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<html> <head> <meta HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=windows-1252"> <title>PSB 2006 Online Proceedings</title> </head> <body LINK="#0000ff" VLINK="#800080"> <table width="100%" border="0" cellspacing="0" align="center"><tr> <td valign="bottom"> <h2>PSB 2006 Online Proceedings</h2> </td> <td align="right"> <a href="http://psb.stanford.edu/"> PSB 2006</a> <img src="nucleosome_psbweb.gif" align="middle"> </td> </tr></table> <a href="http://psb.stanford.edu/psb-online/">PSB Proceedings for All Years</a> <hr> <h3>Contents</h3> <ul> <li><a href="#pharma">Computational Approaches for Pharmacogenomics</a> <li><a href="#proteomics">Computational Proteomics </a> <li><a href="#genstudies">Design and Analysis of Genetic Studies After the HapMap Project </a> <li><a href="#nlp">Linking Biomedical Information Through Text Mining </a> <li><a href="#protein">Protein Interactions in Disease </a> <li><a href="#semantic">Semantic Webs for Life Sciences </a> </ul> <hr> <a href="psb06-prefacev2.pdf">Preface</a> <h3><a name="nlp">Linking Biomedical Information Through Text Mining</a></h3> <dl> <dt><a href="intro-nlp.pdf">Session Introduction</a></dt> <dd>K. Bretonnel Cohen, Olivier Bodenreider, and Lynette Hirschman; Pacific Symposium on Biocomputing 11:1-3(2006)</dd> <dt><a href="chun.pdf">Extraction of Gene-Disease Relations from Medline Using Domain Dictionaries and Machine Learning</a></dt> <dd>Hong-Woo Chun, Yoshimasa Tsuruoka, Jin-Dong Kim, Rie Shiba, Naoki Nagata, Teruyoshi Hishiki, and Jun'ichi Tsujii; Pacific Symposium on Biocomputing 11:4-15(2006)</dd> <dt><a href="hoglund.pdf">Significantly Improved Prediction of Subcellular Localization by Integrating Text and Protein Sequence Data </a></dt> <dd>Annette Hoglund, Torsten Blum, Scott Brady, Pierre Donnes, John San Miguel, Matthew Rocheford, Oliver Kohlbacher, and Hagit Shatkay; Pacific Symposium on Biocomputing 11:16-27(2006)</dd> <dt><a href="johnson.pdf">Evaluation of Lexical Methods for Detecting Relationships Between Concepts from Multiple Ontologies </a></dt> <dd>Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., Zhiyong Lu, Michael Bada, Todd Kester, Hyunmin Kim, and Lawrence Hunter; Pacific Symposium on Biocomputing 11:28-39(2006)</dd> <dt><a href="ling.pdf">Automatically Generating Gene Summaries from Biomedical Literature </a></dt> <dd>Xu Ling, Jing Jiang, Xin He, Qiaozhu Mei, Chengxiang Zhai, and Bruce Schatz; Pacific Symposium on Biocomputing 11:40-51(2006)</dd> <dt><a href="lu.pdf">Finding GeneRIFs via Gene Ontology Annotations </a></dt> <dd>Zhiyong Lu, K. Bretonnel Cohen, and Lawrence Hunter; Pacific Symposium on Biocomputing 11:52-63(2006)</dd> <dt><a href="lussier.pdf">PhenoGO: Assigning Phenotypic Context to Gene Ontology Annotations with Natural Language Processing </a></dt> <dd>Yves Lussier, Tara Borlawsky, Daniel Rappaport, Yang Liu, and Carol Friedman; Pacific Symposium on Biocomputing 11:64-75(2006)</dd> <dt><a href="maguitman.pdf">Large-Scale Testing of Bibliome Informatics Using Pfam Protein Families </a></dt> <dd>Ana G. Maguitman, Andreas Rechtsteiner, Karin Verspoor, Charlie E. Strauss, and Luis M. Rocha; Pacific Symposium on Biocomputing 11:76-87(2006)</dd> <dt><a href="stoica.pdf">Predicting Gene Functions from Text Using a Cross-Species Approach </a></dt> <dd>Emilia Stoica and Marti Hearst; Pacific Symposium on Biocomputing 11:88-99(2006)</dd> <dt><a href="vlachos.pdf">Bootstrapping the Recognition and Anaphoric Linking of Named Entities in Drosophila Articles </a></dt> <dd>Andreas Vlachos, Caroline Gasperin, Ian Lewin, Ted Briscoe; Pacific Symposium on Biocomputing 11:100-111(2006)</dd> </dl> <h3><a name="semantic">Semantic Webs for Life Sciences</a></h3> <dl> <dt><a href="intro-sem.pdf">Session Introduction </a></dt> <dd>Roberts Stevens, Olivier Bodenreider, and Yves A. Lussier; Pacific Symposium on Biocomputing 11:112-115(2006)</dd> <dt><a href="cohen-boulakia.pdf">Selecting Biological Data Sources and Tools with XPR, a Path Language for RDF </a></dt> <dd>Sarah Cohen-Boulakia, Christine Froidevaux, and Emmanuel Pietriga; Pacific Symposium on Biocomputing 11:116-127(2006)</dd> <dt><a href="good.pdf">Fast, Cheap and Out of Control: A Zero Curation Model for Ontology Development </a></dt> <dd>Benjamin M. Good, Erin M. Tranfield, Poh C. Tan, Marlene Shehata, Gurpreet K. Singhera, John Gosselink, Elena B. Okon, and Mark D. Wilkinson; Pacific Symposium on Biocomputing 11:128-139(2006)</dd> <dt><a href="kazic.pdf">Putting Semantics into the Semantic Web: How Well Can It Capture Biology? </a></dt> <dd>Toni Kazic; Pacific Symposium on Biocomputing 11:140-151(2006)</dd> <dt><a href="kushida.pdf">Event Ontology: A Pathway-Centric Ontology for Biological Processes </a></dt> <dd>Tatsuya Kushida, Toshihisa Takagi, and Ken Ichiro Fukuda; Pacific Symposium on Biocomputing 11:152-163(2006)</dd> <dt><a href="mukherjea.pdf">Discovering Biomedical Relations Utilizing the World-Wide Web </a></dt> <dd>Sougata Mukherjea and Saurav Sahay; Pacific Symposium on Biocomputing 11:164-175(2006)</dd> <dt><a href="neumann.pdf">Biodash: A Semantic Web Dashboard for Drug Development </a></dt> <dd>Eric K. Neumann and Dennis Quan; Pacific Symposium on Biocomputing 11:176-187(2006)</dd> <dt><a href="yip.pdf">SemBiosphere: A Semantic Web Approach to Recommending Microarray Clustering Services </a></dt> <dd>Kevin Y. Yip, Peishen Qi, Martin Schultz, David W. Cheung, and Kei-Hoi Cheung; Pacific Symposium on Biocomputing 11:188-199(2006)</dd> <dt><a href="zhang_s.pdf">Experience in Reasoning with the Foundational Model of Anatomy in OWL DL </a></dt> <dd>Songmao Zhang, Olivier Bodenreider, and Christine Golbreich; Pacific Symposium on Biocomputing 11:200-211(2006)</dd> </dl> <h3><a name="proteomics">Computational Proteomics</a></h3> <dl> <dt><a href="intro-proteomics.pdf">Session Introduction </a></dt> <dd>Bobbie-Jo Webb-Robertson, William Cannon, Joshua Adkins, and Deborah Gracio; Pacific Symposium on Biocomputing 11:212-218(2006)</dd> <dt><a href="arnold.pdf">A Machine Learning Approach to Predicting Peptide Fragmentation Spectra </a></dt> <dd>Randy J. Arnold, Narmada