PSB 2002 Online Proceedings

<HTML> <HEAD> <META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=windows-1252"> <TITLE>PSB 2002 Online Proceedings</TITLE> </HEAD> <BODY LINK="#0000ff" VLINK="#800080"> <H2 ALIGN="CENTER"><a href="http://psb.stanford.edu/psb02/">PSB 2002 Online Proceedings</a></H2> NOTE: This site is currently under construction. Approx. 90% of these links are operational, leading to Adobe .pdf files of the papers. Free .pdf readers may be obtained <A HREF="http://www.adobe.com/prodindex/acrobat/readstep.html">here</A>. <a href="http://psb.stanford.edu/psb-online/">PSB Proceedings For All Years</a> <hr> <h3>CONTENTS</h3> <ul> <li><a href="#preface">Preface</a></li> <li><a href="#genome">Human Genome Variation: Disease, Drug Response, and Clinical Phenotypes</a></li> <li><a href="#genomewide">Genome-Wide Analysis and Comparative Genomics</a></li> <li><a href="#glyco">Expanding Proteomics to Glycobiology</a></li> <li><a href="#mining">Literature Data Mining for Biology</a></li> <li><a href="#pathway">Genome, Pathway and Interaction Bioinformatics</a></li> <li><a href="#phylo">Phylogenetic Genomics and Genomic Phylogenetics</a></li> <li><a href="#protein">Proteins: Structure, Function and Evolution</a></a></li> </ul> <hr> <a href="http://www.smi.stanford.edu/projects/helix/psb02/preface.pdf">Preface</a> <h3><a name="genome">Human Genome Variation: Disease, Drug Response, and Clinical Phenotypes</a></h3> <dl> <dt><a href="humangenomeIntro.pdf"> Session Introduction</a> <dd>F.M. De la Vega, I. S. Kohane, J.A. Schneider, and J.C. Stephens; Pacific Symposium on Biocomputing 7:3-5 (2002). <dt><A HREF="benhur.pdf"> A Stability Based Method for Discovering Structure in Clustered Data</a> <dd>A. Ben-Hur, A. Elisseeff, and I. Guyon; Pacific Symposium on Biocomputing 7:6-17 (2002). <dt><A HREF="ghosh.pdf"> Singular Value Decomposition Regression Models for Classification of Tumors from Microarray Experiments</a> <dd>D. Ghosh; Pacific Symposium on Biocomputing 7:18-29 (2002). <dt><A HREF="heil.pdf"> An Automated Computer System to Support Ultra High Throughput SNP Genotyping</a> <dd>J. Heil, S. Glanowski, J. Scott, E. Winn-Deen, I. McMullen, L. Wu, C. Gire, and A. Sprague; Pacific Symposium on Biocomputing 7:30-40 (2002). <dt><A HREF="malin.pdf"> Inferring Genotype from Clinical Phenotype through a Knowledge Based Algorithm</a> <dd>B.A. Malin and L.A. Sweeney; Pacific Symposium on Biocomputing 7:41-52 (2002). <dt><a href="moore.pdf"> A Cellular Automata Approach to Detecting Interactions Among Single-nucleotide Polymorphisms in Complex Multifactorial Diseases</a> <dd>J.H. Moore and L.W. Hahn; Pacific Symposium on Biocomputing 7:53-64 (2002). <dt><a href="oliver.pdf"> Ontology Development for a Pharmacogenetics Knowledge Base</a> <dd>D.E. Oliver, D.L. Rubin, J.M. Stuart, M. Hewett, T.E. Klein, and R.B. Altman; Pacific Symposium on Biocomputing 7:65-76 (2002). <dt><a href="potter.pdf"> A SOFM Approach to Predicting HIV Drug Resistance</a> <dd>R.B. Potter and S. Draghici; Pacific Symposium on Biocomputing 7:77-87 (2002). <dt><a href="rubin.pdf"> Automating Data Acquisition into Ontologies from Pharmacogenetics Relational Data Sources Using Declarative Object Definitions and XML</a> <dd>D.L. Rubin, M. Hewett, D.E. Oliver, T.E. Klein, and R.B. Altman; Pacific Symposium on Biocomputing 7:88-99 (2002). <dt><a href="zhang.pdf"> On a Family-Based Haplotype Pattern Mining Method for Linkage Disequilibrium Mapping</a> <dd>S. Zhang, K. Zhang, J. Li, and H. Zhao; Pacific Symposium on Biocomputing 7:100-111 (2002). </dl> <h3><a name="genomewide">Genome-Wide Analysis and Comparative Genomics</a></h3> <dl> <dt><a href="genome-wideIntro.pdf"> Session