Table of Contents

• Threshold Gradient Descent Method for Censored Data Regression with Applications in PharmacogenomicsJiang Gui, Hongzhe Li. [doi]
• Session Introduction: Computational Approaches for PharmacogenomicsMarylyn D. Ritchie, Michelle W. Carrillo, Russell A. Wilke. [doi]
• PrefaceRuss B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein. [doi]
• Algorithms for Structural Comparison and Statistical Analysis of 3D Protein MotifsBrian Y. Chen, Viacheslav Fofanov, David M. Kristensen, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki. [doi]
• Fast and Cheap Genome Wide Haplotype Construction via Optical MappingThomas S. Anantharaman, Venkatesh Mysore, Bud Mishra. [doi]
• Enhancing Data Sharing in Collaborative Research Projects with DASHThomas E. Ferrin, Conrad C. Huang, Daniel M. Greenblatt, Doug Stryke, Kathleen M. Giacomini, John H. Morris. [doi]
• Representing Structure-Function Relationships in Mechanistically Diverse Enzyme SuperfamiliesScott C.-H. Pegg, Shoshana Brown, Sunil Ojha, Conrad C. Huang, Thomas E. Ferrin, Patricia C. Babbitt. [doi]
• Introduction to Informatics Approaches in Structural Genomics: Modeling and Representation of Function from Macromolecular STructurePatricia C. Babbitt, Philip E. Bourne, Sean D. Mooney. [doi]
• Discovering Transcriptional Modules from Motif, Chip-Chip and Microarray DataTijl De Bie, Patrick Monsieurs, Kristof Engelen, Bart De Moor, Nello Cristianini, Kathleen Marchal. [doi]
• A Bayesian Framework for SNP IdentificationBobbie-Jo M. Webb-Robertson, Susan L. Havre, Deborah A. Payne. [doi]
• Untangling the Effects of Codon Mutation and Amino Acid ExchangeabilityL. Y. Yampolsky, Arlin Stoltzfus. [doi]
• Implications of Compositionality in the Gene Ontology for Its Curation and Usage Philip V. Ogren, K. Bretonnel Cohen, Lawrence Hunter. [doi]
• Session Introduction: Inferring SNP Function Using Evolutionary, Structural and Computational MethodsMatthew W. Dimmic, Shamil R. Sunyaev, Carlos Bustamante. [doi]
• Informative Structure Priors: Joint Learning of Dynamic Regulatory Networks from Multiple Types of DataAllister Bernard, Alexander J. Hartemink. [doi]
• Multi-Aspect Gene Relation AnalysisH. Yamakawa, K. Maruhashi, Y. Nakao. [doi]
• Genome-Scale Protein Function Prediction in Yeast Saccharomyces cerevisiae Through Integrating Multiple Sources of High-Throughput DataYu Chen, Dong Xu. [doi]
• Identification of Genomic Signatures for the Design of Assays for the Detection and Monitoring of Anthrax ThreatsSorin Draghici, Purvesh Khatri, Yanhong Liu, Kitty J. Chase, Elizabeth A. Bode, David A. Kulesh, Leonard P. Wasieloski, David A. Norwood, Jaques Reifman. [doi]
• ModuleFinder: A Tool for Computational Discovery of Cis Regulatory ModulesAnthony A. Philippakis, Fangxue Sherry He, Martha L. Bulyk. [doi]
• Two-Stage Multi-Class Support Vector Machines to Protein Secondary Structure PredictionMinh Ngoc Nguyen 0002, Jagath C. Rajapakse. [doi]
• Improving Functional Annotation of Non-Synonomous SNPs with Information TheoryRachel Karchin, Libusha Kelly, Andrej Sali. [doi]
• GO Molecular Function Terms Are Predictive of Subcellular LocalizationZ. Lu, Lawrence Hunter. [doi]
• GenRate: A Generative Model That Finds and Scores New Genes and Exons in Genomic Microarray DataBrendan J. Frey, Quaid Morris, Wen Zhang, Naveed Mohammad, Timothy R. Hughes. [doi]
• The Use of Common Ontologies and Controlled Vocabularies to Enable Data Exchange and Deposition for Complex Proteomic ExperimentsSandra E. Orchard, Luisa Montecchi-Palazzi, Henning Hermjakob, Rolf Apweiler. [doi]
• The Clinical Bioinformatics Ontology: A Curated Semantic Network Utilizing RefSeq InformationM. Hoffman, C. Arnoldi, I. Chuang. [doi]
