Pacific Symposium on Biocomputing 2006 Maui, Hawaii, 3-7 January 2006

Session introduction / K. Bretonnel Cohen, Olivier Bodenreider, and Lynette Hirschman -- Extraction of gene-disease relations from medline using domain dictionaries and machine learning / Hong-Woo Chun [und weitere] -- Significantly improved prediction of subcellular localization by integrating text and protein sequence data / Annette Höglund [und weitere] -- Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies / Helen L. Johnson [und weitere] -- Automatically generating gene summaries from biomedical literature / Xu Ling [und weitere] -- Finding geneRIFs via gene ontology annotations / Zhiyong Lu, K. Bretonnel Cohen, and Lawrence Hunter -- PhenoGO : assigning phenotypic context to gene ontology annotations with natural language processing / Yves Lussier [und weitere] -- Large-scale testing of bibliome informatics using Pfam protein families / Ana G. Maguitman [und weitere] -- Predicting gene functions from text using a cross-species approach / Emilia Stoica and Marti Hearst -- Bootstrapping the recognition and anaphoric linking of named entities in drosophila articles / Andreas Vlachos [und weitere] -- Session introduction / Robert Stevens, Olivier Bodenreider, and Yves A. Lussier -- Selecting biological data sources and tools with XPR, a path language for RDF / Sarah Cohen-Boulakia, Christine Froidevaux, and Emmanuel Pietriga -- Fast, cheap and out of control : a zero curation model for ontology development / Benjamin M. Good [und weitere] -- Putting semantics into the semantic web : how well can it capture biology? / Toni Kazic -- Event ontology : a pathway-centric ontology for biological processes / Tatsuya Kushida, Toshihisa Takagi, and Ken Ichiro Fukuda -- Discovering biomedical relations utilizing the world-wide web / Sougata Mukherjea and Saurav Sahay -- Biodash : a semantic web dashboard for drug development / Eric K. Neumann and Dennis Quan -- SemBiosphere : a semantic web approach to recommending microarray clustering services / Kevin Y. Yip [und weitere] -- Experience in reasoning with the foundational model of anatomy in OWL DL / Songrnao Zhang, Olivier Bodenreider, and Christine Golbreich -- Session introduction / Bobbie-Jo Webb-Robertson [und weitere] -- A machine learning approach to predicting peptide fragmentation spectra / Randy J. Arnold [und weitere] -- Identifying protein complexes in high-throughput protein interaction screens using an infinite latent feature model / Wei Chu [und weitere] -- High-accuracy peak picking of proteomics data using wavelet techniques / Eva Lange [und weitere] -- Fast De novo peptide sequencing and spectral alignment via tree decomposition / Chunmei Liu [und weitere] -- Experimental design of time series data for learning from dynamic Bayesian networks / David Page and Irene M. Ong -- Finding diagnostic biomarkers in proteomic spectra / Pallavi N. Pratapa, Edward F. Patz, Jr., and Alexander J. Hartemink -- Gaussian mixture modeling of [symbol] helix subclasses : structure and sequence variations / Ashish V. Tendulkar, Babatunde Ogunnaike, and Pramod P. Wangikar -- An SVM scorer for more sensitive and reliable peptide identification via tandem mass spectrometry / Haipeng Wang [und weitere] -- Normalization regarding non-random missing values in high-throughput mass spectrometry data / Pei Wang [und weitere] -- A point-process model for rapid identification of post-translational modifications / Bo Yan [und weitere] -- A new approach for alignment of multiple proteins / Xu Zhang and Tamer Kahveci -- Session introduction / Maricel Kann [und weitere] -- Discovering regulated networks during HIV-1 latency and reactivation / Sourav Bandyopudhyay, Ryan Kelley, and Trey Ideker -- Mining Alzheimer disease relevant proteins from integrated protein interactome data / Jake Yue Chen, Changyu Shen, and Andrey Y. Sivachenko -- Accounting for structural properties and nucleotide co-variations in the quantitative prediction of binding affinities of protein-DNA interactions / Sumedha Gunewardena and Zhaolei Zhang -- Improving computational predictions of cis-regulatory binding sites / Mark Robinson [und weitere] -- Struct2Net : integrating structure into protein-protein interaction prediction / Rohit Singh, Jinbo Xu, and Bonnie Berger -- Identifying interaction sites in "recalcitrant" proteins : predicted protein and RNA binding sites in Rev proteins of HIV-1 and EIAV agree with experimental data / Michael Terribilini [und weitere] -- Modeling and simulation with hybrid functional petri nets of the role of Interleukin-6 in human early haematopoiesis / Sylvie Troncale [und weitere] -- Modeling and analyzing three-dimensional structures of human disease proteins / Yuzhen Ye, Zhanwen Li, and Adam Godzik -- Session introduction / Francisco M. De La Vega [und weitere] -- Relaxing haplotype block models for association testing / Natalie Castellana [und weitere] -- Effect of the Peroxisome Proliferators-Activated Receptor (PPAR) gamma 3 gene on BMI in 1,210 school students from Morelos, Mexico / Lina Chen [und weitere] -- Transferability of tag SNPs to capture common genetic variation in DNA repair genes across multiple populations / Paul I.W. De Bakker [und weitere] -- A tool for selecting SNPs for association studies based on observed linkage disequilibrium patterns / Francisco M. De La Vega, Hadar I. Isaac, and Charles R. Scafe -- Data simulation software for whole-genome association and other studies in human genetics / Scott M. Dudek [und weitere] -- TagSNP selection based on pairwise LD criteria and power analysis in association studies / Shyam Gopalakrishnan and Zhaohui S. Qin -- Efficient two-stage genome-wide association designs based on false positive report probabilities / Peter Kraft -- The whole genome TagSNP selection and transferability among HapMap populations / Reedik Mägi, Lauris Kaplinski, and Maido Remm -- Session introduction / Michelle W. Carrillo, Russell A. Wilke, and Marylyn D. Ritchie -- Class prediction from time series gene expression profiles using dynamical systems kernels / Karsten M. Borgwardt, S.V.N. Vishwanathan, and Hans-Peter Kriegel -- Computational strategy for discovering druggable gene networks from genome-wide RNA expression profiles / Seiya Imoto [und weitere] -- A bivariate functional mapping model for identifying haplotypes that control drug response for systolic and diastolic blood pressures / Min Lin, Rongling Wu, and Julie Johnson -- Risk factor interactions and genetic effects associated with post-operative atrial fibrillation / Alison A. Motsinger [und weitere] -- Learning a predictive model for growth inhibition from the NCI DTP human tumor cell line screening data : does gene expression make a difference? / Lothur Richter, Ulrich Rückert, and Stefan Kramer