Introduction</a> <dd>I. Dubchak, L. Pachter, and L. Wei; Pacific Symposium on Biocomputing 7:112-114 (2002). <dt><a href="chiaromonte.pdf"> Scoring Pairwise Genomic Sequence Alignments</a> <dd>F. Chiaromonte, V.B. Yap, and W. Miller; Pacific Symposium on Biocomputing 7:115-126 (2002). <dt><a href="cline.pdf"> Structure-Based Comparison of Four Eukaryotic Genomes</a> <dd>M. Cline, G. Liu, A.E. Loraine, R. Shigeta, J. Cheng, G. Mei, D. Kulp, and M.A. Siani-Rose; Pacific Symposium on Biocomputing 7:127-138 (2002). <dt><a href="goldberg.pdf"> Constructing Comparative Genome Maps with Unresolved Marker Order</a> <dd>D. Goldberg, S. McCouch, and J. Kleinberg; Pacific Symposium on Biocomputing 7:139-150 (2002). <dt><a href="gherbi.pdf"> Representation and Processing of Complex DNA Spatial Architecture and its Annotated Genomic Content</a> <dd>R. Gherbi and J. Herisson; Pacific Symposium on Biocomputing 7:151-162 (2002). <dt><a href="holmes.pdf"> Pairwise RNA Structure Comparison with Stochastic Context-Free Grammars</a> <dd>I. Holmes and G.M. Rubin; Pacific Symposium on Biocomputing 7:163-174 (2002). <dt><a href="imoto.pdf"> Estimation of Genetic Networks and Functional Structures Between Genes by Using Bayesian Networks and Nonparametric Regression</a> <dd>S. Imoto, T. Goto and S. Miyano; Pacific Symposium on Biocomputing 7:175-186 (2002). <dt><a href="kel-margoulis.pdf"> Automatic Annotation of Genomic Regulatory Sequences by Searching for Composite Clusters</a> <dd>O.V. Kel-Margoulis, T.G. Ivanova, E. Wingender, and A.E. Kel; Pacific Symposium on Biocomputing 7:187-198 (2002). <dt><a href="mulyukov.pdf"> EULER-PCR: Finishing Experiments for Repeat Resolution</a> <dd>Z. Mulyukov and P.A. Pevzner; Pacific Symposium on Biocomputing 7:199-210 (2002). <dt><a href="nakhleh.pdf"> The Accuracy of Fast Phylogenetic Methods for Large Datasets</a> <dd>L. Nakhleh, B.M.E. Moret, U. Roshan, K. St. John, J. Sun, and T. Warnow; Pacific Symposium on Biocomputing 7:211-222 (2002). <dt><a href="patterson.pdf"> Pre-mRNA Secondary Structure Prediction Aids Splice Site Prediction</a> <dd>D.J. Patterson, K. Yasuhara, and W.L. Ruzzo; Pacific Symposium on Biocomputing 7:223-234 (2002). <dt><a href="sze.pdf"> Finding Weak Motifs in DNA Sequences</a> <dd>S.-H. Sze, M.S. Gelfand, and P.A. Pevzner; Pacific Symposium on Biocomputing 7:235-246 (2002). <dt><a href="volkmuth.pdf"> Evidence for Sequence-Independent Evolutionary Traces in Genomics Data</a> <dd>W. Volkmuth, and N. Alexandrov; Pacific Symposium on Biocomputing 7:247-258 (2002). <dt><a href="wu.pdf"> Multiple Genome Rearrangement by Reversals</a> <dd>S. Wu and X. Gu; Pacific Symposium on Biocomputing 7:259-270 (2002). <dt><a href="yamaguchi.pdf"> High Speed Homology Search with FPGAs</a> <dd>Y. Yamaguchi, T. Maruyama, and A. Konagaya; Pacific Symposium on Biocomputing 7:271-282 (2002). </dl> <h3><a name="glyco">Expanding Proteomics to Glycobiology</a></h3> <dl> <dt><a href="expandingIntro.pdf"> Session Introduction</a> <dd>C.-W. von der Lieth; Pacific Symposium on Biocomputing 7:283-284 (2002). <dt><a href="bohne.pdf"> Glycosylation of Proteins: A Computer Based Method for the Rapid Exploration of Comformational Space of N-Glycans</a> <dd>A. Bohne and C.-W. von der Lieth; Pacific Symposium on Biocomputing 7:285-296 (2002). <dt> <a href="cooper.pdf">Data Standardisation in GlycoSuiteDB</a> <dd>C.A. Cooper, M.J. Harrison, J.M. Webster, M.R. Wilkins, and N.H. Packer; Pacific Symposium on Biocomputing 7:297-309 (2002). <dt><a href="gupta.pdf"> Prediction of Glycosylation Across the Human Proteome and the Correlation to Protein Function</a> <dd>R. Gupta and S. Brunak; Pacific Symposium on Biocomputing 7:310-322 (2002). </dl> <h3><a name="mining">Literature Data Mining for Biology</a></h3> <dl> <dt><a href="literatureIntro.pdf"> Session Introduction</a> <dd>L., Hirschman, J.C. Park, J. Tsujii, C. Wu, and L. Wong; Pacific Symposium on Biocomputing 7:323-325 (2002). <dt><a href="ding.pdf"> Mining MEDLINE: Abstracts, Sentences, or Phrases?