Title Pacific Symposium on Biocomputing 2005 : Hawaii, USA, 4-8 January 2005 / edited by Russ B. Altman [and others]

Published Singapore ; Hackensack, NJ : World Scientific, ©2005

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Description 1 online resource (xxi, 542 pages) : illustrations Contents Biogeometry: applications of computational geometry to molecular structure. Session introduction / A. Tropsha and H. Edelsbrunner -- Classification of non-coding RNA using graph representations of secondary structure / Y. Karklin, R.F Meraz, and S.R. Holbrook -- An adaptive dynamic programming algorithm for the side chain placement problem / A. Leaver-Fay, B. Kuhlman, and J. Snoeyink -- Computational design of combinatorial peptide library for modulating protein-protein interactions / X. Li and J. Liang -- Exploring protein folding trajectories using geometric spanners / D. Russel and L. Guibas -- ChainTweak: sampling from the neighbourhood of a protein conformation / R. Singh and B. Berger -- Coarse and reliable geometric alignment for protein docking / Y. Wang [and others] -- Biomedical ontologies. Session introduction / O. Bodenreider, J.A. Mitchell, and A.T. McCray -- Ontology driven dynamic linking of biology resources / S.K. Bechhofer, R.D. Stevens, and P.W. Lord -- Non-lexical approaches to identifying associative relations in the gene ontology / O. Bodenreider, M. Aubry, and A. Burgun -- GenesTrace: phenomic knowledge discovery via structured terminology / M.N. Cantor [and others] -- Integrating genomic knowledge sources through an anatomy ontology / J.H. Gennari, A. Silberfein, and J.C. Wiley -- GOTrees: predicting GO associations from protein domain composition using decision trees / B. Hayete and J.R. Bienkowska -- The clinical bioinformatics ontology: a curated semantic network utilizing RefSeq information / M. Hoffman, C. Arnoldi, and I. Chuang -- GO molecular function terms are predictive of subcellular localization / Z. Lu and L. Hunter -- Linking ontological resources using aggregatable substance identifiers to organize extracted relations / B. Marshall [and others] -- Implications of compositionality in the gene ontology for its curation and usage / 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 / S. Orchard [and others] -- A flexible measure of contextual similarity for biomedical terms / I. Spasić and S. Ananiadou -- Understanding the global properties of functionally-related gene networks using the gene ontology / L. Tari, C. Baral, and P. Dasgupta -- Identification of functional modules in protein complexes hyperclique pattern discovery / H. Xiong [and others] -- Multi-aspect gene relation analysis / H. Yamakawa, K. Maruhashi, and Y. Nakao -- Computational approaches for pharmacogenomics. Session introduction / 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 / S. Draghici [and others] -- Enhancing data sharing in collaborative research projects with DASH / T.E. Ferrin [and others] Threshold gradient descent method for censored data regression with applications in pharmacogenomics / J. Gui and H. Li -- Parameterization of a nonlinear genotype to phenotype map using molecular networks / J. Peccoud and K. Vander Velden -- Exploratory visual analysis of pharmacogenomic results / D.M. Reif [and others] -- Study of effect of drug lexicons on medication extraction from electronic medical records / E. Sirohi and P. Peissig -- Informatics approaches in structural genomics: modeling and representation of function from macromolecular structure. Session introduction / P.C. Babbitt, P. Bourne, and S.D. Mooney -- Subfamily HMMS in functional genomics / D. Brown [and others] -- Algorithms for structural comparison and statistical analysis of 3D protein motifs / B.Y. Chen [and others] -- Two-stage multi-class support vector machines to protein secondary structure prediction / M.N. Nguyen and J.C. Rajapakse -- Representing structure-function relationships in mechanistically diverse enzyme superfamilies / S.C.-H. Pegg [and others] -- Discovering sequence-structure motifs from protein segments and two applications / T. Tang, J. Xu, and M. Li -- Inferring SNP function using evolutionary, structual, and computational methods. Session introduction / M. Dimmic, S. Sunyaev, and C. Bustamante -- Fast and cheap genome wide haplotype construction via optical mapping / T.S. Anantharaman, V. Mysore, and B. Mishra -- Improving functional annotation of non-synonomous SNPs with information theory / R. Karchin, L. Kelly, and A. Sali -- From context-dependence of mutations to molecular mechanisms of mutagenesis / I.B. Rogozin [and others] -- A Bayesian framework for SNP identification / B.M. Webb-Robertson, S.L. Havre, and D.A. Payne -- Untangling the effects of codon mutation and amino acid exchangeability / L.Y. Yampolsky and A. Stoltzfus -- Joint learning from multiple types of genomic data. Session introduction / A.J. Hartemink and E. Segal -- Sparse factorizations of gene expression data guided by binding data / L. Badea and D. Tilivea -- Informative structure priors: joint learning of dynamic regulatory networks from multiple types of data / A. Bernard and A.J. Hartemink -- Genome-scale protein function prediction in yeast saccharomyces cerevisiae through integrating multiple sources of high-throughput data / Y. Chen and D. Xu -- Discovering transcriptional modules from motif, chip-chip and microarray data / T. De Bie [and others] -- GenRate: a generative model that finds and scores new genes and exons in genomic microarray data / B. Frey [and others] -- Bayesian joint prediction of associated transcription factors in bacillus subtilis / Y. Makita [and others] -- ModuleFinder: a tool for computational discovery of Cis regulatory modules / A.A. Philippakis, F.S. He, and M.L. Bulyk -- Random forest similarity for protein-protein interaction prediction from multiple sources / Y. Qi, J. Klein-Seetharaman, and Z. Bar-Joseph Summary The Pacific Symposium on Biocomputing (PSB 2005) 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. This latest volume in the prestigious conference series contains the contributions of top researchers from the US, the Asia-Pacific region and around the world. Sections are devoted to 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 book is an essential source of ideas, discoveries and references for academics in biocomputing, bioinformatics researchers and computer scientists Analysis Biocomputing PSB Bibliography Includes bibliographical references Notes English Print version record Subject Biology -- Mathematical models -- Congresses Biology -- Computer simulation -- Congresses Molecular biology -- Mathematical models -- Congresses Molecular biology -- Computer simulation -- Congresses NATURE -- Reference. SCIENCE -- Life Sciences -- Biology. SCIENCE -- Life Sciences -- General. Biology -- Computer simulation Biology -- Mathematical models Molecular biology -- Computer simulation Molecular biology -- Mathematical models Genre/Form Conference papers and proceedings Form Electronic book Author Altman, Russ. ISBN 9789812702456 9812702458 1281898503 9781281898500 9786611898502 6611898506

Other Titles Biocomputing 2005

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