Table of Contents

• PrefaceRuss B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein. [doi]
• Human Genome Variation: Disease, Drug Response, and Clinical Phenotypes - Session IntroductionFrancisco M. de la Vega, Isaac S. Kohane, J. A. Schneider, J. C. Stephens. 3-5 [doi]
• A Stability Based Method for Discovering Structure in Clustered DataAsa Ben-Hur, André Elisseeff, Isabelle Guyon. 6-17 [doi]
• Singular Value Decomposition Regression Models for Classification of Tumors from Microarray ExperimentsDebashis Ghosh. 18-29 [doi]
• An Automated Computer System to Support Ultra High Throughput SNP GenotypingJ. Heil, S. Glanowski, J. Scott, E. Winn-Deen, I. McMullen, L. Wu, C. Gire, A. Sprague. 30-40 [doi]
• Inferring Genotype from Clinical Phenotype through a Knowledge Based AlgorithmBradley Malin, Latanya Sweeney. 41-52 [doi]
• A Cellular Automata Approach to Detecting Interactions Among Single-nucleotide Polymorphisms in Complex Multifactorial DiseasesJason H. Moore, Lance W. Hahn. 53-64 [doi]
• Ontology Development for a Pharmacogenetics Knowledge BaseDiane E. Oliver, Daniel L. Rubin, Joshua M. Stuart, Micheal Hewett, Teri E. Klein, Russ B. Altman. 65-76 [doi]
• A SOFM Approach to Predicting HIV Drug ResistanceR. Brian Potter, Sorin Draghici. 77-87 [doi]
• Automating Data Acquisition into Ontologies from Pharmacogenetics Relational Data Sources Using Declarative Object Definitions and XMLDaniel L. Rubin, Micheal Hewett, Diane E. Oliver, Teri E. Klein, Russ B. Altman. 88-99 [doi]
• On a Family-Based Haplotype Pattern Mining Method for Linkage Disequilibrium MappingShuanglin Zhang, Kui Zhang, Jinming Li, Hongyu Zhao. 100-111 [doi]
• Scoring Pairwise Genomic Sequence AlignmentsF. Chiaromonte, V. B. Yap, W. Miller. 115-126 [doi]
• Structure-Based Comparison of Four Eukaryotic GenomesMelissa S. Cline, Guoying Liu, Ann E. Loraine, Ron Shigeta, Jill Cheng, Gangwu Mei, David Kulp, Michael A. Siani-Rose. 127-138 [doi]
• Representation and Processing of Complex DNA Spatial Architecture and its Annotated Genomic ContentRachid Gherbi, Joan Hérisson. 151-162 [doi]
• Pairwise RNA Structure Comparison with Stochastic Context-Free GrammarsIan Holmes, Gerald M. Rubin. 163-174 [doi]
• Estimation of Genetic Networks and Functional Structures Between Genes by Using Bayesian Networks and Nonparametric RegressionSeiya Imoto, Takao Goto, Satoru Miyano. 175-186 [doi]
• Automatic Annotation of Genomic Regulatory Sequences by Searching for Composite ClustersOlga V. Kel-Margoulis, T. G. Ivanova, Edgar Wingender, Alexander E. Kel. 187-198 [doi]
• EULER-PCR: Finishing Experiments for Repeat ResolutionZufar Mulyukov, Pavel A. Pevzner. 199-210 [doi]
• The Accuracy of Fast Phylogenetic Methods for Large DatasetsLuay Nakhleh, Bernard M. E. Moret, Usman Roshan, Katherine St. John, Jerry Sun, Tandy Warnow. 211-222 [doi]
• Pre-mRNA Secondary Structure Prediction Aids Splice Site PredictionDonald J. Patterson, Ken Yasuhara, Walter L. Ruzzo. 223-234 [doi]
• Finding Weak Motifs in DNA SequencesSing-Hoi Sze, Mikhail S. Gelfand, Pavel A. Pevzner. 235-246 [doi]
• Evidence for Sequence-Independent Evolutionary Traces in Genomics DataWayne Volkmuth, N. Alexandrov. 247-258 [doi]
• Multiple Genome Rearrangement by ReversalsShiquan Wu, Xun Gu. 259-270 [doi]
• High Speed Homology Search with FPGAsYoshiki Yamaguchi, Tsutomu Maruyama, Akihiko Konagaya. 271-282 [doi]
• Expanding Proteomics to Glycobiology - Session IntroductionClaus-Wilhelm von der Lieth. 283-284 [doi]
• Glycosylation of Proteins: A Computer Based Method for the Rapid Exploration of Comformational Space of N-GlycansAndreas Bohne, Claus-Wilhelm von der Lieth. 285-296 [doi]
• Data Standardisation in GlycoSuiteDBCatherine A. Cooper, Mathew J. Harrison, J. M. Webster, Marc R. Wilkins, Nicolle H. Packer. 297-309
• Prediction of Glycosylation Across the Human Proteome and the Correlation to Protein FunctionRamneek Gupta, Søren Brunak. 310-322 [doi]
• Literature Data Mining for Biology - Session IntroductionLynette Hirschman, Jong C. Park, Jun-ichi Tsujii, Cathy H. Wu, Limsoon Wong. 323-325 [doi]
• Mining MEDLINE: Abstracts, Sentences, or Phrases?Jing Ding, Daniel Berleant, Dan Nettleton, Eve Syrkin Wurtele. 326-337 [doi]
