CONTENTS

• Preface
• Human Genome Variation: Disease, Drug Response, and Clinical Phenotypes
• Genome-Wide Analysis and Comparative Genomics
• Expanding Proteomics to Glycobiology
• Literature Data Mining for Biology
• Genome, Pathway and Interaction Bioinformatics
• Phylogenetic Genomics and Genomic Phylogenetics
• Proteins: Structure, Function and Evolution

Preface

Human Genome Variation: Disease, Drug Response, and Clinical Phenotypes

Session Introduction

F.M. De la Vega, I. S. Kohane, J.A. Schneider, and J.C. Stephens; Pacific Symposium on Biocomputing 7:3-5 (2002).

A Stability Based Method for Discovering Structure in Clustered Data

A. Ben-Hur, A. Elisseeff, and I. Guyon; Pacific Symposium on Biocomputing 7:6-17 (2002).

Singular Value Decomposition Regression Models for Classification of Tumors from Microarray Experiments

D. Ghosh; Pacific Symposium on Biocomputing 7:18-29 (2002).

An Automated Computer System to Support Ultra High Throughput SNP Genotyping

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).

Inferring Genotype from Clinical Phenotype through a Knowledge Based Algorithm

B.A. Malin and L.A. Sweeney; Pacific Symposium on Biocomputing 7:41-52 (2002).

A Cellular Automata Approach to Detecting Interactions Among Single-nucleotide Polymorphisms in Complex Multifactorial Diseases

J.H. Moore and L.W. Hahn; Pacific Symposium on Biocomputing 7:53-64 (2002).

Ontology Development for a Pharmacogenetics Knowledge Base

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).

A SOFM Approach to Predicting HIV Drug Resistance

R.B. Potter and S. Draghici; Pacific Symposium on Biocomputing 7:77-87 (2002).

Automating Data Acquisition into Ontologies from Pharmacogenetics Relational Data Sources Using Declarative Object Definitions and XML

D.L. Rubin, M. Hewett, D.E. Oliver, T.E. Klein, and R.B. Altman; Pacific Symposium on Biocomputing 7:88-99 (2002).

On a Family-Based Haplotype Pattern Mining Method for Linkage Disequilibrium Mapping

S. Zhang, K. Zhang, J. Li, and H. Zhao; Pacific Symposium on Biocomputing 7:100-111 (2002).

Genome-Wide Analysis and Comparative Genomics

Session Introduction

I. Dubchak, L. Pachter, and L. Wei; Pacific Symposium on Biocomputing 7:112-114 (2002).

Scoring Pairwise Genomic Sequence Alignments

F. Chiaromonte, V.B. Yap, and W. Miller; Pacific Symposium on Biocomputing 7:115-126 (2002).

Structure-Based Comparison of Four Eukaryotic Genomes

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).

Constructing Comparative Genome Maps with Unresolved Marker Order

D. Goldberg, S. McCouch, and J. Kleinberg; Pacific Symposium on Biocomputing 7:139-150 (2002).

Representation and Processing of Complex DNA Spatial Architecture and its Annotated Genomic Content

R. Gherbi and J. Herisson; Pacific Symposium on Biocomputing 7:151-162 (2002).

Pairwise RNA Structure Comparison with Stochastic Context-Free Grammars

I. Holmes and G.M. Rubin; Pacific Symposium on Biocomputing 7:163-174 (2002).

Estimation of Genetic Networks and Functional Structures Between Genes by Using Bayesian Networks and Nonparametric Regression

S. Imoto, T. Goto and S. Miyano; Pacific Symposium on Biocomputing 7:175-186 (2002).

Automatic Annotation of Genomic Regulatory Sequences by Searching for Composite Clusters

O.V. Kel-Margoulis, T.G. Ivanova, E. Wingender, and A.E. Kel; Pacific Symposium on Biocomputing 7:187-198 (2002).

EULER-PCR: Finishing Experiments for Repeat Resolution

Z. Mulyukov and P.A. Pevzner; Pacific Symposium on Biocomputing 7:199-210 (2002).

The Accuracy of Fast Phylogenetic Methods for Large Datasets

L. Nakhleh, B.M.E. Moret, U. Roshan, K. St. John, J. Sun, and T. Warnow; Pacific Symposium on Biocomputing 7:211-222 (2002).

Pre-mRNA Secondary Structure Prediction Aids Splice Site Prediction

D.J. Patterson, K. Yasuhara, and W.L. Ruzzo; Pacific Symposium on Biocomputing 7:223-234 (2002).

