Pacific Symposium on Biocomputing 2005: Hawaii, USA 4 - 8 January 2005

by Altman, Russ B.

• ISBN13: 9789812560469
• ISBN10: 9812560467
• Edition: 1st
• Format: Hardcover
• Copyright: 2004-12-01
• Publisher: World Scientific Pub Co Inc

Summary

"The book is an essential source of ideas, discoveries and references for academics in biocomputing, bioinformatics researchers and computer scientists."--BOOK JACKET.

Table of Contents

Preface	v
BIOGEOMETRY: APPLICATIONS OF COMPUTATIONAL GEOMETRY TO MOLECULAR STRUCTURE
Session Introduction	1	(3)
A. Tropsha and H. Edelsbrunner
Classification of Non-Coding RNA Using Graph Representations of Secondary Structure	4	(12)
Y. Karklin, R.F. Meraz, and S.R. Holbrook
An Adaptive Dynamic Programming Algorithm for the Side Chain Placement Problem	16	(12)
A. Leaver-Fay, B. Kuhlman, and J. Snoeyink
Computational Design of Combinatorial Peptide Library for Modulating Protein-Protein Interactions	28	(12)
X. Li and J. Liang
Exploring Protein Folding Trajectories Using Geometric Spanners	40	(12)
D. Russel and L. Guibas
ChainTweak: Sampling from the Neighbourhood of a Protein Conformation	52	(12)
R. Singh and B. Berger
Coarse and Reliable Geometric Alignment for Protein Docking	64	(12)
Y. Wang, P.K. Agarwal, P. Brown, H. Edelsbrunner, and J. Rudolph
BIOMEDICAL ONTOLOGIES
Session Introduction	76	(3)
O. Bodenreider, J.A. Mitchell, and A.T. McCray
Ontology Driven Dynamic Linking of Biology Resources	79	(12)
S.K. Bechhofer, R.D. Stevens, and P.W. Lord
Non-Lexical Approaches to Identifying Associative Relations in the Gene Ontology	91	(12)
O. Bodenreider, M. Aubry, and A. Burgun
GenesTrace: Phenomic Knowledge Discovery via Structured Terminology	103	(12)
M.N. Cantor, I.N. Sarkar, O. Bodenreider, and Y.A. Lussier
Integrating Genomic Knowledge Sources Through an Anatomy Ontology	115	(12)
J.H. Gennari, A. Silberfein, and J.C. Wiley
GOTrees: Predicting GO Associations from Protein Domain Composition Using Decision Trees	127	(12)
B. Hayete and J.R. Bienkowska
The Clinical Bioinformatics Ontology: A Curated Semantic Network Utilizing RefSeq Information	139	(12)
M. Hoffman, C. Arnoldi, and I. Chuang
GO Molecular Function Terms Are Predictive of Subcellular Localization	151	(11)
Z. Lu and L. Hunter
Linking Ontological Resources Using Aggregatable Substance Identifiers to Organize Extracted Relations	162	(12)
B. Marshall, H. Su, D. McDonald, and H. Chen
Implications of Compositionality in the Gene Ontology for Its Curation and Usage	174	(12)
P.V. Ogren, K.B. Cohen, and L. Hunter
The Use of Common Ontologies and Controlled Vocabularies to Enable Data Exchange and Deposition for Complex Proteomic Experiments	186	(11)
S. Orchard, L. Montecchi-Palazzi, H. Hermjakob, and R. Apweiler
A Flexible Measure of Contextual Similarity for Biomedical Terms	197	(12)
I. Spasic and S. Ananiadou
Understanding the Global Properties of Functionally-Related Gene Networks Using the Gene Ontology	209	(12)
L. Tari, C. Baral, and P. Dasgupta
Identification of Functional Modules in Protein Complexes via Hyperclique Pattern Discovery	221	(12)
H. Xiong, X. He, C. Ding, Y. Zhang, V Kumar, and S.R. Holbrook
Multi-Aspect Gene Relation Analysis	233	(12)
H. Yamakawa, K. Maruhashi, and Y. Nakao
COMPUTATIONAL APPROACHES FOR PHARMACOGENOMICS
Session Introduction	245	(3)
M.D. Ritchie, M.W. Carrillo, and R.A. Wilke
Identification of Genomic Signatures for the Design of Assays for the Detection and Monitoring of Anthrax Threats	248	(12)
S. Draghici, P. Khatri, Y. Liu, K.J. Chase, E.A. Bode, D.A. Kulesh, L.P. Wasieloski, D.A. Norwood, and J. Reifman
