10. PSB 2005: Big Island of Hawaii, USA

• 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
  
• M. 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
  
• M. Hoffman, C. Arnoldi, I. Chuang:
  The Clinical Bioinformatics Ontology: A Curated Semantic Network Utilizing RefSeq Information.
  
• Z. 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.
  
• H. Yamakawa, K. Maruhashi, Y. Nakao:
  Multi-Aspect Gene Relation Analysis.
  

Computational Approaches for Pharmacogenomics

• Marylyn D. Ritchie, Michelle W. 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, P. 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 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 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 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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