Abstract is missing.
- Preface [doi]
- Session IntroductionK. Bretonnel Cohen, Olivier Bodenreider, Lynette Hirschman. 1-3 [doi]
- Extraction of Gene-Disease Relations from Medline Using Domain Dictionaries and Machine LearningHong-Woo Chun, Yoshimasa Tsuruoka, Jin-Dong Kim, Rie Shiba, Naoki Nagata, Teruyoshi Hishiki, Jun-ichi Tsujii. 4-15 [doi]
- Significantly Improved Prediction of Subcellular Localization by Integrating Text and Protein Sequence Data Annette Höglund, Torsten Blum, Scott Brady, Pierre Dönnes, John San Miguel, Matthew Rocheford, Oliver Kohlbacher, Hagit Shatkay. 16-27 [doi]
- Evaluation of Lexical Methods for Detecting Relationships Between Concepts from Multiple OntologiesHelen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., Zhiyong Lu, Michael Bada, Todd Kester, Hyunmin Kim, Lawrence Hunter. 28-39 [doi]
- Automatically Generating Gene Summaries from Biomedical LiteratureXu Ling, Jing Jiang, Xin He, Qiaozhu Mei, ChengXiang Zhai, Bruce R. Schatz. 40-51 [doi]
- Finding GeneRIFs via Gene Ontology AnnotationsZhiyong Lu, K. Bretonnel Cohen, Lawrence Hunter. 52-63 [doi]
- PhenoGO: Assigning Phenotypic Context to Gene Ontology Annotations with Natural Language ProcessingYves A. Lussier, Tara Borlawsky, Daniel Rappaport, Yang Liu, Carol Friedman. 64-75 [doi]
- Large-Scale Testing of Bibliome Informatics Using Pfam Protein FamiliesAna Gabriela Maguitman, Andreas Rechtsteiner, Karin Verspoor, Charlie E. M. Strauss, Luis Mateus Rocha. 76-87 [doi]
- Predicting Gene Functions from Text Using a Cross-Species ApproachEmilia Stoica, Marti A. Hearst. 88-99 [doi]
- Bootstrapping the Recognition and Anaphoric Linking of Named Entities in Drosophila ArticlesAndreas Vlachos, Caroline Gasperin, Ian Lewin, Ted Briscoe. 100-111 [doi]
- Session IntroductionRobert Stevens, Olivier Bodenreider, Yves A. Lussier. 112-115 [doi]
- Selecting Biological Data Sources and Tools with XPR, a Path Language for RDFSarah Cohen Boulakia, Christine Froidevaux, Emmanuel Pietriga. 116-127 [doi]
- Fast, Cheap and Out of Control: A Zero Curation Model for Ontology DevelopmentBenjamin M. Good, Erin M. Tranfield, Poh C. Tan, Marlene Shehata, Gurpreet K. Singhera, John Gosselink, Elena B. Okon, Mark D. Wilkinson. 128-139 [doi]
- Putting Semantics into the Semantic Web: How Well Can It Capture Biology?Toni Kazic. 140-151 [doi]
- Event Ontology: A Pathway-Centric Ontology for Biological ProcessesTatsuya Kushida, Toshihisa Takagi, Ken-ichiro Fukuda. 152-163 [doi]
- Discovering Biomedical Relations Utilizing the World-Wide WebSougata Mukherjea, Saurav Sahay. 164-175 [doi]
- Biodash: A Semantic Web Dashboard for Drug DevelopmentEric K. Neumann, Dennis Quan. 176-187 [doi]
- SemBiosphere: A Semantic Web Approach to Recommending Microarray Clustering ServicesKevin Y. Yip, Peishen Qi, Martin H. Schultz, David W. Cheung, Kei-Hoi Cheung. 188-199 [doi]
- Experience in Reasoning with the Foundational Model of Anatomy in OWL DLSongmao Zhang, Olivier Bodenreider, Christine Golbreich. 200-211 [doi]
- Session IntroductionBobbie-Jo M. Webb-Robertson, William R. Cannon, Joshua N. Adkins, Deborah K. Gracio. 212-218 [doi]
- A Machine Learning Approach to Predicting Peptide Fragmentation SpectraRandy J. Arnold, Narmada Jayasankar, Divya Aggarwal, Haixu Tang, Predrag Radivojac. 219-230 [doi]
- Identifying Protein Complexes in High-Throughput Protein Interaction Screens Using an Infinite Latent Feature ModelWei Chu, Zoubin Ghahramani, Roland Krause, David L. Wild. 231-242 [doi]
- High-Accuracy Peak Picking of Proteomics Data Using Wavelet TechniquesEva Lange, Clemens Gröpl, Knut Reinert, Oliver Kohlbacher, Andreas Hildebrandt. 243-254 [doi]
- Fast De novo Peptide Sequencing and Spectral Alignment via Tree DecompositionChunmei Liu, Yinglei Song, Bo Yan, Ying Xu, Liming Cai. 255-266 [doi]
- Experimental Design of Time Series Data for Learning from Dynamic Bayesian NetworksC. David Page Jr., Irene M. Ong. 267-278 [doi]
- Finding Diagnostic Biomarkers in Proteomic SpectraPallavi N. Pratapa, Edward F. Patz Jr., Alexander J. Hartemink. 279-290 [doi]
- Gaussian Mixture Modeling of Helix Subclasses: Structure and Sequence VariationsAshish V. Tendulkar, Babatunde Ogunnaike, Pramod P. Wangikar. 291-302 [doi]
- An SVM Scorer for More Sensitive and Reliable Peptide Identification via Tandem Mass SpectrometryHaipeng Wang, Yan Fu, Ruixiang Sun, Simin He, Rong Zeng, Wen Gao. 303-314 [doi]
- Normalization Regarding Non-Random Missing Values in High-Throughput Mass Spectrometry DataPei Wang, Hua Tang, Heidi Zhang, Jeffrey Whiteaker, Amanda G. Paulovich, Martin McIntosh. 315-326 [doi]