Finding Weak Motifs in DNA Sequences

S.-H. Sze, M.S. Gelfand, and P.A. Pevzner; Pacific Symposium on Biocomputing 7:235-246 (2002).

Evidence for Sequence-Independent Evolutionary Traces in Genomics Data

W. Volkmuth, and N. Alexandrov; Pacific Symposium on Biocomputing 7:247-258 (2002).

Multiple Genome Rearrangement by Reversals

S. Wu and X. Gu; Pacific Symposium on Biocomputing 7:259-270 (2002).

High Speed Homology Search with FPGAs

Y. Yamaguchi, T. Maruyama, and A. Konagaya; Pacific Symposium on Biocomputing 7:271-282 (2002).

Expanding Proteomics to Glycobiology

Session Introduction

C.-W. von der Lieth; Pacific Symposium on Biocomputing 7:283-284 (2002).

Glycosylation of Proteins: A Computer Based Method for the Rapid Exploration of Comformational Space of N-Glycans

A. Bohne and C.-W. von der Lieth; Pacific Symposium on Biocomputing 7:285-296 (2002).

Data Standardisation in GlycoSuiteDB

C.A. Cooper, M.J. Harrison, J.M. Webster, M.R. Wilkins, and N.H. Packer; Pacific Symposium on Biocomputing 7:297-309 (2002).

Prediction of Glycosylation Across the Human Proteome and the Correlation to Protein Function

R. Gupta and S. Brunak; Pacific Symposium on Biocomputing 7:310-322 (2002).

Literature Data Mining for Biology

Session Introduction

L., Hirschman, J.C. Park, J. Tsujii, C. Wu, and L. Wong; Pacific Symposium on Biocomputing 7:323-325 (2002).

Mining MEDLINE: Abstracts, Sentences, or Phrases?

J. Ding, D. Berleant, D. Nettleton, and E. Wurtele; Pacific Symposium on Biocomputing 7:326-337 (2002).

Creating Knowledge Repositories from Biomedical Reports: The MEDSYNDIKATE Text Mining System

U. Hahn, M. Romacker, and S. Schulz; Pacific Symposium on Biocomputing 7:338-349 (2002).

Filling Preposition-Based Templates to Capture Information from Medical Abstracts

G. Leroy and H. Chen; Pacific Symposium on Biocomputing 7:350-361 (2002).

Robust Relational Parsing Over Biomedical Literature: Extracting Inhibit Relations

J. Pustejovsky, J. Castaño, J. Zhang, M. Kotecki, and B. Cochran; Pacific Symposium on Biocomputing 7:362-373 (2002).

Predicting the Sub-Cellular Location of Proteins from Text Using Support Vector Machines

B.J. Stapley, L.A. Kelley, and M.J.E. Sternberg; Pacific Symposium on Biocomputing 7:374-385 (2002).

A Thematic Analysis of the AIDS Literature

W.J. Wilbur; Pacific Symposium on Biocomputing 7:386-397 (2002).

Genome, Pathway and Interaction Bioinformatics

Session Introduction

P. Karp, P.R. Romero, and E. Neumann; Pacific Symposium on Biocomputing 7:398-399 (2002).

Pathway Logic: Symbolic Analysis of Biological Signaling

S. Eker, M. Knapp, K. Laderoute, P. Lincoln, J. Meseguer, and K. Sonmez; Pacific Symposium on Biocomputing 7:400-412 (2002).

Towards the Prediction of Complete Protein-Protein Interaction Networks

S.M. Gomez and A. Rzhetsky; Pacific Symposium on Biocomputing 7:413-424 (2002).

Identifying Muscle Regulatory Elements and Genes in the Nematode Caenorhabditis Elegans

D. Guhathakurta, L.A. Schriefer, M.C. Hresko, R.H. Waterston, and G.D. Stormo; Pacific Symposium on Biocomputing 7:425-436 (2002).

Combining Location and Expression Data for Principled Discovery of Genetic Regulatory Network Models

A.J. Hartemink, D.K. Gifford, T.S. Jaakkola, and R.A. Young; Pacific Symposium on Biocomputing 7:437-449 (2002).

The ERATO Systems Biology Workbench: Enabling Interaction and Exchange Between Software Tools for Computational Biology

M. Hucka, A. Finney, H.M. Sauro, H. Bolouri, J. Doyle, and H. Kitano; Pacific Symposium on Biocomputing 7:450-461 (2002).