</a> <dd>J. Ding, D. Berleant, D. Nettleton, and E. Wurtele; Pacific Symposium on Biocomputing 7:326-337 (2002). <dt><a href="hahn.pdf"> Creating Knowledge Repositories from Biomedical Reports: The MEDSYNDIKATE Text Mining System</a> <dd>U. Hahn, M. Romacker, and S. Schulz; Pacific Symposium on Biocomputing 7:338-349 (2002). <dt><a href="leroy.pdf"> Filling Preposition-Based Templates to Capture Information from Medical Abstracts</a> <dd>G. Leroy and H. Chen; Pacific Symposium on Biocomputing 7:350-361 (2002). <dt><a href="pustejovsk.pdf"> Robust Relational Parsing Over Biomedical Literature: Extracting Inhibit Relations</a> <dd>J. Pustejovsky, J. Casta駉, J. Zhang, M. Kotecki, and B. Cochran; Pacific Symposium on Biocomputing 7:362-373 (2002). <dt><a href="stapley.pdf"> Predicting the Sub-Cellular Location of Proteins from Text Using Support Vector Machines</a> <dd>B.J. Stapley, L.A. Kelley, and M.J.E. Sternberg; Pacific Symposium on Biocomputing 7:374-385 (2002). <dt><a href="wilbur.pdf"> A Thematic Analysis of the AIDS Literature</a> <dd>W.J. Wilbur; Pacific Symposium on Biocomputing 7:386-397 (2002). </dl> <h3><a name="pathway">Genome, Pathway and Interaction Bioinformatics</a></h3> <dl> <dt><a href="genomepathwayIntro.pdf"> Session Introduction</a> <dd>P. Karp, P.R. Romero, and E. Neumann; Pacific Symposium on Biocomputing 7:398-399 (2002). <dt><a href="eker.pdf"> Pathway Logic: Symbolic Analysis of Biological Signaling</a> <dd>S. Eker, M. Knapp, K. Laderoute, P. Lincoln, J. Meseguer, and K. Sonmez; Pacific Symposium on Biocomputing 7:400-412 (2002). <dt><a href="gomez.pdf"> Towards the Prediction of Complete Protein-Protein Interaction Networks</a> <dd>S.M. Gomez and A. Rzhetsky; Pacific Symposium on Biocomputing 7:413-424 (2002). <dt><a href="guhathakurta.pdf"> Identifying Muscle Regulatory Elements and Genes in the Nematode Caenorhabditis Elegans</a> <dd>D. Guhathakurta, L.A. Schriefer, M.C. Hresko, R.H. Waterston, and G.D. Stormo; Pacific Symposium on Biocomputing 7:425-436 (2002). <dt><a href="hartemink.pdf"> Combining Location and Expression Data for Principled Discovery of Genetic Regulatory Network Models</a> <dd>A.J. Hartemink, D.K. Gifford, T.S. Jaakkola, and R.A. Young; Pacific Symposium on Biocomputing 7:437-449 (2002). <dt><a href="hucka.pdf"> The ERATO Systems Biology Workbench: Enabling Interaction and Exchange Between Software Tools for Computational Biology</a> <dd>M. Hucka, A. Finney, H.M. Sauro, H. Bolouri, J. Doyle, and H. Kitano; Pacific Symposium on Biocomputing 7:450-461 (2002). <dt><a href="kurhekar.pdf"> Genome-Wide Pathway Analysis and Visualization Using Gene Expression Data</a> <dd>M.P. Kurhekar, S. Adak, S. Jhunjhunwala, and K. Raghupathy; Pacific Symposium on Biocomputing 7:462-473 (2002). <dt><a href="pavlidis.pdf"> Exploring Gene Expression Data with Class Scores</a> <dd>P. Pavlidis, D.P. Lewis, and W.S. Noble; Pacific Symposium on Biocomputing 7:474-485 (2002). <dt><a href="shrager.pdf"> Guiding Revision of Regulatory Models with Expression Data</a> <dd>J. Shrager, P. Langley, and A. Pohorille; Pacific Symposium on Biocomputing 7:486-497 (2002). <dt><a href="yoo.pdf"> Discovery of Causal Relationships in a Gene-Regulation Pathway from a Mixture of Experimental and Observational DNA Microarray Data</a> <dd>C. Yoo, V. Thorsson, and G.F. Cooper; Pacific Symposium on Biocomputing 7:498-509 (2002). </dl> <h3><a name="phylo">Phylogenetic Genomics and Genomic Phylogenetics</a></h3> <dl> <dt><a href="phylogeneticIntro.pdf"> Session Introduction</a> <dd>S. Stanley and B.A. Salisbury; Pacific Symposium on Biocomputing 7:510-511 (2002). <dt><a href="zilvermit.pdf"> Shallow Genomics, Phylogenetics, and Evolution in the Family Drosophilidae</a> <dd>M. Zilversmit, P. O'Grady, and R. Desalle; Pacific Symposium on Biocomputing 7:512-523 (2002). <dt><a href="wang.pdf"> Fast Phylogenetic Methods for the Analysis of Genome Rearrangement Data: An Empirical Study</a> <dd>L.