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10. PSB 2005: Big Island of Hawaii, USA
- Russ B. Altman, Tiffany A. Jung, Teri E. Klein, A. Keith Dunker, Lawrence Hunter:
Biocomputing 2005, Proceedings of the Pacific Symposium, Hawaii, USA, 4-8 January 2005. World Scientific 2005, ISBN 981-256-046-7 - Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein:
Preface.
Biogeometry: Applications of Computational Geometry to Molecular Structure
- Alexander Tropsha, Herbert Edelsbrunner:
Session Introduction: Biogeometry: Applications of Computational Geometry to Molecular Structure. 3-4 - Yan Karklin, Richard F. Meraz, Stephen R. Holbrook:
Classification of Non-Coding RNA Using Graph Representations of Secondary Structure. 5-16 - Andrew Leaver-Fay, Brian Kuhlman, Jack Snoeyink:
An Adaptive Dynamic Programming Algorithm for the Side Chain Placement Problem. 17-28 - Xiang Li, Jie Liang:
Computational Design of Combinatorial Peptide Library for Modulating Protein-Protein Interactions. 29-41 - Daniel Russel, Leonidas J. Guibas:
Exploring Protein Folding Trajectories Using Geometric Spanners. 42-53 - Rohit Singh, Bonnie Berger:
ChainTweak: Sampling from the Neighbourhood of a Protein Conformation. 54-65 - Yusu Wang, Pankaj K. Agarwal, P. Brown, Herbert Edelsbrunner, Johannes Rudolph:
Coarse and Reliable Geometric Alignment for Protein Docking. 66-77
Biomedical Ontologies
- Olivier Bodenreider, Joyce A. Mitchell, Alexa T. McCray:
Session Introduction: Biomedical Ontologies. 89-92 - Sean Bechhofer, Robert D. Stevens, Phillip W. Lord:
Ontology Driven Dynamic Linking of Biology Resources. 93-103 - Olivier Bodenreider, Marc Aubry, Anita Burgun:
Non-Lexical Approaches to Identifying Associative Relations in the Gene Ontology. 104-115 - Michael N. Cantor, Indra Neil Sarkar, Olivier Bodenreider, Yves A. Lussier:
GenesTrace: Phenomic Knowledge Discovery via Structured Terminology. 116-127 - John H. Gennari, Adam Silberfein, Jesse C. Wiley:
Integrating Genomic Knowledge Sources Through an Anatomy Ontology. 128-139 - Boris Hayete, Jadwiga R. Bienkowska:
GOTrees: Predicting GO Associations from Protein Domain Composition Using Decision Trees. 140-151 - Mark Hoffman, C. Arnoldi, I. Chuang:
The Clinical Bioinformatics Ontology: A Curated Semantic Network Utilizing RefSeq Information. - Zhiyong Lu, Lawrence Hunter:
GO Molecular Function Terms Are Predictive of Subcellular Localization. - Byron Marshall, Hua Su, Daniel McDonald, Hsinchun Chen:
Linking Ontological Resources Using Aggregatable Substance Identifiers to Organize Extracted Relations. - Philip V. Ogren, K. Bretonnel Cohen, Lawrence Hunter:
Implications of Compositionality in the Gene Ontology for Its Curation and Usage . - Sandra E. Orchard, Luisa Montecchi-Palazzi, Henning Hermjakob, Rolf Apweiler:
The Use of Common Ontologies and Controlled Vocabularies to Enable Data Exchange and Deposition for Complex Proteomic Experiments. - Irena Spasic, Sophia Ananiadou:
A Flexible Measure of Contextual Similarity for Biomedical Terms. - Luis Tari, Chitta Baral, P. Dasgupta:
Understanding the Global Properties of Functionally-Related Gene Networks Using the Gene Ontology. - Hui Xiong, Xiaofeng He, Chris H. Q. Ding, Ya Zhang, Vipin Kumar, Stephen R. Holbrook:
Identification of Functional Modules in Protein Complexes via Hyperclique Pattern Discovery. - Hiroshi Yamakawa, Koji Maruhashi, Yoshio Nakao, Mutsuyo Yamaguchi:
Multi-Aspect Gene Relation Analysis.
