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6. PSB 2001: Hawaii, USA
- Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein:
Proceedings of the 6th Pacific Symposium on Biocomputing, PSB 2001, Hawaii, USA, January 3-7, 2001. 2001 - Preface.
Human Genome Variation: Linking Genotypes to Clinical Phenotypes
- Francisco M. de la Vega, Martin Kreitman, Isaac S. Kohane:
Human Genome Variation: Linking Genotypes to Clinical Phenotypes - Session Introduction. 3-5 - Atul J. Butte, J. Ye, G. Niederfellner, K. Rett, H. U. Häring, M. F. White, Isaac S. Kohane:
Determining Significant Fold Differences in Gene Expression Analysis. 6-17 - Derek Gordon, Jürg Ott:
Assessment and Management of Single Nucleotide Polymorphism Genotype Errors in Genetic Association. 18-29 - Ju-Han Kim, Lucila Ohno-Machado, Isaac S. Kohane:
Unsupervised Learning from Complex Data: The Matrix Incision Tree Algorithm. 30-41 - Gregory T. Klus, Andrew Song, Ari Schick, Mattias Wahde, Zoltan Szallasi:
Mutual Information Analysis as a Tool to Assess the Role of Aneuploidy in the Generation of Cancer-Associated Differential Gene Expression Patterns. 42-51 - Peter J. Park, Marcello Pagano, Marco Bonetti:
A Nonparametric Scoring Algorithm for Identifying Informative Genes from Microarray Data. 52-63
Disorder and Flexibility in Protein Structure and Function
- Clay Bracken, Malin M. Young, A. Keith Dunker:
Disorder and Flexibility in Protein Structure and Function - Session Introduction. 64-66 - Andrei T. Alexandrescu:
An NMR-Based Quenched Hydrogen Exchange Investigation of Model Amyloid Fibrils Formed by Cold Shock Protein A. 67-78 - J. J. Prompers, S. F. Lienin, R. Brüschweiler:
Collective Reorientational Motion and Nuclear Spin Relaxation in Proteins. 79-88 - R. M. Williams, Zoran Obradovic, V. Mathura, W. Braun, E. C. Garner, J. Young, S. Takayama, Celeste J. Brown, A. Keith Dunker:
The Protein Non-Folding Problem: Amino Acid Determinants of Intrinsic Order and Disorder. 89-100
DNA Structure, Protein-DNA Interactions, and DNA-Protein Expression
- Pierre Baldi, Richard H. Lathrop:
DNA Structure, Protein-DNA Interactions, and DNA-Protein Expression - Session Introduction. 101-102 - Craig J. Benham:
Stress-Induced DNA Duplex Destabilization in Transcriptional Initiation. 103-114 - Panayiotis V. Benos, Alan S. Lapedes, D. S. Fields, Gary D. Stormo:
SAMIE: Statistical Algorithm for Modeling Interaction Energies. 115-126 - X. Liu, Douglas L. Brutlag, Jun S. Liu:
BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes. 127-138 - Yael Mandel-Gutfreund, A. Baron, Hanah Margalit:
A Structure-Based Approach for Prediction of Protein Binding Sites in Gene-Upstream Regions. 139-150 - Paul Pavlidis, Terrence S. Furey, M. Liberto, David Haussler, William Noble Grundy:
Promoter Region-Based Classification of Genes. 151-164
Structures, Phylogenies, and Genomes: The Integrated Study of Protein Evolution
- Richard A. Goldstein, David D. Pollock, Jeffrey L. Thorne:
Structures, Phylogenies, and Genomes: The Integrated Study of Protein Evolution - Session Introduction. 164-166 - John S. Conery, Michael Lynch:
Nucleotide Substitutions and the Evolution of Duplicate Genes. 167-178 - Jotun Hein:
An Algorithm for Statistical Alignment of Sequences Related by a Binary Tree. 179-190 - Jeffrey M. Koshi, Richard A. Goldstein:
Analyzing Rate Heterogeneity During Protein Evolution. 191-202 - Andrey Rzhetsky, Pavel Morozov:
Markov Chain Monte Carlo Computation of Confidence Intervals for Substitution-Rate Variation in Proteins. 203-214 - Simon Tavaré, Dean C. Adams, Olivier Fedrigo, Gavin J. P. Naylor:
A Model for Phylogenetic Inference Using Structural and Chemical Covariates. 215-225 - Ziheng Yang:
Maximum Likelihood Analysis of Adaptive Evolution in HIV-1 Gp120 env Gene. 226-237
High Performance Computing for Computational Biology
- Thomas E. Ferrin, Bruce A. Foster, Richard Hughey:
High Performance Computing for Computational Biology - Session Introduction. 238-239 - D. Rey Banatao, Conrad C. Huang, Patricia C. Babbitt, Russ B. Altman, Teri E. Klein:
ViewFeature: Integrated Feature Analysis and Visualization. 240-250 - Alexander Dimitrov, John P. Miller:
Analyzing Sensory Systems with the Information Distortion Function. 251-262 - Leslie Grate, Mark Diekhans, David M. Dahle, Richard Hughey:
Sequence Analysis With the Kestrel SIMD Parallel Processor. 263-274 - Chittibabu Guda, Eric D. Scheeff, Philip E. Bourne, Ilya N. Shindyalov:
