L. Rubin, Joshua M. Stuart, Micheal Hewett, Teri E. Klein, Russ B. Altman:
  Ontology Development for a Pharmacogenetics Knowledge Base. 65-76
  
• R. Brian Potter, Sorin Draghici:
  A SOFM Approach to Predicting HIV Drug Resistance. 77-87
  
• Daniel L. Rubin, Micheal Hewett, Diane E. Oliver, Teri E. Klein, Russ B. Altman:
  Automating Data Acquisition into Ontologies from Pharmacogenetics Relational Data Sources Using Declarative Object Definitions and XML. 88-99
  
• Shuanglin Zhang, Kui Zhang, Jinming Li, Hongyu Zhao:
  On a Family-Based Haplotype Pattern Mining Method for Linkage Disequilibrium Mapping. 100-111
  

Genome-Wide Analysis and Comparative Genomics

• Inna Dubchak, Lior Pachter, Liping Wei:
  Genome-Wide Analysis and Comparative Genomics - Session Introduction. 112-114
  
• F. Chiaromonte, V. B. Yap, W. Miller:
  Scoring Pairwise Genomic Sequence Alignments. 115-126
  
• Melissa S. Cline, Guoying Liu, Ann E. Loraine, Ron Shigeta, Jill Cheng, Gangwu Mei, David Kulp, Michael A. Siani-Rose:
  Structure-Based Comparison of Four Eukaryotic Genomes. 127-138
  
• Debra Goldberg, Susan McCouch, Jon M. Kleinberg:
  Constructing Comparative Genome Maps with Unresolved Marker Order. 139-150
  
• Rachid Gherbi, Joan Hérisson:
  Representation and Processing of Complex DNA Spatial Architecture and its Annotated Genomic Content. 151-162
  
• Ian Holmes, Gerald M. Rubin:
  Pairwise RNA Structure Comparison with Stochastic Context-Free Grammars. 163-174
  
• Seiya Imoto, Takao Goto, Satoru Miyano:
  Estimation of Genetic Networks and Functional Structures Between Genes by Using Bayesian Networks and Nonparametric Regression. 175-186
  
• Olga V. Kel-Margoulis, T. G. Ivanova, Edgar Wingender, Alexander E. Kel:
  Automatic Annotation of Genomic Regulatory Sequences by Searching for Composite Clusters. 187-198
  
• Zufar Mulyukov, Pavel A. Pevzner:
  EULER-PCR: Finishing Experiments for Repeat Resolution. 199-210
  
• Luay Nakhleh, Bernard M. E. Moret, Usman Roshan, Katherine St. John, Jerry Sun, Tandy Warnow:
  The Accuracy of Fast Phylogenetic Methods for Large Datasets. 211-222
  
• Donald J. Patterson, Ken Yasuhara, Walter L. Ruzzo:
  Pre-mRNA Secondary Structure Prediction Aids Splice Site Prediction. 223-234
  
• Sing-Hoi Sze, Mikhail S. Gelfand, Pavel A. Pevzner:
  Finding Weak Motifs in DNA Sequences. 235-246
  
• Wayne Volkmuth, N. Alexandrov:
  Evidence for Sequence-Independent Evolutionary Traces in Genomics Data. 247-258
  
• Shiquan Wu, Xun Gu:
  Multiple Genome Rearrangement by Reversals. 259-270
  
• Yoshiki Yamaguchi, Tsutomu Maruyama, Akihiko Konagaya:
  High Speed Homology Search with FPGAs. 271-282
  

Expanding Proteomics to Glycobiology

• Claus-Wilhelm von der Lieth:
  Expanding Proteomics to Glycobiology - Session Introduction. 283-284
  
• Andreas Bohne, Claus-Wilhelm von der Lieth:
  Glycosylation of Proteins: A Computer Based Method for the Rapid Exploration of Comformational Space of N-Glycans. 285-296
  
• Catherine A. Cooper, Mathew J. Harrison, J. M. Webster, Marc R. Wilkins, Nicolle H. Packer: Data Standardisation in GlycoSuiteDB. 297-309
• Ramneek Gupta, Søren Brunak:
  Prediction of Glycosylation Across the Human Proteome and the Correlation to Protein Function. 310-322
  

Literature Data Mining for Biology

• Lynette Hirschman, Jong C. Park, Jun-ichi Tsujii, Cathy H. Wu, Limsoon Wong:
  Literature Data Mining for Biology - Session Introduction. 323-325
  
• Jing Ding, Daniel Berleant, Dan Nettleton, Eve Syrkin Wurtele:
  Mining MEDLINE: Abstracts, Sentences, or Phrases? 326-337
  
• Udo Hahn, Martin Romacker, Stefan Schulz:
  Creating Knowledge Repositories from Biomedical Reports: The MEDSYNDIKATE Text Mining System. 338-349
  
• Gondy Leroy, Hsinchun Chen:
  Filling Preposition-Based Templates to Capture Information from Medical Abstracts. 350-361
  
• James Pustejovsky, José M. Castaño, Jason Zhang, M. Kotecki, B. Cochran:
  Robust Relational Parsing Over Biomedical Literature: Extracting Inhibit Relations. 362-373
  