Enhancing Data Sharing in Collaborative Research Projects with DASH	260	(12)
T.E. Ferrin, C.C. Huang, D.M. Greenblatt, D. Stryke, K.M. Giacomini, and J.H. Morris
Threshold Gradient Descent Method for Censored Data Regression with Applications in Pharmacogenomics	272	(12)
J. Gui and H. Li
Parameterization of a Nonlinear Genotype to Phenotype Map Using Molecular Networks	284	(12)
J. Peccoud and K. Vander Velden
Exploratory Visual Analysis of Pharmacogenomic Results	296	(12)
D.M. Reif, S.M. Dudek, C.M. Shaffer, J. Wang, and J.H. Moore
Study of Effect of Drug Lexicons on Medication Extraction from Electronic Medical Records	308	(11)
E. Sirohi and P. Peissig
INFORMATICS APPROACHES IN STRUCTURAL GENOMICS: MODELING AND REPRESENTATION OF FUNCTION FROM MACROMOLECULAR STRUCTURE
Session Introduction	319	(3)
P.C. Babbitt, P. Bourne, and S.D. Mooney
Subfamily HMMS in Functional Genomics	322	(12)
D. Brown, N. Krishnamurthy, J.M. Dale, W. Christopher, and K. Sjölander
Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs	334	(12)
B.Y. Chen, V.Y. Fofanov, D.M. Kristensen, M. Kimmel, O. Lichtarge, and L.E. Kavraki
Two-Stage Multi-Class Support Vector Machines to Protein Secondary Structure Prediction	346	(12)
M.N. Nguyen and J.C. Rajapakse
Representing Structure-Function Relationships in Mechanistically Diverse Enzyme Superfamilies	358	(12)
S.C.-H. Pegg, S. Brown, S. Ojha, C.C. Huang, T.E. Ferrin, and P.C. Babbitt
Discovering Sequence-Structure Motifs from Protein Segments and Two Applications	370	(12)
T. Tang, J. Xu, and M. Li
INFERRING SNP FUNCTION USING EVOLUTIONARY, STRUCTURAL, AND COMPUTATIONAL METHODS
Session Introduction	382	(3)
M. Dimmic, S. Sunyaev, and C. Bustamante
Fast and Cheap Genome Wide Haplotype Construction via Optical Mapping	385	(12)
T.S. Anantharaman, V. Mysore, and B. Mishra
Improving Functional Annotation of Non-Synonomous SNPs with Information Theory	397	(12)
R. Karchin, L. Kelly, and A. Sali
From Context-Dependence of Mutations to Molecular Mechanisms of Mutagenesis	409	(12)
I.B. Rogozin, B.A. Malyarchuk, Y.I. Pavlov, and L. Milanesi
A Bayesian Framework for SNP Identification	421	(12)
B.M. Webb-Robertson, S.L. Havre, and D.A. Payne
Untangling the Effects of Codon Mutation and Amino Acid Exchangeability	433	(12)
L.Y. Yampolsky and A. Stoltzfus
JOINT LEARNING FROM MULTIPLE TYPES OF GENOMIC DATA
Session Introduction	445	(2)
A.J. Hartemink and E. Segal
Sparse Factorizations of Gene Expression Data Guided by Binding Data	447	(12)
L. Badea and D. Tilivea
Informative Structure Priors: Joint Learning of Dynamic Regulatory Networks from Multiple Types of Data	459	(12)
A. Bernard and A.J. Hartemink
knonnc-Scale Protein Function Prediction in Yeast Saccharomyces cerevisiae Through Integrating Multiple Sources of High-Throughput Data	471	(12)
Y. Chen and D. Xu
Discovering Transcriptional Modules from Motif, Chip-Chip and Microarray Data	483	(12)
T. De Bie, P. Monsieurs, K. Engelen, B. De Moor, N. Cristianini, and K. Marchal
GenRate: A Generative Model That Finds and Scores New Genes and Exons in Genomic Microarray Data	495	(12)
B. Frey, Q. Morris, W. Zhang, N. Mohammad, and T. Hughes
Bayesian Joint Prediction of Associated Transcription Factors in Bacillus subtilis	507	(12)
Y. Makita, M.J.L. De Hoon, N. Ogasawara, S. Miyano, and K. Nakai
ModuleFinder: A Tool for Computational Discovery of Cis Regulatory Modules	519	(12)
A.A. Philippakis, F.S. He, and M.L. Bulyk
Random Forest Similarity for Protein-Protein Interaction Prediction from Multiple Sources	531
Y. Qi, J. Klein-Seetharaman, and Z. Bar-Joseph