A New Algorithm for the Alignment of Multiple Protein Structures Using Monte Carlo Optimization. 275-286 - Tai Hsu, Paul Cull:
Gene Verification and Discovery by Walking Tree Method. 287-298 - Torgeir R. Hvidsten, Henryk Jan Komorowski, Arne K. Sandvik, Astrid Lægreid:
Predicting Gene Function from Gene Expressions and Ontologies. 299-310 - Wellington Santos Martins, Juan del Cuvillo, F. J. Useche, Kevin B. Theobald, Guang R. Gao:
A Multithreaded Parallel Implementation of a Dynamic Programming Algorithm for Sequence Comparison. 311-322 - Eric Rice, Richard Hughey:
Molecular Fingerprinting on the SIMD Parallel Processor Kestrel. 323-334 - Roman Sásik, Terence Hwa, N. Iranfar, W. F. Loomis:
Percolation Clustering: A Novel Algorithm Applied to the Clustering of Gene Expression Patterns in Dictyostelium Development. 335-347 - Rimli Sengupta, Martin Tompa:
Quality Control in Manufacturing Oligo Arrays: A Combinatorial Design Approach. 348-359 - Allison Waugh, Glenn A. Williams, Liping Wei, Russ B. Altman:
Using Metacomputing Tools to Facilitate Large Scale Analyses of Biological Databases. 360-371
Natural Language Processing for Biology
- Jun'ichi Tsujii, Limsoon Wong:
Natural Language Processing for Biology - Session Introduction. 372-373 - Jeffrey T. Chang, Soumya Raychaudhuri, Russ B. Altman:
Including Biological Literature Improves Homology Search. 374-383 - Ioannis Iliopoulos, Anton J. Enright, Christos A. Ouzounis:
TEXTQUEST: Document Clustering of MEDLINE Abstracts For Concept Discovery In Molecular Biology. 384-395 - Jong C. Park, Hyun Sook Kim, Jung-Jae Kim:
Bidirectional Incremental Parsing for Automatic Pathway Identification with Combinatory Categorial Grammar. 396-407 - Akane Yakushiji, Yuka Tateisi, Yusuke Miyao, Jun'ichi Tsujii:
Event Extraction from Biomedical Papers Using a Full Parser. 408-419
Genome, Pathway and Interaction Bioinformatics
- Peter D. Karp, Eric P. Neumann, Pedro Romero:
Genome, Pathway and Interaction Bioinformatics - Session Introduction. 420-421 - Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, Richard A. Young:
Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks. 422-433 - John R. Koza, William Mydlowec, Guido Lanza, Jessen Yu, Martin A. Keane:
Reverse Engineering of Metabolic Pathways from Observed Data Using Genetic Programming. 434-445 - Yukihiro Maki, Daisuke Tominaga, Masahiro Okamoto, Shoji Watanabe, Yukihiro Eguchi:
Development of a System for the Inference of Large Scale Genetic Networks. 446-458 - Aviv Regev, William Silverman, Ehud Shapiro:
Representation and Simulation of Biochemical Processes Using the pi-Calculus Process Algebra. 459-470 - Pedro Romero, Peter D. Karp:
Nutrition-Related Analysis of Pathway/Genome Databases. 470-482 - Matthew J. Stephens, Mathew J. Palakal, Snehasis Mukhopadhyay, Rajeev R. Raje, Javed Mostafa:
Detecting Gene Relations from MEDLINE Abstracts. 483-496 - Christine L. Tsien, T. A. Libermann, X. Gu, Isaac S. Kohane:
On Reporting Fold Differences. 496-507 - Lodewyk F. A. Wessels, Eugene P. van Someren, Marcel J. T. Reinders:
A Comparison of Genetic Network Models. 508-519 - Limsoon Wong:
PIES, A Protein Interaction Extraction System. 520-531 - Lingchong You, John Yin:
Simulating the Growth of Viruses. 532-543
Phylogenetics in the Post-Genomic Era
- Jennifer E. Steinbachs, Paul E. Kearney:
Phylogenetics in the Post-Genomic Era - Session Introduction. 544-546 - Olaf R. P. Bininda-Emonds, S. G. Brady, J. Kim, Michael J. Sanderson:
Scaling of Accuracy in Extremely Large Phylogenetic Trees. 547-558 - Patricia A. Evans, Harold T. Wareham:
Exact Algorithms for Computing Pairwise Alignments and 3-Medians From Structure-Annotated Sequences (Extended Abstract). 559-570 - Junhyong Kim, Benjamin A. Salisbury:
A Tree Obscured By Vines: Horizontal Gene Transfer and the Median Tree Method of Estimating Species Phylogeny. 571-582 - Bernard M. E. Moret, Stacia K. Wyman, David A. Bader
, Tandy J. Warnow, Mi Yan:
A New Implmentation and Detailed Study of Breakpoint Analysis. 583-594 - Fengrong Ren, Soichi Ogishima, Hiroshi Tanaka:
A New Algorithm for Analysis of Within-Host HIV-1 Evolution. 595-605 - Jennifer E. Steinbachs, Nikolaos V. Schizas, J. W. O. Ballard:
Efficiencies of Genes and Accuracy of Tree-Building Methods in Recovering a Known Drosophila Genealogy. 606-617
Bioethics, Fiction Science, and the Future of Mankind
- Pierre Baldi, Søren Brunak:
Bioethics, Fiction Science, and the Future of Mankind - Session Introduction. Pacific Symposium on Biocomputing 2001
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