Abstract is missing.
- Bioethics, Fiction Science, and the Future of Mankind - Session IntroductionPierre Baldi, Søren Brunak.
- Human Genome Variation: Linking Genotypes to Clinical Phenotypes - Session IntroductionFrancisco M. de la Vega, Martin Kreitman, Isaac S. Kohane. 3-5 [doi]
- Determining Significant Fold Differences in Gene Expression AnalysisAtul J. Butte, J. Ye, G. Niederfellner, K. Rett, H. U. Häring, M. F. White, Isaac S. Kohane. 6-17 [doi]
- Assessment and Management of Single Nucleotide Polymorphism Genotype Errors in Genetic AssociationDerek Gordon, Jürg Ott. 18-29 [doi]
- Unsupervised Learning from Complex Data: The Matrix Incision Tree AlgorithmJu Han Kim, Lucila Ohno-Machado, Isaac S. Kohane. 30-41 [doi]
- Mutual Information Analysis as a Tool to Assess the Role of Aneuploidy in the Generation of Cancer-Associated Differential Gene Expression PatternsGregory T. Klus, Andrew Song, Ari Schick, Mattias Wahde, Zoltan Szallasi. 42-51 [doi]
- The Protein Non-Folding Problem: Amino Acid Determinants of Intrinsic Order and DisorderR. M. Williams, Zoran Obradovic, V. Mathura, W. Braun, E. C. Garner, J. Young, S. Takayama, Celeste J. Brown, A. Keith Dunker. 89-100 [doi]
- DNA Structure, Protein-DNA Interactions, and DNA-Protein Expression - Session IntroductionP. F. Baldi, Richard H. Lathrop. 101-102 [doi]
- Stress-Induced DNA Duplex Destabilization in Transcriptional InitiationCraig J. Benham. 103-114 [doi]
- SAMIE: Statistical Algorithm for Modeling Interaction EnergiesPanayiotis V. Benos, Alan S. Lapedes, D. S. Fields, Gary D. Stormo. 115-126 [doi]
- BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed GenesX. Liu, Douglas L. Brutlag, Jun S. Liu. 127-138 [doi]
- An Algorithm for Statistical Alignment of Sequences Related by a Binary TreeJotun Hein. 179-190 [doi]
- Analyzing Rate Heterogeneity During Protein EvolutionJeffrey M. Koshi, Richard A. Goldstein. 191-202 [doi]
- Markov Chain Monte Carlo Computation of Confidence Intervals for Substitution-Rate Variation in ProteinsAndrey Rzhetsky, Pavel Morozov. 203-214 [doi]
- A Model for Phylogenetic Inference Using Structural and Chemical CovariatesSimon Tavaré, Dean C. Adams, Olivier Fedrigo, Gavin J. P. Naylor. 215-225 [doi]
- Maximum Likelihood Analysis of Adaptive Evolution in HIV-1 Gp120 env GeneZiheng Yang. 226-237 [doi]
- High Performance Computing for Computational Biology - Session IntroductionThomas E. Ferrin, Bruce A. Foster, Richard Hughey. 238-239 [doi]
- ViewFeature: Integrated Feature Analysis and VisualizationD. Rey Banatao, Conrad C. Huang, Patricia C. Babbitt, Russ B. Altman, Teri E. Klein. 240-250 [doi]
- Analyzing Sensory Systems with the Information Distortion FunctionAlexander Dimitrov, John P. Miller. 251-262 [doi]
- Sequence Analysis With the Kestrel SIMD Parallel ProcessorLeslie Grate, Mark Diekhans, David M. Dahle, Richard Hughey. 263-274 [doi]
- A New Algorithm for the Alignment of Multiple Protein Structures Using Monte Carlo OptimizationChittibabu Guda, Eric D. Scheeff, Philip E. Bourne, Ilya N. Shindyalov. 275-286 [doi]
- Gene Verification and Discovery by Walking Tree MethodTai Hsu, Paul Cull. 287-298 [doi]
- Predicting Gene Function from Gene Expressions and OntologiesTorgeir R. Hvidsten, Henryk Jan Komorowski, Arne K. Sandvik, Astrid Lægreid. 299-310 [doi]
- A Multithreaded Parallel Implementation of a Dynamic Programming Algorithm for Sequence ComparisonW. S. Martins, Juan del Cuvillo, F. J. Useche, Kevin B. Theobald, Guang R. Gao. 311-322 [doi]
- Molecular Fingerprinting on the SIMD Parallel Processor KestrelEric Rice, Richard Hughey. 323-334 [doi]