Genome-Wide Pathway Analysis and Visualization Using Gene Expression Data

M.P. Kurhekar, S. Adak, S. Jhunjhunwala, and K. Raghupathy; Pacific Symposium on Biocomputing 7:462-473 (2002).

Exploring Gene Expression Data with Class Scores

P. Pavlidis, D.P. Lewis, and W.S. Noble; Pacific Symposium on Biocomputing 7:474-485 (2002).

Guiding Revision of Regulatory Models with Expression Data

J. Shrager, P. Langley, and A. Pohorille; Pacific Symposium on Biocomputing 7:486-497 (2002).

Discovery of Causal Relationships in a Gene-Regulation Pathway from a Mixture of Experimental and Observational DNA Microarray Data

C. Yoo, V. Thorsson, and G.F. Cooper; Pacific Symposium on Biocomputing 7:498-509 (2002).

Phylogenetic Genomics and Genomic Phylogenetics

Session Introduction

S. Stanley and B.A. Salisbury; Pacific Symposium on Biocomputing 7:510-511 (2002).

Shallow Genomics, Phylogenetics, and Evolution in the Family Drosophilidae

M. Zilversmit, P. O'Grady, and R. Desalle; Pacific Symposium on Biocomputing 7:512-523 (2002).

Fast Phylogenetic Methods for the Analysis of Genome Rearrangement Data: An Empirical Study

L.-S. Wang, R.K. Jansen, B.M.E. Moret, L.A. Raubeson, and T. Warnow; Pacific Symposium on Biocomputing 7:524-535 (2002).

Vertebrate Phylogenomics: Reconciled Trees and Gene Duplications

R.D.M. Page and J.A. Cotton; Pacific Symposium on Biocomputing 7:536-547 (2002).

Proteins: Structure, Function and Evolution

Session Introduction

P. Clote, G.J.P. Naylor, and Z. Yang; Pacific Symposium on Biocomputing 7:548-551 (2002).

Screened Charge Electrostatic Model in Protein-Protein Docking Simulations

J. Fernandez-Recio, M. Totrov, and R. Abagyan; Pacific Symposium on Biocomputing 7:552-565 (2002).

The Spectrum Kernel: A String Kernel for SVM Protein Classification

C. Leslie, E. Eskin, and W.S. Noble; Pacific Symposium on Biocomputing 7:566-575 (2002).

Detecting Positively Selected Amino Acid Sites Using Posterior Predictive P-Values

R. Nielsen and J. P Huelsenbeck; Pacific Symposium on Biocomputing 7:576-588 (2002).

Improving Sequence Alignments For Intrinsically Disordered Proteins

P. Radivojac, Z. Obradovic, C.J. Brown, and A.K. Dunker; Pacific Symposium on Biocomputing 7:589-600 (2002).

ab initio Folding of Multiple-Chain Proteins

J.A. Saunders, K.D. Gibson, and H.A. Scheraga; Pacific Symposium on Biocomputing 7:601-612 (2002).

Investigating Evolutionary Lines of Least Resistance Using the Inverse Protein-Folding Problem

J. Schonfeld, O. Eulenstein, K. Vander Velden, and G.J.P. Naylor; Pacific Symposium on Biocomputing 7:613-624 (2002).

Using Evolutionary Methods to Study G-Protein Coupled Receptors

O. Soyer, M.W. Dimmic, R.R. Neubig, and R.A. Goldstein; Pacific Symposium on Biocomputing 7:625-636 (2002).

Progress in Predicting Protein Function from Structure: Unique Features of O-Glycosidases

E.W. Stawiski, Y. Mandel-Gutfreund, A.C. Lowenthal, and L.M. Gregoret; Pacific Symposium on Biocomputing 7:637-648 (2002).

Support Vector Machine Prediction of Signal Peptide Cleavage Site Using a New Class of Kernels for Strings

J.-P. Vert; Pacific Symposium on Biocomputing 7:649-660 (2002).

Constraint-Based Hydrophobic Core Construction for Protein Structure Prediction in the Face-Centered-Cubic Lattice

S. Will; Pacific Symposium on Biocomputing 7:661-672 (2002).

Detecting Native Protein Folds Among Large Decoy Sets with Hydrophobic Moment Profiling

R. Zhou and B.D. Silverman; Pacific Symposium on Biocomputing 7:673-684 (2002).