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7. PSB 2002: Lihue, Hawaii, USA
- Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein:
Proceedings of the 7th Pacific Symposium on Biocomputing, PSB 2002, Lihue, Hawaii, USA, January 3-7, 2002. 2002 - 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, Julie A. Schneider, J. Claiborne 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 - Jeremy Heil, Stephen Glanowski, J. Scott, Emily S. Winn-Deen, Ivy McMullen, L. Wu, C. Gire, A. Sprague:
An Automated Computer System to Support Ultra High Throughput SNP Genotyping. 30-40 - Bradley A. 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 J. 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. Pacific Symposium on Biocomputing 2002: 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, Maciej Kotecki, Brent Cochran:
Robust Relational Parsing Over Biomedical Literature: Extracting Inhibit Relations. 362-373 - Benjamin 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 S. 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, Suchit 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 J. 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 - Rasmus 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 - Eric 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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