PSB 2005 Online Proceedings

 PSB 2005

PSB Proceedings for All Years

CONTENTS

Preface

Biogeometry: Applications of Computational Geometry to Molecular Structure

Session Introduction
A. Tropsha and H. Edelsbrunner; Pacific Symposium on Biocomputing 10:1-3(2005)
Classification of Non-Coding RNA Using Graph Representations of Secondary Structure
Y. Karklin, R.F. Meraz, and S.R. Holbrook; Pacific Symposium on Biocomputing 10:4-15(2005)
An Adaptive Dynamic Programming Algorithm for the Side Chain Placement Problem
A. Leaver-Fay, B. Kuhlman, and J. Snoeyink; Pacific Symposium on Biocomputing 10:16-27(2005)
Computational Design of Combinatorial Peptide Library for Modulating Protein-Protein Interactions
X. Li and J. Liang; Pacific Symposium on Biocomputing 10:28-39(2005)
Exploring Protein Folding Trajectories Using Geometric Spanners
D. Russel and L. Guibas; Pacific Symposium on Biocomputing 10:40-51(2005)
ChainTweak: Sampling from the Neighbourhood of a Protein Conformation
R. Singh and B. Berger; Pacific Symposium on Biocomputing 10:52-63(2005)
Coarse and Reliable Geometric Alignment for Protein Docking
Y. Wang, P.K.Agarwal, P.Brown, H. Edelsbrunner, and J. Rudolph; Pacific Symposium on Biocomputing 10:64-75(2005)

Biomedical Ontologies

Session Introduction
O. Bodenreider, J.A.. Mitchell, and A.T. McCray; Pacific Symposium on Biocomputing 10:76-78(2005)
Ontology Driven Dynamic Linking of Biology Resources
S.K. Bechhofer, R.D. Stevens, and P.W. Lord; Pacific Symposium on Biocomputing 10:79-90(2005)
Non-Lexical Approaches to Identifying Associative Relations in the Gene Ontology
O. Bodenreider, M Aubry, and A. Burgun; Pacific Symposium on Biocomputing 10:91-102(2005)
GenesTrace: Phenomic Knowledge Discovery via Structured Terminology
M.N. Cantor, I.N. Sarkar, O. Bodenreider, and Y.A. Lussier; Pacific Symposium on Biocomputing 10:103-114(2005)
Integrating Genomic Knowledge Sources Through an Anatomy Ontology
J.H. Gennari, A. Silberfein, and J.C. Wiley ; Pacific Symposium on Biocomputing 10:115-126(2005)
GOTrees: Predicting GO Associations from Protein Domain Composition Using Decision Trees
B. Hayete and J.R. Bienkowska; Pacific Symposium on Biocomputing 10:127-138(2005)
The Clinical Bioinformatics Ontology: A Curated Semantic Network Utilizing RefSeq Information
M. Hoffman, C. Arnoldi, and I. Chuang; Pacific Symposium on Biocomputing 10:139-150(2005)
GO Molecular Function Terms Are Predictive of Subcellular Localization
Z. Lu and L. Hunter; Pacific Symposium on Biocomputing 10:151-161(2005)
Linking Ontological Resources Using Aggregatable Substance Identifiers to Organize Extracted Relations
B. Marshall, H. Su, D. McDonald, and H. Chen; Pacific Symposium on Biocomputing 10:162-173(2005)
Implications of Compositionality in the Gene Ontology for Its Curation and Usage
P.V. Ogren, K.B. Cohen, and L. Hunter; Pacific Symposium on Biocomputing 10:174-185(2005)
The Use of Common Ontologies and Controlled Vocabularies to Enable Data Exchange and Deposition for Complex Proteomic Experiments
S. Orchard, L. Montecchi-Palazzi, H. Hermjakob, and R. Apweiler; Pacific Symposium on Biocomputing 10:186-196(2005)
A Flexible Measure of Contextual Similarity for Biomedical Terms
I. Spasic and S. Ananiadou; Pacific Symposium on Biocomputing 10:197-208(2005)
Understanding the Global Properties of Functionally-Related Gene Networks Using the Gene Ontology
L. Tari, C. Baral, and P. Dasgupta; Pacific Symposium on Biocomputing 10:209-220(2005)
Identification of Functional Modules in Protein Complexes via Hyperclique Pattern Discovery
H. Xiong, X. He, C. Ding, Y. Zhang, V. Kumar, and S.R. Holbrook; Pacific Symposium on Biocomputing 10:221-232(2005)
Multi-Aspect Gene Relation Analysis
H. Yamakawa, K. Maruhashi, and Y.Nakao; Pacific Symposium on Biocomputing 10:233-244(2005)

