• 
  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.
• 
  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.
• 
  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 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.

last updated on Wed May 22 05:01:25 2013 by the dblp team
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