- A Point-Process Model for Rapid Identification of Post-Translational ModificationsBo Yan, Tong Zhou, Peng Wang, Zhijie Liu, Vincent A. Emanuele II, Victor Olman, Ying Xu. 327-338 [doi]
- A New Approach for Alignment of Multiple ProteinsXu Zhang, Tamer Kahveci. 339-350 [doi]
- Session IntroductionMaricel G. Kann, Yanay Ofran, Marco Punta, Predrag Radivojac. 351-353 [doi]
- Discovering Regulated Networks During HIV-1 Latency and ReactivationSourav Bandyopadhyay, Ryan M. Kelley, Trey Ideker. 354-366 [doi]
- Mining Alzheimer Disease Relevant Proteins from Integrated Protein Interactome DataJake Yue Chen, Changyu Shen, Andrey Y. Sivachenko. 367-378 [doi]
- Accounting for Structural Properties and Nucleotide Co-variations in the Quantitative Prediction of Binding Affinities of Protein-DNA InteractionsSumedha Gunewardena, Zhaolei Zhang. 379-390 [doi]
- Improving Computational Predictions of Cis- Regulatory Binding SitesMark Robinson, Yi Sun, Rene te Boekhorst, Paul Kaye, Rod Adams, Neil Davey, Alistair G. Rust. 391-402 [doi]
- Struct2Net: Integrating Structure into Protein-Protein Interaction PredictionRohit Singh, Jinbo Xu, Bonnie Berger. 403-414 [doi]
- Identifying Interaction Sites in Recalcitrant Proteins: Predicted Protein and RNA Binding Sites in Rev Proteins of HIV-1 and EIAV Agree with Experimental DataMichael Terribilini, Jae-Hyung Lee, Changhui Yan, Robert L. Jernigan, Susan Carpenter. 415-426 [doi]
- Modeling and Simulation with Hybrid Functional Petri Nets of the Role of Interleukin-6 in Human Early HaematopoiesisSylvie Troncale, Fariza Tahi, David Campard, Jean-Pierre Vannier, Janine Guespin. 427-438 [doi]
- Modeling and Analyzing Three-Dimensional Structures of Human Disease ProteinsYuzhen Ye, Zhanwen Li, Adam Godzik. 439-450 [doi]
- Session IntroductionFrancisco M. de la Vega, Andrew G. Clark, Andrew Collins, Kenneth K. Kidd. 451-453 [doi]
- Relaxing Haplotype Block Models for Association TestingNatalie Castellana, Kedar Dhamdhere, Srinath Sridhar, Russell Schwartz. 454-466 [doi]
- Effect of the Peroxisome Proliferators-Activated Receptor (PPAR) Gamma 3 Gene on BMI in 1, 210 School Students from Morelos, MexicoLina Chen, H. Eduardo Velasco Mondragón, Eduardo Lazcano-Ponce, Andrew Collins, Yin Yao Shugart. 467-477 [doi]
- Transferability of Tag SNPs to Capture Common Genetic Variation in DNA Repair Genes Across Multiple PopulationsPaul I. W. de Bakker, Robert R. Graham, David Altshuler, Brian E. Henderson, Christopher A. Haiman. 478-486 [doi]
- A Tool for Selecting SNPs for Association Studies Based on Observed Linkage Disequilibrium PatternsFrancisco M. de la Vega, Hadar I. Isaac, Charles R. Scafe. 487-498 [doi]
- Data Simulation Software for Whole-Genome Association and Other Studies in Human GeneticsScott M. Dudek, Alison A. Motsinger, Digna R. Velez, Scott M. Williams, Marylyn D. Ritchie. 499-510 [doi]
- TagSNP Selection Based on Pairwise LD Criteria and Power Analysis in Association StudiesShyam Gopalakrishnan, Zhaohui S. Qin. 511-522 [doi]
- Efficient Two-Stage Genome-Wide Association Designs Based on False Positive Report ProbabilitiesPeter Kraft. 523-534 [doi]
- The Whole Genome TagSNP Selection and Transferability Among HapMap PopulationsReedik Magi, Lauris Kaplinski, Maido Remm. 535-543 [doi]
- Session IntroductionMichelle W. Carrillo, Russell A. Wilke, Marylyn D. Ritchie. 544-546 [doi]
- Class Prediction from Time Series Gene Expression Profiles Using Dynamical Systems KernelsKarsten M. Borgwardt, S. V. N. Vishwanathan, Hans-Peter Kriegel. 547-558 [doi]
- Computational Strategy for Discovering Druggable Gene Networks from Genome-Wide RNA Expression ProfilesSeiya Imoto, Yoshinori Tamada, Hiromitsu Araki, Kaori Yasuda, Cristin G. Print, Stephen D. Charnock-Jones, Deborah Sanders, Christopher J. Savoie, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano. 559-571 [doi]
- A Bivariate Functional Mapping Model for Identifying Haplotypes that Control Drug Response for Systolic and Diastolic Blood PressuresMin Lin, Rongling Wu, Julie A. Johnson. 572-583 [doi]
- Risk Factor Interactions and Genetic Effects Associated with Post-Operative Atrial FibrillationAlison A. Motsinger, Brian S. Donahue, Nancy J. Brown, Dan M. Roden, Marylyn D. Ritchie. 584-595 [doi]
- Learning a Predictive Model for Growth Inhibition from the NCI DTP Human Tumor Cell Line Screening Data: Does Gene Expression Make a Difference?Lothar Richter, Ulrich Rückert, Stefan Kramer. 596-607 [doi]