• B. J. Stapley, Lawrence A. Kelley, Michael J. E. Sternberg:
  Predicting the Sub-Cellular Location of Proteins from Text Using Support Vector Machines. 374-385
  
• W. John Wilbur:
  A Thematic Analysis of the AIDS Literature. 386-397
  

Genome, Pathway and Interaction Bioinformatics

• Peter D. Karp, Pedro Romero, Eric P. Neumann:
  Genome, Pathway and Interaction Bioinformatics - Session Introduction. 398-399
  
• Steven Eker, Merrill Knapp, Keith Laderoute, Patrick Lincoln, José Meseguer, M. Kemal Sönmez:
  Pathway Logic: Symbolic Analysis of Biological Signaling. 400-412
  
• Shawn M. Gomez, Andrey Rzhetsky:
  Towards the Prediction of Complete Protein-Protein Interaction Networks. 413-424
  
• D. Guhathakurta, L. A. Schriefer, M. C. Hresko, R. H. Waterston, Gary D. Stormo:
  Identifying Muscle Regulatory Elements and Genes in the Nematode Caenorhabditis Elegans. 425-436
  
• Alexander J. Hartemink, David K. Gifford, Tommi Jaakkola, Richard A. Young:
  Combining Location and Expression Data for Principled Discovery of Genetic Regulatory Network Models. 437-449
  
• Michael Hucka, Andrew Finney, Herbert M. Sauro, H. Bolouri, John C. Doyle, Hiroaki Kitano:
  The ERATO Systems Biology Workbench: Enabling Interaction and Exchange Between Software Tools for Computational Biology. 450-461
  
• Manish P. Kurhekar, Sudeshna Adak, S. Jhunjhunwala, K. Raghupathy:
  Genome-Wide Pathway Analysis and Visualization Using Gene Expression Data. 462-473
  
• Paul Pavlidis, Darrin P. Lewis, William Stafford Noble:
  Exploring Gene Expression Data with Class Scores. 474-485
  
• Jeff Shrager, Pat Langley, Andrew Pohorille:
  Guiding Revision of Regulatory Models with Expression Data. 486-497
  
• Changwon Yoo, Vesteinn Thorsson, Gregory F. Cooper:
  Discovery of Causal Relationships in a Gene-Regulation Pathway from a Mixture of Experimental and Observational DNA Microarray Data. 498-509
  

Phylogenetic Genomics and Genomic Phylogenetics

• Scott Stanley, Benjamin A. Salisbury:
  Phylogenetic Genomics and Genomic Phylogenetics - Session Introduction. 510-511
  
• M. Zilversmit, P. O'Grady, Robert DeSalle:
  Shallow Genomics, Phylogenetics, and Evolution in the Family Drosophilidae. 512-523
  
• Li-San Wang, Robert K. Jansen, Bernard M. E. Moret, Linda A. Raubeson, Tandy Warnow:
  Fast Phylogenetic Methods for the Analysis of Genome Rearrangement Data: An Empirical Study. 524-535
  
• Roderic D. M. Page, J. A. Cotton:
  Vertebrate Phylogenomics: Reconciled Trees and Gene Duplications. 536-547
  

Proteins: Structure, Function and Evolution

• Peter Clote, Gavin J. P. Naylor, Ziheng Yang:
  Proteins: Structure, Function and Evolution - Session Introduction. 548-551
  
• Juan Fernández-Recio, Maxim Totrov, Ruben Abagyan:
  Screened Charge Electrostatic Model in Protein-Protein Docking Simulations. 552-565
  
• Christina S. Leslie, Eleazar Eskin, William Stafford Noble:
  The Spectrum Kernel: A String Kernel for SVM Protein Classification. 566-575
  
• R. Nielsen, John P. Huelsenbeck:
  Detecting Positively Selected Amino Acid Sites Using Posterior Predictive P-Values. 576-588
  
• Predrag Radivojac, Zoran Obradovic, Celeste J. Brown, A. Keith Dunker:
  Improving Sequence Alignments For Intrinsically Disordered Proteins. 589-600
  
• J. A. Saunders, Kenneth D. Gibson, Harold A. Scheraga:
  Ab Initio Folding of Multiple-Chain Proteins. 601-612
  
• J. Schonfeld, Oliver Eulenstein, Kent Vander Velden, Gavin J. P. Naylor:
  Investigating Evolutionary Lines of Least Resistance Using the Inverse Protein-Folding Problem. 613-624
  
• Orkun Soyer, Matthew W. Dimmic, Richard R. Neubig, Richard A. Goldstein:
  Using Evolutionary Methods to Study G-Protein Coupled Receptors. 625-636
  
• E. W. Stawiski, Yael Mandel-Gutfreund, A. C. Lowenthal, L. M. Gregoret:
  Progress in Predicting Protein Function from Structure: Unique Features of O-Glycosidases. 637-648
  
• Jean-Philippe Vert:
  Support Vector Machine Prediction of Signal Peptide Cleavage Site Using a New Class of Kernels for Strings. 649-660
  
• Sebastian Will:
  Constraint-Based Hydrophobic Core Construction for Protein Structure Prediction in the Face-Centered-Cubic Lattice. 661-672
  
• Ruhong Zhou, B. David Silverman:
  Detecting Native Protein Folds Among Large Decoy Sets with Hydrophobic Moment Profiling. 673-684