-S. Wang, R.K. Jansen, B.M.E. Moret, L.A. Raubeson, and T. Warnow; Pacific Symposium on Biocomputing 7:524-535 (2002). <dt><a href="page.pdf"> Vertebrate Phylogenomics: Reconciled Trees and Gene Duplications</a> <dd>R.D.M. Page and J.A. Cotton; Pacific Symposium on Biocomputing 7:536-547 (2002). </dl> <h3><a name="protein">Proteins: Structure, Function and Evolution</a></h3> <dl> <dt><a href="proteinsIntro.pdf"> Session Introduction</a> <dd>P. Clote, G.J.P. Naylor, and Z. Yang; Pacific Symposium on Biocomputing 7:548-551 (2002). <dt><a href="fernandez-recio.pdf"> Screened Charge Electrostatic Model in Protein-Protein Docking Simulations</a> <dd>J. Fernandez-Recio, M. Totrov, and R. Abagyan; Pacific Symposium on Biocomputing 7:552-565 (2002). <dt><a href="leslie.pdf"> The Spectrum Kernel: A String Kernel for SVM Protein Classification</a> <dd>C. Leslie, E. Eskin, and W.S. Noble; Pacific Symposium on Biocomputing 7:566-575 (2002). <dt><a href="nielsen.pdf"> Detecting Positively Selected Amino Acid Sites Using Posterior Predictive P-Values</a> <dd>R. Nielsen and J. P Huelsenbeck; Pacific Symposium on Biocomputing 7:576-588 (2002). <dt><a href="radivojac.pdf"> Improving Sequence Alignments For Intrinsically Disordered Proteins</a> <dd>P. Radivojac, Z. Obradovic, C.J. Brown, and A.K. Dunker; Pacific Symposium on Biocomputing 7:589-600 (2002). <dt><a href="saunders.pdf"> ab initio Folding of Multiple-Chain Proteins</a> <dd>J.A. Saunders, K.D. Gibson, and H.A. Scheraga; Pacific Symposium on Biocomputing 7:601-612 (2002). <dt><a href="schonfeld.pdf"> Investigating Evolutionary Lines of Least Resistance Using the Inverse Protein-Folding Problem</a> <dd>J. Schonfeld, O. Eulenstein, K. Vander Velden, and G.J.P. Naylor; Pacific Symposium on Biocomputing 7:613-624 (2002). <dt><a href="soyer.pdf"> Using Evolutionary Methods to Study G-Protein Coupled Receptors</a> <dd>O. Soyer, M.W. Dimmic, R.R. Neubig, and R.A. Goldstein; Pacific Symposium on Biocomputing 7:625-636 (2002). <dt><a href="stawiski.pdf"> Progress in Predicting Protein Function from Structure: Unique Features of O-Glycosidases</a> <dd>E.W. Stawiski, Y. Mandel-Gutfreund, A.C. Lowenthal, and L.M. Gregoret; Pacific Symposium on Biocomputing 7:637-648 (2002). <dt><a href="vert.pdf"> Support Vector Machine Prediction of Signal Peptide Cleavage Site Using a New Class of Kernels for Strings</a> <dd>J.-P. Vert; Pacific Symposium on Biocomputing 7:649-660 (2002). <dt><a href="will.pdf"> Constraint-Based Hydrophobic Core Construction for Protein Structure Prediction in the Face-Centered-Cubic Lattice</a> <dd>S. Will; Pacific Symposium on Biocomputing 7:661-672 (2002). <dt><a href="zhou.pdf"> Detecting Native Protein Folds Among Large Decoy Sets with Hydrophobic Moment Profiling</a> <dd>R. Zhou and B.D. Silverman; Pacific Symposium on Biocomputing 7:673-684 (2002). </dl> <hr> <table width="100%" border="0" cellspacing="0" align="center"><tr> <td align="left"><a href="http://www-smi.stanford.edu/projects/helix/psb-online/">Back to the PSB Online Proceedings page</a></td> <td align="right">Updated: February 19, 2002</td> </tr></table> </body> </html>

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PSB 2002 Online Proceedings