11. PSB 2006: Wailea, Maui, Hawaii, USA

• Preface.
  

Linking Biomedical Information Through Text Mining

• K. Bretonnel Cohen, Olivier Bodenreider, Lynette Hirschman:
  Session Introduction. 1-3
  
• Hong-Woo Chun, Yoshimasa Tsuruoka, Jin-Dong Kim, Rie Shiba, Naoki Nagata, Teruyoshi Hishiki, Jun'ichi Tsujii:
  Extraction of Gene-Disease Relations from Medline Using Domain Dictionaries and Machine Learning. 4-15
  
• Annette Höglund, Torsten Blum, Scott Brady, Pierre Dönnes, John San Miguel, Matthew Rocheford, Oliver Kohlbacher, Hagit Shatkay:
  Significantly Improved Prediction of Subcellular Localization by Integrating Text and Protein Sequence Data . 16-27
  
• Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., Zhiyong Lu, Michael Bada, Todd Kester, Hyunmin Kim, Lawrence Hunter:
  Evaluation of Lexical Methods for Detecting Relationships Between Concepts from Multiple Ontologies. 28-39
  
• Xu Ling, Jing Jiang, Xin He, Qiaozhu Mei, ChengXiang Zhai, Bruce R. Schatz:
  Automatically Generating Gene Summaries from Biomedical Literature. 40-51
  
• Zhiyong Lu, K. Bretonnel Cohen, Lawrence Hunter:
  Finding GeneRIFs via Gene Ontology Annotations. 52-63
  
• Yves A. Lussier, Tara Borlawsky, Daniel Rappaport, Yang Liu, Carol Friedman:
  PhenoGO: Assigning Phenotypic Context to Gene Ontology Annotations with Natural Language Processing. 64-75
  
• Ana Gabriela Maguitman, Andreas Rechtsteiner, Karin Verspoor, Charlie E. M. Strauss, Luis Mateus Rocha:
  Large-Scale Testing of Bibliome Informatics Using Pfam Protein Families. 76-87
  
• Emilia Stoica, Marti A. Hearst:
  Predicting Gene Functions from Text Using a Cross-Species Approach. 88-99
  
• Andreas Vlachos, Caroline Gasperin, Ian Lewin, Ted Briscoe:
  Bootstrapping the Recognition and Anaphoric Linking of Named Entities in Drosophila Articles. 100-111
  

Semantic Webs for Life Sciences

• Robert Stevens, Olivier Bodenreider, Yves A. Lussier:
  Session Introduction. 112-115
  
• Sarah Cohen Boulakia, Christine Froidevaux, Emmanuel Pietriga:
  Selecting Biological Data Sources and Tools with XPR, a Path Language for RDF. 116-127
  
• Benjamin M. Good, Erin M. Tranfield, Poh C. Tan, Marlene Shehata, Gurpreet K. Singhera, John Gosselink, Elena B. Okon, Mark D. Wilkinson:
  Fast, Cheap and Out of Control: A Zero Curation Model for Ontology Development. 128-139
  
• Toni Kazic:
  Putting Semantics into the Semantic Web: How Well Can It Capture Biology? 140-151
  
• Tatsuya Kushida, Toshihisa Takagi, Ken-ichiro Fukuda:
  Event Ontology: A Pathway-Centric Ontology for Biological Processes. 152-163
  
• Sougata Mukherjea, Saurav Sahay:
  Discovering Biomedical Relations Utilizing the World-Wide Web. 164-175
  
• Eric K. Neumann, Dennis Quan:
  Biodash: A Semantic Web Dashboard for Drug Development. 176-187
  
• Kevin Y. Yip, Peishen Qi, Martin H. Schultz, David W. Cheung, Kei-Hoi Cheung:
  SemBiosphere: A Semantic Web Approach to Recommending Microarray Clustering Services. 188-199
  
