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11. PSB 2006: Wailea, Maui, Hawaii, USA
- Russ B. Altman, Tiffany Murray, Teri E. Klein, A. Keith Dunker, Lawrence Hunter:
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
- 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 M. 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, G. 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 Mägi, Lauris Kaplinski, Maido Remm:
The Whole Genome TagSNP Selection and Transferability Among HapMap Populations. 535-543
Computational Approaches for Pharmacogenomics
- Michelle Whirl 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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