Pacific Symposium on Biocomputing 2004: Hawaii, USA 6-10 January 2004

by Altman, Russ B.

• ISBN13: 9789812385987
• ISBN10: 9812385983
• Edition: 1st
• Format: Hardcover
• Copyright: 2004-03-01
• Publisher: WORLD SCIENTIFIC PUB CO INC

Summary

The Pacific Symposium on Biocomputing (PSB 2004) is an international, multidisciplinary conference for the presentation and discussion of current research on the theory and application of computational methods in problems of biological significance. The rigorously peer-reviewed papers and presentations are collected in this archival proceedings volume. PSB is a forum for the presentation of work on databases, algorithms, interfaces, visualization, modeling and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology. PSB 2004 brings together top researchers from the US, the Asia-Pacific region and the rest of the world to exchange research findings and address open issues in all aspects of computational biology.

Table of Contents

Preface
Design of a High-Throughput Assay for Alternative Splicing Using Polymerase Colonies	p. 5
The Effects of Alternative Splicing on Transmembrane Proteins in the Mouse Genome	p. 17
Genome-Wide Detection of Alternative Splicing in Expressed Sequences Using Partial Order Multiple Sequence Alignment Graphs	p. 29
Detection of Novel Splice Forms in Human and Mouse Using Cross-Species Approach	p. 42
Extensive Search for Discriminative Features of Alternative Splicing	p. 54
Transcriptome and Genome Conservation of Alternative Splicing Events in Humans and Mice	p. 66
A Database Designed to Computationally Aid an Experimental Approach to Alternative Splicing	p. 78
Pedigree Generation for Analysis of Genetic Linkage and Association	p. 93
A Markov Chain Approach to Reconstruction of Long Haplotypes	p. 104
Tradeoff Between No-Call Reduction in Genotyping Error Rate and Loss of Sample Size for Genetic Case/Control Association Studies	p. 116
A Comparison of Different Strategies for Computing Confidence Intervals of the Linkage Disequilibrium Measure D'	p. 128
Multiplexing Schemes for Generic SNP Genotyping Assays	p. 140
Haplotype Block Definition and Its Application	p. 152
Part-of Relations in Anatomy Ontologies: A Proposal for RDFS and OWL Formalisations	p. 166
Building Mouse Phenotype Ontologies	p. 178
An Evidence Ontology for Use in Pathway/Genome Databases	p. 190
Terminological Mapping for High Throughput Comparative Biology of Phenotypes	p. 202
The Compositional Structure of Gene Ontology Terms	p. 214
Defaults, Context, and Knowledge: Alternatives for OWL-Indexed Knowledge Bases	p. 226
Biological Nomenclatures: A Source of Lexical Knowledge and Ambiguity	p. 238
Investigating Implicit Knowledge in Ontologies with Application to the Anatomical Domain	p. 250
ProGreSS: Simultaneous Searching of Protein Databases by Sequence and Structure	p. 264
Predicting the Operon Structure of Bacillus subtilis Using Operon Length, Intergene Distance, and Gene Expression Information	p. 276
Combining Text Mining and Sequence Analysis to Discover Protein Functional Regions	p. 288
Kernel-Based Data Fusion and Its Application to Protein Function Prediction in Yeast	p. 300
Discovery of Binding Motif Pairs from Protein Complex Structural Data and Protein Interaction Sequence Data	p. 312
Phylogenetic Motif Detection by Expectation-Maximization on Evolutionary Mixtures	p. 324
Using Protein-Protein Interactions for Refining Gene Networks Estimated from Microarray Data by Bayesian Networks	p. 336
Motif Discovery in Heterogeneous Sequence Data	p. 348
Negative Information for Motif Discovery	p. 360
The Status of Structural Genomics Defined Through the Analysis of Current Targets and Structures	p. 375
Protein Structure and Fold Prediction Using Tree-Augmented Naive Bayesian Classifier	p. 387
Clustering Protein Sequence and Structure Space with Infinite Gaussian Mixture Models	p. 399
Accurate Classification of Protein Structural Families Using Coherent Subgraph Analysis	p. 411
Identifying Good Predictions of RNA Secondary Structure	p. 423
Exploring Bias in the Protein Data Bank Using Contrast Classifiers	p. 435
Geometric Analysis of Cross-Linkability for Protein Fold Discrimination	p. 447
Protein Fold Recognition Through Application of Residual Dipolar Coupling Data	p. 459
A Mixed Integer Linear Programming (MILP) Framework for Inferring Time Delay in Gene Regulatory Networks	p. 474
Robust Identification of Large Genetic Networks	p. 486
Reconstructing Chain Functions in Genetic Networks	p. 498
Inferring Gene Regulatory Networks from Raw Data - A Molecular Epistemics Approach	p. 510
A Biospi Model of Lymphocyte-Endothelial Interactions in Inflamed Brain Venules	p. 521
Modeling Cellular Processes with Variational Bayesian Cooperative Vector Quantizer	p. 533
Symbolic Inference of Xenobiotic Metabolism	p. 545
Finding Optimal Models for Small Gene Networks	p. 557
Pathway Logic Modeling of Protein Functional Domains in Signal Transduction	p. 568
Modeling Gene Expression from Microarray Expression Data with State-Space Equations	p. 581
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