• Random Forest Similarity for Protein-Protein Interaction Prediction from Multiple SourcesYanjun Qi, Judith Klein-Seetharaman, Ziv Bar-Joseph. [doi]
• Session Introduction: Joint Learning from Multiple Types of Genomic DataAlexander J. Hartemink, Eran Segal. [doi]
• Sparse Factorizations of Gene Expression Guided by Binding DataLiviu Badea, Doina Tilivea. [doi]
• Exploratory Visual Analysis of Pharmacogenomic ResultsDavid M. Reif, Scott M. Dudek, Christian M. Shaffer, Janey Wang, Jason H. Moore. [doi]
• Parameterization of a Nonlinear Genotype to Phenotype Map Using Molecular NetworksJean Peccoud, Kent Vander Velden. [doi]
• A Flexible Measure of Contextual Similarity for Biomedical TermsIrena Spasic, Sophia Ananiadou. [doi]
• From Context-Dependence of Mutations to Molecular Mechanisms of MutagenesisIgor B. Rogozin, B. A. Malyarchuk, Youri I. Pavlov, Luciano Milanesi. [doi]
• Subfamily HMMS in Functional GenomicsDuncan Brown, Nandini Krishnamurthy, Joseph M. Dale, Wayne Christopher, Kimmen Sjölander. [doi]
• Linking Ontological Resources Using Aggregatable Substance Identifiers to Organize Extracted RelationsByron Marshall, Hua Su, Daniel McDonald, Hsinchun Chen. [doi]
• Identification of Functional Modules in Protein Complexes via Hyperclique Pattern DiscoveryHui Xiong, Xiaofeng He, Chris H. Q. Ding, Ya Zhang, Vipin Kumar, Stephen R. Holbrook. [doi]
• Understanding the Global Properties of Functionally-Related Gene Networks Using the Gene OntologyLuis Tari, Chitta Baral, P. Dasgupta. [doi]
• Discovering Sequence-Structure Motifs from Protein Segments and Two ApplicationsThomas Tang, Jinbo Xu, Ming Li. [doi]
• Bayesian Joint Prediction of Associated Transcription Factors in Bacillus subtilisYuko Makita, Michiel J. L. de Hoon, Naotake Ogasawara, Satoru Miyano, Kenta Nakai. [doi]
• Study of Effect of Drug Lexicons on Medication Extraction from Electronic Medical RecordsE. Sirohi, P. Peissig. [doi]
• Session Introduction: Biogeometry: Applications of Computational Geometry to Molecular StructureAlexander Tropsha, Herbert Edelsbrunner. 3-4 [doi]
• Classification of Non-Coding RNA Using Graph Representations of Secondary StructureYan Karklin, Richard F. Meraz, Stephen R. Holbrook. 5-16 [doi]
• An Adaptive Dynamic Programming Algorithm for the Side Chain Placement ProblemAndrew Leaver-Fay, Brian Kuhlman, Jack Snoeyink. 17-28 [doi]
• Computational Design of Combinatorial Peptide Library for Modulating Protein-Protein InteractionsXiang Li, Jie Liang. 29-41 [doi]
• Exploring Protein Folding Trajectories Using Geometric SpannersDaniel Russel, Leonidas J. Guibas. 42-53 [doi]
• ChainTweak: Sampling from the Neighbourhood of a Protein ConformationRohit Singh, Bonnie Berger. 54-65 [doi]
• Coarse and Reliable Geometric Alignment for Protein DockingYusu Wang, Pankaj K. Agarwal, P. Brown, Herbert Edelsbrunner, Johannes Rudolph. 66-77 [doi]
• Session Introduction: Biomedical OntologiesOlivier Bodenreider, Joyce A. Mitchell, Alexa T. McCray. 89-92 [doi]
• Ontology Driven Dynamic Linking of Biology ResourcesSean Bechhofer, Robert D. Stevens, Phillip W. Lord. 93-103 [doi]
• Non-Lexical Approaches to Identifying Associative Relations in the Gene OntologyOlivier Bodenreider, Marc Aubry, Anita Burgun. 104-115 [doi]
• GenesTrace: Phenomic Knowledge Discovery via Structured TerminologyM. N. Cantor, Indra Neil Sarkar, Olivier Bodenreider, Yves A. Lussier. 116-127 [doi]
• Integrating Genomic Knowledge Sources Through an Anatomy OntologyJohn H. Gennari, Adam Silberfein, Jesse C. Wiley. 128-139 [doi]
• GOTrees: Predicting GO Associations from Protein Domain Composition Using Decision TreesBoris Hayete, Jadwiga R. Bienkowska. 140-151 [doi]