• Creating Knowledge Repositories from Biomedical Reports: The MEDSYNDIKATE Text Mining SystemUdo Hahn, Martin Romacker, Stefan Schulz. 338-349 [doi]
• Robust Relational Parsing Over Biomedical Literature: Extracting Inhibit RelationsJames Pustejovsky, José M. Castaño, Jason Zhang, M. Kotecki, B. Cochran. 362-373 [doi]
• Predicting the Sub-Cellular Location of Proteins from Text Using Support Vector MachinesB. J. Stapley, Lawrence A. Kelley, Michael J. E. Sternberg. 374-385 [doi]
• Genome, Pathway and Interaction Bioinformatics - Session IntroductionPeter D. Karp, Pedro Romero, Eric P. Neumann. 398-399 [doi]
• Pathway Logic: Symbolic Analysis of Biological SignalingSteven Eker, Merrill Knapp, Keith Laderoute, Patrick Lincoln, José Meseguer, M. Kemal Sönmez. 400-412 [doi]
• Towards the Prediction of Complete Protein-Protein Interaction NetworksShawn M. Gomez, Andrey Rzhetsky. 413-424 [doi]
• Identifying Muscle Regulatory Elements and Genes in the Nematode Caenorhabditis ElegansD. Guhathakurta, L. A. Schriefer, M. C. Hresko, R. H. Waterston, Gary D. Stormo. 425-436 [doi]
• Combining Location and Expression Data for Principled Discovery of Genetic Regulatory Network ModelsAlexander J. Hartemink, David K. Gifford, Tommi Jaakkola, Richard A. Young. 437-449 [doi]
• The ERATO Systems Biology Workbench: Enabling Interaction and Exchange Between Software Tools for Computational BiologyMichael Hucka, Andrew Finney, Herbert M. Sauro, H. Bolouri, John C. Doyle, Hiroaki Kitano. 450-461 [doi]
• Genome-Wide Pathway Analysis and Visualization Using Gene Expression DataManish P. Kurhekar, Sudeshna Adak, S. Jhunjhunwala, K. Raghupathy. 462-473 [doi]
• Exploring Gene Expression Data with Class ScoresPaul Pavlidis, Darrin P. Lewis, William Stafford Noble. 474-485 [doi]
• Guiding Revision of Regulatory Models with Expression DataJeff Shrager, Pat Langley, Andrew Pohorille. 486-497 [doi]
• Discovery of Causal Relationships in a Gene-Regulation Pathway from a Mixture of Experimental and Observational DNA Microarray DataChangwon Yoo, Vesteinn Thorsson, Gregory F. Cooper. 498-509 [doi]
• Phylogenetic Genomics and Genomic Phylogenetics - Session IntroductionScott Stanley, Benjamin A. Salisbury. 510-511 [doi]
• Shallow Genomics, Phylogenetics, and Evolution in the Family DrosophilidaeM. Zilversmit, P. O Grady, Robert DeSalle. 512-523 [doi]
• Fast Phylogenetic Methods for the Analysis of Genome Rearrangement Data: An Empirical StudyLi-San Wang, Robert K. Jansen, Bernard M. E. Moret, Linda A. Raubeson, Tandy Warnow. 524-535 [doi]
• Vertebrate Phylogenomics: Reconciled Trees and Gene DuplicationsRoderic D. M. Page, J. A. Cotton. 536-547 [doi]
• Proteins: Structure, Function and Evolution - Session IntroductionPeter Clote, Gavin J. P. Naylor, Ziheng Yang. 548-551 [doi]
• Screened Charge Electrostatic Model in Protein-Protein Docking SimulationsJuan Fernández-Recio, Maxim Totrov, Ruben Abagyan. 552-565 [doi]
• The Spectrum Kernel: A String Kernel for SVM Protein ClassificationChristina S. Leslie, Eleazar Eskin, William Stafford Noble. 566-575 [doi]
• Detecting Positively Selected Amino Acid Sites Using Posterior Predictive P-ValuesR. Nielsen, John P. Huelsenbeck. 576-588 [doi]
• Ab Initio Folding of Multiple-Chain ProteinsJ. A. Saunders, Kenneth D. Gibson, Harold A. Scheraga. 601-612 [doi]
• Investigating Evolutionary Lines of Least Resistance Using the Inverse Protein-Folding ProblemJ. Schonfeld, Oliver Eulenstein, Kent Vander Velden, Gavin J. P. Naylor. 613-624 [doi]
• Using Evolutionary Methods to Study G-Protein Coupled ReceptorsOrkun Soyer, Matthew W. Dimmic, Richard R. Neubig, Richard A. Goldstein. 625-636 [doi]
• Progress in Predicting Protein Function from Structure: Unique Features of O-GlycosidasesE. W. Stawiski, Yael Mandel-Gutfreund, A. C. Lowenthal, L. M. Gregoret. 637-648 [doi]
• Support Vector Machine Prediction of Signal Peptide Cleavage Site Using a New Class of Kernels for StringsJean-Philippe Vert. 649-660 [doi]
• Constraint-Based Hydrophobic Core Construction for Protein Structure Prediction in the Face-Centered-Cubic LatticeSebastian Will. 661-672 [doi]
• Detecting Native Protein Folds Among Large Decoy Sets with Hydrophobic Moment ProfilingRuhong Zhou, B. David Silverman. 673-684 [doi]