Jayasankar, Divya Aggarwal, Haixu Tang, and Predrag Radivojac; Pacific Symposium on Biocomputing 11:219-230(2006)</dd> <dt><a href="chu.pdf">Identifying Protein Complexes in High-Throughput Protein Interaction Screens Using an Infinite Latent Feature Model </a></dt> <dd>Wei Chu, Zoubin Ghahramani, Roland Krause, and David L. Wild; Pacific Symposium on Biocomputing 11:231-242(2006)</dd> <dt><a href="lange.pdf">High-Accuracy Peak Picking of Proteomics Data Using Wavelet Techniques </a></dt> <dd>Eva Lange, Clemens Gropl, Knut Reinert, Oliver Kohlbacher, and Andreas Hildebrandt; Pacific Symposium on Biocomputing 11:243-254(2006)</dd> <dt><a href="liu.pdf">Fast De novo Peptide Sequencing and Spectral Alignment via Tree Decomposition </a></dt> <dd>Chunmei Liu, Yinglei Song, Bo Yan, Ying Xu, and Liming Cai; Pacific Symposium on Biocomputing 11:255-266(2006)</dd> <dt><a href="page.pdf">Experimental Design of Time Series Data for Learning from Dynamic Bayesian Networks </a></dt> <dd>David Page and Irene M. Ong; Pacific Symposium on Biocomputing 11:267-278(2006)</dd> <dt><a href="pratapa.pdf">Finding Diagnostic Biomarkers in Proteomic Spectra </a></dt> <dd>Pallavi N. Pratapa, Edward F. Patz, Jr., Alexander J. Hartemink; Pacific Symposium on Biocomputing 11:279-290(2006)</dd> <dt><a href="tendulkar.pdf">Gaussian Mixture Modeling of Helix Subclasses: Structure and Sequence Variations </a></dt> <dd>Ashish V. Tendulkar, Babatunde Ogunnaike, and Pramod P. Wangikar; Pacific Symposium on Biocomputing 11:291-302(2006)</dd> <dt><a href="wang_h.pdf">An SVM Scorer for More Sensitive and Reliable Peptide Identification via Tandem Mass Spectrometry </a></dt> <dd>Haipeng Wang, Yan Fu, Ruixiang Sun, Simin He, Rong Zeng, and Wen Gao; Pacific Symposium on Biocomputing 11:303-314(2006)</dd> <dt><a href="wang_p.pdf">Normalization Regarding Non-Random Missing Values in High-Throughput Mass Spectrometry Data </a></dt> <dd>Pei Wang, Hua Tang, Heidi Zhang, Jeffrey Whiteaker, Amanda G. Paulovich, and Martin Mcintosh ; Pacific Symposium on Biocomputing 11:315-326(2006)</dd> <dt><a href="yan.pdf">A Point-Process Model for Rapid Identification of Post-Translational Modifications </a></dt> <dd>Bo Yan, Tong Zhou, Peng Wang, Zhijie Liu, Vincent A. Emanuele II, Victor Olman, and Ying Xu; Pacific Symposium on Biocomputing 11:327-338(2006)</dd> <dt><a href="zhang_x.pdf">A New Approach for Alignment of Multiple Proteins </a></dt> <dd>Xu Zhang and Tamer Kahveci; Pacific Symposium on Biocomputing 11:339-350(2006)</dd> </dl> <h3><a name="protein">Protein Interactions in Disease</a></h3> <dl> <dt><a href="intro-protein.pdf">Session Introduction </a></dt> <dd>Maricel Kann, Yanay Ofran, Marco Punta, and Predrag Radivojac; Pacific Symposium on Biocomputing 11:351-353(2006)</dd> <dt><a href="bandyopadhyay.pdf">Discovering Regulated Networks During HIV-1 Latency and Reactivation </a></dt> <dd>Sourav Bandyopadhyay, Ryan Kelley, and Trey Ideker; Pacific Symposium on Biocomputing 11:354-366(2006)</dd> <dt><a href="chen_j.pdf">Mining Alzheimer Disease Relevant Proteins from Integrated