- Percolation Clustering: A Novel Algorithm Applied to the Clustering of Gene Expression Patterns in Dictyostelium DevelopmentR. Sásik, Terence Hwa, N. Iranfar, W. F. Loomis. 335-347 [doi]
- Quality Control in Manufacturing Oligo Arrays: A Combinatorial Design ApproachRimli Sengupta, Martin Tompa. 348-359 [doi]
- Using Metacomputing Tools to Facilitate Large Scale Analyses of Biological DatabasesAllison Waugh, Glenn A. Williams, Liping Wei, Russ B. Altman. 360-371 [doi]
- Natural Language Processing for Biology - Session IntroductionJun-ichi Tsujii, Limsoon Wong. 372-373 [doi]
- Including Biological Literature Improves Homology SearchJeffrey T. Chang, Soumya Raychaudhuri, Russ B. Altman. 374-383 [doi]
- TEXTQUEST: Document Clustering of MEDLINE Abstracts For Concept Discovery In Molecular BiologyIoannis Iliopoulos, Anton J. Enright, Christos A. Ouzounis. 384-395 [doi]
- Bidirectional Incremental Parsing for Automatic Pathway Identification with Combinatory Categorial GrammarJong C. Park, Hyun Sook Kim, Jung-jae Kim. 396-407 [doi]
- Event Extraction from Biomedical Papers Using a Full ParserAkane Yakushiji, Yuka Tateisi, Yusuke Miyao, Jun-ichi Tsujii. 408-419 [doi]
- Genome, Pathway and Interaction Bioinformatics - Session IntroductionPeter D. Karp, Eric P. Neumann, Pedro Romero. 420-421 [doi]
- Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory NetworksAlexander J. Hartemink, David K. Gifford, Tommi Jaakkola, Richard A. Young. 422-433 [doi]
- Reverse Engineering of Metabolic Pathways from Observed Data Using Genetic ProgrammingJohn R. Koza, William Mydlowec, Guido Lanza, Jessen Yu, Martin A. Keane. 434-445 [doi]
- Development of a System for the Inference of Large Scale Genetic NetworksYukihiro Maki, Daisuke Tominaga, Masahiro Okamoto, Shoji Watanabe, Yukihiro Eguchi. 446-458 [doi]
- Representation and Simulation of Biochemical Processes Using the pi-Calculus Process AlgebraAviv Regev, William Silverman, Ehud Y. Shapiro. 459-470 [doi]
- Nutrition-Related Analysis of Pathway/Genome DatabasesPedro Romero, Peter D. Karp. 470-482 [doi]
- Detecting Gene Relations from MEDLINE AbstractsMatthew Stephens, Mathew J. Palakal, Snehasis Mukhopadhyay, Rajeev R. Raje, Javed Mostafa. 483-496 [doi]
- On Reporting Fold DifferencesChristine L. Tsien, T. A. Libermann, X. Gu, Isaac S. Kohane. 496-507 [doi]
- A Comparison of Genetic Network ModelsLodewyk F. A. Wessels, Eugene P. van Someren, Marcel J. T. Reinders. 508-519 [doi]
- PIES, A Protein Interaction Extraction SystemLimsoon Wong. 520-531 [doi]
- Simulating the Growth of VirusesLingchong You, John Yin. 532-543 [doi]
- Phylogenetics in the Post-Genomic Era - Session IntroductionJennifer E. Steinbachs, Paul E. Kearney. 544-546 [doi]
- Scaling of Accuracy in Extremely Large Phylogenetic TreesOlaf R. P. Bininda-Emonds, S. G. Brady, J. Kim, Michael J. Sanderson. 547-558 [doi]
- Exact Algorithms for Computing Pairwise Alignments and 3-Medians From Structure-Annotated Sequences (Extended Abstract)Patricia A. Evans, Harold T. Wareham. 559-570 [doi]
- A Tree Obscured By Vines: Horizontal Gene Transfer and the Median Tree Method of Estimating Species PhylogenyJunhyong Kim, Benjamin A. Salisbury. 571-582 [doi]
- A New Implmentation and Detailed Study of Breakpoint AnalysisBernard M. E. Moret, Stacia K. Wyman, David A. Bader, Tandy Warnow, Mi Yan. 583-594 [doi]
- A New Algorithm for Analysis of Within-Host HIV-1 EvolutionFengrong Ren, Soichi Ogishima, Hiroshi Tanaka. 595-605 [doi]
- Efficiencies of Genes and Accuracy of Tree-Building Methods in Recovering a Known Drosophila GenealogyJennifer E. Steinbachs, Nikolaos V. Schizas, J. W. O. Ballard. 606-617 [doi]