• 
  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
• 
  Francesca 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 S. 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

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