Protein Interactome Data </a></dt> <dd>Jake Yue Chen, Changyu Shen, and Andrey Y. Sivachenko; Pacific Symposium on Biocomputing 11:367-378(2006)</dd> <dt><a href="gunewardena.pdf">Accounting for Structural Properties and Nucleotide Co-variations in the Quantitative Prediction of Binding Affinities of Protein-DNA Interactions </a></dt> <dd>Sumedha Gunewardena and Zhaolei Zhang; Pacific Symposium on Biocomputing 11:379-390(2006)</dd> <dt><a href="robinson.pdf">Improving Computational Predictions of Cis- Regulatory Binding Sites </a></dt> <dd>Mark Robinson, Yi Sun, Rene Te Boekhorst, Paul Kaye, Rod Adams, Neil Davey, and Alistair G. Rust ; Pacific Symposium on Biocomputing 11:391-402(2006)</dd> <dt><a href="singh.pdf">Struct2Net: Integrating Structure into Protein-Protein Interaction Prediction </a></dt> <dd>Rohit Singh, Jinbo Xu, and Bonnie Berger; Pacific Symposium on Biocomputing 11:403-414(2006)</dd> <dt><a href="terribilini.pdf">Identifying Interaction Sites in "Recalcitrant" Proteins: Predicted Protein and RNA Binding Sites in Rev Proteins of HIV-1 and EIAV Agree with Experimental Data </a></dt> <dd>Michael Terribilini, Jae-Hyung Lee, Changhui Yan, Robert L. Jernigan, Susan Carpenter, Vasant Honavar, and Drena Dobbs; Pacific Symposium on Biocomputing 11:415-426(2006)</dd> <dt><a href="troncale.pdf">Modeling and Simulation with Hybrid Functional Petri Nets of the Role of Interleukin-6 in Human Early Haematopoiesis </a></dt> <dd>Sylvie Troncale, Fariza Tahi, David Campard, Jean-Pierre Vannier, and Janine Guespin; Pacific Symposium on Biocomputing 11:427-438(2006)</dd> <dt><a href="ye.pdf">Modeling and Analyzing Three-Dimensional Structures of Human Disease Proteins </a></dt> <dd>Yuzhen Ye, Zhanwen Li, and Adam Godzik; Pacific Symposium on Biocomputing 11:439-450(2006)</dd> </dl> <h3><a name="genstudies">Design and Analysis of Genetic Studies After the Hapmap Project</a></h3> <dl> <dt><a href="intro-genstudies.pdf">Session Introduction </a></dt> <dd>Francisco M. De La Vega, Andrew G. Clark, Andrew Collins, and Kenneth K. Kidd; Pacific Symposium on Biocomputing 11:451-453(2006)</dd> <dt><a href="castellana.pdf">Relaxing Haplotype Block Models for Association Testing </a></dt> <dd>Natalie Castellana, Kedar Dhamdhere, Srinath Sridhar, and Russell Schwartz; Pacific Symposium on Biocomputing 11:454-466(2006)</dd> <dt><a href="chen_l.pdf">Effect of the Peroxisome Proliferators-Activated Receptor (PPAR) Gamma 3 Gene on BMI in 1,210 School Students from Morelos, Mexico </a></dt> <dd>Lina Chen, H. Eduardo Velasco Mondragon, Eduardo Lazcano-Ponce, Andrew Collins, and Yin Yao Shugart; Pacific Symposium on Biocomputing 11:467-477(2006)</dd> <dt><a href="debakker.pdf">Transferability of Tag SNPs to Capture Common Genetic Variation in DNA Repair Genes Across Multiple Populations </a></dt> <dd>Paul I.W. De Bakker, Robert R. Graham, David Altshuler, Brian E. Henderson, and Christopher A. Haiman; Pacific Symposium on Biocomputing 11:478-486(2006)</dd> <dt><a href="delavega.pdf">A Tool for Selecting SNPs for Association Studies Based on Observed Linkage