• Songmao Zhang, Olivier Bodenreider, Christine Golbreich:
  Experience in Reasoning with the Foundational Model of Anatomy in OWL DL. 200-211
  

Computational Proteomics

• Bobbie-Jo M. Webb-Robertson, William R. Cannon, Joshua N. Adkins, Deborah K. Gracio:
  Session Introduction. 212-218
  
• Randy J. Arnold, Narmada Jayasankar, Divya Aggarwal, Haixu Tang, Predrag Radivojac:
  A Machine Learning Approach to Predicting Peptide Fragmentation Spectra. 219-230
  
• Wei Chu, Zoubin Ghahramani, Roland Krause, David L. Wild:
  Identifying Protein Complexes in High-Throughput Protein Interaction Screens Using an Infinite Latent Feature Model. 231-242
  
• Eva Lange, Clemens Gröpl, Knut Reinert, Oliver Kohlbacher, Andreas Hildebrandt:
  High-Accuracy Peak Picking of Proteomics Data Using Wavelet Techniques. 243-254
  
• Chunmei Liu, Yinglei Song, Bo Yan, Ying Xu, Liming Cai:
  Fast De novo Peptide Sequencing and Spectral Alignment via Tree Decomposition. 255-266
  
• C. David Page Jr., Irene M. Ong:
  Experimental Design of Time Series Data for Learning from Dynamic Bayesian Networks. 267-278
  
• Pallavi N. Pratapa, Edward F. Patz Jr., Alexander J. Hartemink:
  Finding Diagnostic Biomarkers in Proteomic Spectra. 279-290
  
• Ashish V. Tendulkar, Babatunde Ogunnaike, Pramod P. Wangikar:
  Gaussian Mixture Modeling of Helix Subclasses: Structure and Sequence Variations. 291-302
  
• Haipeng Wang, Yan Fu, Ruixiang Sun, Simin He, Rong Zeng, Wen Gao:
  An SVM Scorer for More Sensitive and Reliable Peptide Identification via Tandem Mass Spectrometry. 303-314
  
• Pei Wang, Hua Tang, Heidi Zhang, Jeffrey Whiteaker, Amanda G. Paulovich, Martin McIntosh:
  Normalization Regarding Non-Random Missing Values in High-Throughput Mass Spectrometry Data. 315-326
  
• Bo Yan, Tong Zhou, Peng Wang, Zhijie Liu, Vincent A. Emanuele II, Victor Olman, Ying Xu:
  A Point-Process Model for Rapid Identification of Post-Translational Modifications. 327-338
  
• Xu Zhang, Tamer Kahveci:
  A New Approach for Alignment of Multiple Proteins. 339-350
  

Protein Interactions in Disease

• Maricel G. Kann, Yanay Ofran, Marco Punta, Predrag Radivojac:
  Session Introduction. 351-353
  
• Sourav Bandyopadhyay, Ryan M. Kelley, Trey Ideker:
  Discovering Regulated Networks During HIV-1 Latency and Reactivation. 354-366
  
• Jake Yue Chen, Changyu Shen, Andrey Y. Sivachenko:
  Mining Alzheimer Disease Relevant Proteins from Integrated Protein Interactome Data. 367-378
  
• Sumedha Gunewardena, Zhaolei Zhang:
  Accounting for Structural Properties and Nucleotide Co-variations in the Quantitative Prediction of Binding Affinities of Protein-DNA Interactions. 379-390
  
• Mark Robinson, Yi Sun, Rene te Boekhorst, Paul Kaye, Rod Adams, Neil Davey, Alistair G. Rust:
  Improving Computational Predictions of Cis- Regulatory Binding Sites. 391-402
  
• Rohit Singh, Jinbo Xu, Bonnie Berger:
  Struct2Net: Integrating Structure into Protein-Protein Interaction Prediction. 403-414
  
