11. PSB 2006: Wailea, Maui, Hawaii, USA
Russ B. Altman, Tiffany Murray, Teri E. Klein, A. Keith Dunker, Lawrence Hunter (Eds.): Biocomputing 2006, Proceedings of the Pacific Symposium, Maui, Hawaii, USA, 3-7 January 2006. World Scientific 2006 ISBN 981-256-463-2- Preface.
Linking Biomedical Information Through Text Mining
- 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
- 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
- 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
Protein Interactions in Disease
- 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
- 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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last updated on 2013-06-18T214307 by the dblp team