Disequilibrium Patterns </a></dt> <dd>Francisco M. De La Vega, Hadar I. Isaac, and Charles R. Scafe; Pacific Symposium on Biocomputing 11:487-498(2006)</dd> <dt><a href="dudek.pdf">Data Simulation Software for Whole-Genome Association and Other Studies in Human Genetics </a></dt> <dd>Scott M. Dudek, Alison A. Motsinger, Digna R. Velez, Scott M. Williams, and Marylyn D. Ritchie; Pacific Symposium on Biocomputing 11:499-510(2006)</dd> <dt><a href="gopalakrishnan.pdf">TagSNP Selection Based on Pairwise LD Criteria and Power Analysis in Association Studies </a></dt> <dd>Shyam Gopalakrishnan and Zhaohui S. Qin; Pacific Symposium on Biocomputing 11:511-522(2006)</dd> <dt><a href="kraft.pdf">Efficient Two-Stage Genome-Wide Association Designs Based on False Positive Report Probabilities </a></dt> <dd>Peter Kraft; Pacific Symposium on Biocomputing 11:523-534(2006)</dd> <dt><a href="magi.pdf">The Whole Genome TagSNP Selection and Transferability Among HapMap Populations </a></dt> <dd>Reedik Magi, Lauris Kaplinski, and Maido Remm; Pacific Symposium on Biocomputing 11:535-543(2006)</dd> </dl> <h3><a name="pharma">Computational Approaches for Pharmacogenomics</a></h3> <dl> <dt><a href="intro-pharma.pdf">Session Introduction </a></dt> <dd>Michelle W. Carrillo, Russell A. Wilke, and Marylyn D. Ritchie; Pacific Symposium on Biocomputing 11:544-546(2006)</dd> <dt><a href="borgwardt.pdf">Class Prediction from Time Series Gene Expression Profiles Using Dynamical Systems Kernels </a></dt> <dd>Karsten M. Borgwardt, S.V.N. Vishwanathan, and Hans-Peter Kriegel; Pacific Symposium on Biocomputing 11:547-558(2006)</dd> <dt><a href="imoto.pdf">Computational Strategy for Discovering Druggable Gene Networks from Genome-Wide RNA Expression Profiles </a></dt> <dd>Seiya Imoto, Yoshinori Tamada, Hiromitsu Araki, Kaori Yasuda, Cristin G. Print, Stephen D. Charnock-Jones, Deborah Sanders, Christopher J. Savoie, Kousuke Tashiro, Satoru Kuhara, and Satoru Miyano; Pacific Symposium on Biocomputing 11:559-571(2006)</dd> <dt><a href="lin.pdf">A Bivariate Functional Mapping Model for Identifying Haplotypes that Control Drug Response for Systolic and Diastolic Blood Pressures </a></dt> <dd>Min Lin, Rongling Wu, and Julie Johnson; Pacific Symposium on Biocomputing 11:572-583(2006)</dd> <dt><a href="motsinger.pdf">Risk Factor Interactions and Genetic Effects Associated with Post-Operative Atrial Fibrillation </a></dt> <dd>Alison A. Motsinger, Brian S. Donahue, Nancy J. Brown, Dan M. Roden, and Marylyn D. Ritchie; Pacific Symposium on Biocomputing 11:584-595(2006)</dd> <dt><a href="richter.pdf">Learning a Predictive Model for Growth Inhibition from the NCI DTP Human Tumor Cell Line Screening Data: Does Gene Expression Make a Difference? </a></dt> <dd>Lothar Richter, Ulrich Ruckert, and Stefan Kramer; Pacific Symposium on Biocomputing 11:596-607(2006)</dd> </dl> <hr> <table width="100%" border="0" cellspacing="0" align="center"><tr> <td align="left"><a href="index.html">Back to the main PSB page</a></td> <td align="right">Updated: February 3, 2006</td> </tr></table> </body> </html>