Computational Approaches for Pharmacogenomics

Session Introduction
M.D. Ritchie, M.W. Carrillo, and R.A. Wilke; Pacific Symposium on Biocomputing 10:245-247(2005)
Identification of Genomic Signatures for the Design of Assays for the Detection and Monitoring of Anthrax Threats
S. Draghici, P. Khatri, Y. Liu, K.J. Chase, E.A. Bode, D.A. Kulesh, L.P. Wasieloski, D.A. Norwood, and J. Reifman; Pacific Symposium on Biocomputing 10:248-259(2005)
Enhancing Data Sharing in Collaborative Research Projects with DASH
T.E. Ferrin, C.C. Huang, D.M. Greenblatt, D. Stryke, K.M. Giacomini, and J.H. Morris; Pacific Symposium on Biocomputing 10:260-271(2005)
Threshold Gradient Descent Method for Censored Data Regression with Applications in Pharmacogenomics
J. Gui and H. Li; Pacific Symposium on Biocomputing 10:272-283(2005)
Parameterization of a Nonlinear Genotype to Phenotype Map Using Molecular Networks
J. Peccoud and K. Vander Velden; Pacific Symposium on Biocomputing 10:284-295(2005)
Exploratory Visual Analysis of Pharmacogenomic Results
D.M. Reif, S.M. Dudek, C.M. Shaffer, J. Wang, and J.H. Moore; Pacific Symposium on Biocomputing 10:296-307(2005)
Study of Effect of Drug Lexicons on Medication Extraction from Electronic Medical Records
E. Sirohi and P. Peissig; Pacific Symposium on Biocomputing 10:308-318(2005)

Inferring Function from Structural Genomics Targets

Session Introduction
P.C. Babbitt, P. Bourne, and S.D. Mooney; Pacific Symposium on Biocomputing 10:319-321(2005)
Subfamily HMMS in Functional Genomics
D. Brown, N. Krishnamurthy, J.M. Dale, W. Christopher, and K. Sjölander; Pacific Symposium on Biocomputing 10:322-333(2005)
Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs
B.Y. Chen, V.Y. Fofanov, D.M. Kristensen, M. Kimmel, O. Lichtarge, and L.E. Kavraki; Pacific Symposium on Biocomputing 10:334-345(2005)
Two-Stage Multi-Class Support Vector Machines to Protein Secondary Structure Prediction
M.N. Nguyen and J.C. Rajapakse; Pacific Symposium on Biocomputing 10:346-357(2005)
Representing Structure-Function Relationships in Mechanistically Diverse Enzyme Superfamilies
S.C.-H. Pegg, S. Brown, S. Ojha, C.C. Huang, T.E. Ferrin, and P.C. Babbitt; Pacific Symposium on Biocomputing 10:358-369(2005)
Discovering Sequence-Structure Motifs from Protein Segments and Two Applications
T. Tang, J. Xu, and M. Li; Pacific Symposium on Biocomputing 10:370-381(2005)

Inferring SNP Function Using Evolutionary, Structural and Computational Methods

Session Introduction
M. Dimmic, S. Sunyaev, and C. Bustamante; Pacific Symposium on Biocomputing 10:382-384(2005)
Fast and Cheap Genome Wide Haplotype Construction via Optical Mapping
T.S. Anantharaman, V. Mysore, and B. Mishra; Pacific Symposium on Biocomputing 10:385-396(2005)
Improving Functional Annotation of Non-Synonomous SNPs with Information Theory
R. Karchin, L.Kelly, and A. Sali; Pacific Symposium on Biocomputing 10:397-408(2005)
From Context-Dependence of Mutations to Molecular Mechanisms of Mutagenesis
I.B. Rogozin, B.A. Malyarchuk, Y.I. Pavlov, and L. Milanesi; Pacific Symposium on Biocomputing 10:409-420(2005)
A Bayesian Framework for SNP Identification
B.M. Webb-Robertson, S.L. Havre, and D.A. Payne; Pacific Symposium on Biocomputing 10:421-432(2005)
Untangling the Effects of Codon Mutation and Amino Acid Exchangeability
L.Y. Yampolsky and A. Stoltzfus; Pacific Symposium on Biocomputing 10:433-444(2005)

Joint Learning from Multiple Types of Genomic Data

Session Introduction
A.J. Hartemink and E. Segal; Pacific Symposium on Biocomputing 10:445-446(2005)
Sparse Factorizations of Gene Expression Guided by Binding Data
L. Badea and D. Tilivea; Pacific Symposium on Biocomputing 10:447-458(2005)
Informative Structure Priors: Joint Learning of Dynamic Regulatory Networks from Multiple Types of Data
A. Bernard and A.J. Hartemink; Pacific Symposium on Biocomputing 10:459-470(2005)
Genome-Scale Protein Function Prediction in Yeast Saccharomyces cerevisiae Through Integrating Multiple Sources of High-Throughput Data
Y. Chen and D. Xu; Pacific Symposium on Biocomputing 10:471-482(2005)
Discovering Transcriptional Modules from Motif, Chip-Chip and Microarray Data
T. De Bie, P. Monsieurs, K. Engelen, B. De Moor, N. Cristianini, and K. Marchal; Pacific Symposium on Biocomputing 10:483-494(2005)
GenRate: A Generative Model That Finds and Scores New Genes and Exons in Genomic Microarray Data
B. Frey, Q. Morris, W. Zhang, N. Mohammad, and T. Hughes; Pacific Symposium on Biocomputing 10:495-506(2005)
Bayesian Joint Prediction of Associated Transcription Factors in Bacillus subtilis
Y. Makita, M.J.L. De Hoon, N. Ogasawara, S. Miyano, and K. Nakai; Pacific Symposium on Biocomputing 10:507-518(2005)
ModuleFinder: A Tool for Computational Discovery of Cis Regulatory Modules
A.A. Philippakis, F.S. He, and M.L. Bulyk; Pacific Symposium on Biocomputing 10:519-530(2005)
Random Forest Similarity for Protein-Protein Interaction Prediction from Multiple Sources
Y. Qi, J. Klein-Seetharaman, and Z. Bar-Joseph ; Pacific Symposium on Biocomputing 10:531-542(2005)
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