• Michael Terribilini, Jae-Hyung Lee, Changhui Yan, Robert L. Jernigan, Susan Carpenter:
  Identifying Interaction Sites in "Recalcitrant" Proteins: Predicted Protein and RNA Binding Sites in Rev Proteins of HIV-1 and EIAV Agree with Experimental Data. 415-426
  
• Sylvie Troncale, Fariza Tahi, David Campard, Jean-Pierre Vannier, Janine Guespin:
  Modeling and Simulation with Hybrid Functional Petri Nets of the Role of Interleukin-6 in Human Early Haematopoiesis. 427-438
  
• Yuzhen Ye, Zhanwen Li, Adam Godzik:
  Modeling and Analyzing Three-Dimensional Structures of Human Disease Proteins. 439-450
  

Design and Analysis of Genetic Studies After the Hapmap Project

• Francisco M. de la Vega, Andrew G. Clark, Andrew Collins, Kenneth K. Kidd:
  Session Introduction. 451-453
  
• Natalie Castellana, Kedar Dhamdhere, Srinath Sridhar, Russell Schwartz:
  Relaxing Haplotype Block Models for Association Testing. 454-466
  
• Lina Chen, H. Eduardo Velasco Mondragón, Eduardo Lazcano-Ponce, Andrew Collins, Yin Yao Shugart:
  Effect of the Peroxisome Proliferators-Activated Receptor (PPAR) Gamma 3 Gene on BMI in 1, 210 School Students from Morelos, Mexico. 467-477
  
• Paul I. W. De Bakker, Robert R. Graham, David Altshuler, Brian E. Henderson, Christopher A. Haiman:
  Transferability of Tag SNPs to Capture Common Genetic Variation in DNA Repair Genes Across Multiple Populations. 478-486
  
• Francisco M. de la Vega, Hadar I. Isaac, Charles R. Scafe:
  A Tool for Selecting SNPs for Association Studies Based on Observed Linkage Disequilibrium Patterns. 487-498
  
• Scott M. Dudek, Alison A. Motsinger, Digna R. Velez, Scott M. Williams, Marylyn D. Ritchie:
  Data Simulation Software for Whole-Genome Association and Other Studies in Human Genetics. 499-510
  
• Shyam Gopalakrishnan, Zhaohui S. Qin:
  TagSNP Selection Based on Pairwise LD Criteria and Power Analysis in Association Studies. 511-522
  
• Peter Kraft:
  Efficient Two-Stage Genome-Wide Association Designs Based on False Positive Report Probabilities. 523-534
  
• Reedik Magi, Lauris Kaplinski, Maido Remm:
  The Whole Genome TagSNP Selection and Transferability Among HapMap Populations. 535-543
  

Computational Approaches for Pharmacogenomics

• Michelle W. Carrillo, Russell A. Wilke, Marylyn D. Ritchie:
  Session Introduction. 544-546
  
• Karsten M. Borgwardt, S. V. N. Vishwanathan, Hans-Peter Kriegel:
  Class Prediction from Time Series Gene Expression Profiles Using Dynamical Systems Kernels. 547-558
  
• Seiya 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:
  Computational Strategy for Discovering Druggable Gene Networks from Genome-Wide RNA Expression Profiles. 559-571
  
• Min Lin, Rongling Wu, Julie A. Johnson:
  A Bivariate Functional Mapping Model for Identifying Haplotypes that Control Drug Response for Systolic and Diastolic Blood Pressures. 572-583
  
• Alison A. Motsinger, Brian S. Donahue, Nancy J. Brown, Dan M. Roden, Marylyn D. Ritchie:
  Risk Factor Interactions and Genetic Effects Associated with Post-Operative Atrial Fibrillation. 584-595
  
• Lothar Richter, Ulrich Rückert, Stefan Kramer:
  Learning a Predictive Model for Growth Inhibition from the NCI DTP Human Tumor Cell Line Screening Data: Does Gene Expression Make a Difference? 596-607
  

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