Pacific Symposium on Biocomputing 2006 : Proceedings of the Pacific Symposium Maui, Hawaii 3 - 7 January 2006

by Altman, Russ B.

• ISBN13: 9789812564634
• ISBN10: 9812564632
• Format: Hardcover
• Copyright: 2005-12-31
• Publisher: World Scientific Pub Co Inc

Summary

The Pacific Symposium on Biocomputing (PSB) 2006 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2006 will be held January 3?7, 2006 at the Grand Wailea, Maui. Tutorials will be offered prior to the start of the conference. PSB 2006 will bring together top researchers from the US, the Asian Pacific nations, and around the world to exchange research results and address open issues in all aspects of computational biology. It is a forum for the presentation of work in 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. The PSB has been designed to be responsive to the need for critical mass in

Table of Contents

Extraction of gene-disease relations from medline using domain dictionaries and machine learning	p. 4
Significantly improved prediction of subcellular localization by integrating text and protein sequence data	p. 16
Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies	p. 28
Automatically generating gene summaries from biomedical literature	p. 40
Finding GeneRIFs via gene ontology annotations	p. 52
PhenoGO : assigning phenotypic context to gene ontology annotations with natural language processing	p. 64
Large-scale testing of bibliome informatics using Pfam protein families	p. 76
Predicting gene functions from text using a cross-species approach	p. 88
Bootstrapping the recognition and anaphoric linking of named entities in Drosophila articles	p. 100
Selecting biological data sources and tools with XPR, a path language for RDF	p. 116
Fast, cheap and out of control : a zero curation model for ontology development	p. 128
Putting semantics into the semantic Web : how well can it capture biology?	p. 140
Event ontology : a pathway-centric ontology for biological processes	p. 152
Discovering biomedical relations utilizing the World-Wide Web	p. 164
Biodash : a semantic Web dashboard for drug development	p. 176
SemBiosphere : a semantic Web approach to recommending microarray clustering services	p. 188
Experience in reasoning with the foundational model of anatomy in OWL DL	p. 200
A machine learning approach to predicting peptide fragmentation spectra	p. 219
Identifying protein complexes in high-throughput protein interaction screens using an infinite latent feature model	p. 231
High-accuracy peak picking of proteomics data using wavelet techniques	p. 243
Fast De novo peptide sequencing and spectral alignment via tree decomposition	p. 255
Experimental design of time series data for learning from dynamic Bayesian networks	p. 267
Finding diagnostic biomarkers in proteomic spectra	p. 279
Gaussian mixture modeling of [alpha]-[tau] helix subclasses : structure and sequence variations	p. 291
An SVM scorer for more sensitive and reliable peptide identification via tandem mass spectrometry	p. 303
Normalization regarding non-random missing values in high-throughput mass spectrometry data	p. 315
A point-process model for rapid identification of post-translational modifications	p. 327
A new approach for alignment of multiple proteins	p. 339
Discovering regulated networks during HIV-1 latency and reactivation	p. 354
Mining Alzheimer disease relevant proteins from integrated protein interactome data	p. 367
Accounting for structural properties and nucleotide co-variations in the quantitative prediction of binding affinities of protein-DNA interactions	p. 379
Improving computational predictions of Cis-regulatory binding sites	p. 391
Struct2Net : integrating structure into protein-protein interaction prediction	p. 403
Identifying interaction sites in "recalcitrant" proteins : predicted protein and RNA binding sites in rev proteins of HIV-1 and EIAV agree with experimental data	p. 415
Modeling and simulation with hybrid functional Petri nets of the role of interleukin-6 in human early haematopoiesis	p. 427
Modeling and analyzing three-dimensional structures of human disease proteins	p. 439
Relaxing haplotype block models for association testing	p. 454
Effect of the peroxisome proliferators-activated receptor (PPAR) gamma 3 gene on BMI in 1,210 school students from Morelos, Mexico	p. 467
Transferability of tag SNPs to capture common genetic variation in DNA repair genes across multiple populations	p. 478
A tool for selecting SNPs for association studies based on observed linkage disequilibrium patterns	p. 487
Data simulation software for whole-genome association and other studies in human genetics	p. 499
TagSNP selection based on pairwise LD criteria and power analysis in association studies	p. 511
Efficient two-stage genome-wide association designs based on false positive report probabilities	p. 523
The whole genome TagSNP selection and transferability among HapMap populations	p. 535
Class prediction from time series gene expression profiles using dynamical systems kernels	p. 547
Computational strategy for discovering druggable gene networks from genome-wide RNA expression profiles	p. 559
A bivariate functional mapping model for identifying haplotypes that control drug response for systolic and diastolic blood pressures	p. 572
Risk factor interactions and genetic effects associated with post-operative atrial fibrillation	p. 584
Learning a predictive model for growth inhibition from the NCI DTP human tumor cell line screening data : does gene expression make a difference?	p. 596
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