Computational Approaches for Pharmacogenomics
- Marylyn D. Ritchie, Michelle Whirl Carrillo, Russell A. Wilke:
Session Introduction: Computational Approaches for Pharmacogenomics. - Sorin Draghici, Purvesh Khatri, Yanhong Liu, Kitty J. Chase, Elizabeth A. Bode, David A. Kulesh, Leonard P. Wasieloski, David A. Norwood, Jaques Reifman:
Identification of Genomic Signatures for the Design of Assays for the Detection and Monitoring of Anthrax Threats. - Thomas E. Ferrin, Conrad C. Huang, Daniel M. Greenblatt, Doug Stryke, Kathleen M. Giacomini, John H. Morris:
Enhancing Data Sharing in Collaborative Research Projects with DASH. - Jiang Gui, Hongzhe Li:
Threshold Gradient Descent Method for Censored Data Regression with Applications in Pharmacogenomics. - Jean Peccoud, Kent Vander Velden:
Parameterization of a Nonlinear Genotype to Phenotype Map Using Molecular Networks. - David M. Reif, Scott M. Dudek, Christian M. Shaffer, Janey Wang, Jason H. Moore:
Exploratory Visual Analysis of Pharmacogenomic Results. - E. Sirohi, Peggy L. Peissig:
Study of Effect of Drug Lexicons on Medication Extraction from Electronic Medical Records.
Inferring Function from Structural Genomics Targets
- Patricia C. Babbitt, Philip E. Bourne, Sean D. Mooney:
Introduction to Informatics Approaches in Structural Genomics: Modeling and Representation of Function from Macromolecular STructure. - Duncan P. Brown, Nandini Krishnamurthy, Joseph M. Dale, Wayne Christopher, Kimmen Sjölander:
Subfamily HMMS in Functional Genomics. - Brian Y. Chen, Viacheslav Fofanov, David M. Kristensen, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki:
Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs. - Minh Ngoc Nguyen, Jagath C. Rajapakse:
Two-Stage Multi-Class Support Vector Machines to Protein Secondary Structure Prediction. - Scott C.-H. Pegg, Shoshana D. Brown, Sunil Ojha, Conrad C. Huang, Thomas E. Ferrin, Patricia C. Babbitt:
Representing Structure-Function Relationships in Mechanistically Diverse Enzyme Superfamilies. - Thomas Tang, Jinbo Xu, Ming Li:
Discovering Sequence-Structure Motifs from Protein Segments and Two Applications.
Inferring SNP Function Using Evolutionary, Structural and Computational Methods
- Matthew W. Dimmic, Shamil R. Sunyaev, Carlos D. Bustamante:
Session Introduction: Inferring SNP Function Using Evolutionary, Structural and Computational Methods. - Thomas S. Anantharaman, Venkatesh Mysore, Bud Mishra:
Fast and Cheap Genome Wide Haplotype Construction via Optical Mapping. - Rachel Karchin, Libusha Kelly, Andrej Sali:
Improving Functional Annotation of Non-Synonomous SNPs with Information Theory. - Igor B. Rogozin, B. A. Malyarchuk, Youri I. Pavlov, Luciano Milanesi:
From Context-Dependence of Mutations to Molecular Mechanisms of Mutagenesis. - Bobbie-Jo M. Webb-Robertson, Susan L. Havre, Deborah A. Payne:
A Bayesian Framework for SNP Identification. - L. Y. Yampolsky, Arlin Stoltzfus:
Untangling the Effects of Codon Mutation and Amino Acid Exchangeability.
Joint Learning from Multiple Types of Genomic Data
- Alexander J. Hartemink, Eran Segal:
Session Introduction: Joint Learning from Multiple Types of Genomic Data. - Liviu Badea, Doina Tilivea:
Sparse Factorizations of Gene Expression Guided by Binding Data. - Allister Bernard, Alexander J. Hartemink:
Informative Structure Priors: Joint Learning of Dynamic Regulatory Networks from Multiple Types of Data. - Yu Chen, Dong Xu:
Genome-Scale Protein Function Prediction in Yeast Saccharomyces cerevisiae Through Integrating Multiple Sources of High-Throughput Data. - Tijl De Bie, Patrick Monsieurs, Kristof Engelen, Bart De Moor, Nello Cristianini, Kathleen Marchal:
Discovering Transcriptional Modules from Motif, Chip-Chip and Microarray Data. - Brendan J. Frey, Quaid Morris, Wen Zhang, Naveed Mohammad, Timothy R. Hughes:
GenRate: A Generative Model That Finds and Scores New Genes and Exons in Genomic Microarray Data. - Yuko Makita, Michiel J. L. de Hoon, Naotake Ogasawara, Satoru Miyano, Kenta Nakai:
Bayesian Joint Prediction of Associated Transcription Factors in Bacillus subtilis. - Anthony A. Philippakis, Fangxue Sherry He, Martha L. Bulyk:
ModuleFinder: A Tool for Computational Discovery of Cis Regulatory Modules. - Yanjun Qi, Judith Klein-Seetharaman, Ziv Bar-Joseph:
Random Forest Similarity for Protein-Protein Interaction Prediction from Multiple Sources.
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