Contents

• Computational Approaches for Pharmacogenomics
• Computational Proteomics
• Design and Analysis of Genetic Studies After the HapMap Project
• Linking Biomedical Information Through Text Mining
• Protein Interactions in Disease
• Semantic Webs for Life Sciences

Preface

Linking Biomedical Information Through Text Mining

Session Introduction

K. Bretonnel Cohen, Olivier Bodenreider, and Lynette Hirschman; Pacific Symposium on Biocomputing 11:1-3(2006)

Extraction of Gene-Disease Relations from Medline Using Domain Dictionaries and Machine Learning

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)

Significantly Improved Prediction of Subcellular Localization by Integrating Text and Protein Sequence Data

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)

Evaluation of Lexical Methods for Detecting Relationships Between Concepts from Multiple Ontologies

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)

Automatically Generating Gene Summaries from Biomedical Literature

Xu Ling, Jing Jiang, Xin He, Qiaozhu Mei, Chengxiang Zhai, and Bruce Schatz; Pacific Symposium on Biocomputing 11:40-51(2006)

Finding GeneRIFs via Gene Ontology Annotations

Zhiyong Lu, K. Bretonnel Cohen, and Lawrence Hunter; Pacific Symposium on Biocomputing 11:52-63(2006)

PhenoGO: Assigning Phenotypic Context to Gene Ontology Annotations with Natural Language Processing

Yves Lussier, Tara Borlawsky, Daniel Rappaport, Yang Liu, and Carol Friedman; Pacific Symposium on Biocomputing 11:64-75(2006)

Large-Scale Testing of Bibliome Informatics Using Pfam Protein Families

Ana G. Maguitman, Andreas Rechtsteiner, Karin Verspoor, Charlie E. Strauss, and Luis M. Rocha; Pacific Symposium on Biocomputing 11:76-87(2006)

Predicting Gene Functions from Text Using a Cross-Species Approach

Emilia Stoica and Marti Hearst; Pacific Symposium on Biocomputing 11:88-99(2006)

Bootstrapping the Recognition and Anaphoric Linking of Named Entities in Drosophila Articles

Andreas Vlachos, Caroline Gasperin, Ian Lewin, Ted Briscoe; Pacific Symposium on Biocomputing 11:100-111(2006)

Semantic Webs for Life Sciences

Session Introduction

Roberts Stevens, Olivier Bodenreider, and Yves A. Lussier; Pacific Symposium on Biocomputing 11:112-115(2006)

Selecting Biological Data Sources and Tools with XPR, a Path Language for RDF

Sarah Cohen-Boulakia, Christine Froidevaux, and Emmanuel Pietriga; Pacific Symposium on Biocomputing 11:116-127(2006)

Fast, Cheap and Out of Control: A Zero Curation Model for Ontology Development

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)

Putting Semantics into the Semantic Web: How Well Can It Capture Biology?

Toni Kazic; Pacific Symposium on Biocomputing 11:140-151(2006)

Event Ontology: A Pathway-Centric Ontology for Biological Processes

Tatsuya Kushida, Toshihisa Takagi, and Ken Ichiro Fukuda; Pacific Symposium on Biocomputing 11:152-163(2006)

Discovering Biomedical Relations Utilizing the World-Wide Web

Sougata Mukherjea and Saurav Sahay; Pacific Symposium on Biocomputing 11:164-175(2006)

Biodash: A Semantic Web Dashboard for Drug Development

Eric K. Neumann and Dennis Quan; Pacific Symposium on Biocomputing 11:176-187(2006)

SemBiosphere: A Semantic Web Approach to Recommending Microarray Clustering Services

Kevin Y. Yip, Peishen Qi, Martin Schultz, David W. Cheung, and Kei-Hoi Cheung; Pacific Symposium on Biocomputing 11:188-199(2006)

Experience in Reasoning with the Foundational Model of Anatomy in OWL DL

Songmao Zhang, Olivier Bodenreider, and Christine Golbreich; Pacific Symposium on Biocomputing 11:200-211(2006)

Computational Proteomics

Session Introduction

Bobbie-Jo Webb-Robertson, William Cannon, Joshua Adkins, and Deborah Gracio; Pacific Symposium on Biocomputing 11:212-218(2006)

A Machine Learning Approach to Predicting Peptide Fragmentation Spectra

Randy J. Arnold, Narmada Jayasankar, Divya Aggarwal, Haixu Tang, and Predrag Radivojac; Pacific Symposium on Biocomputing 11:219-230(2006)

Identifying Protein Complexes in High-Throughput Protein Interaction Screens Using an Infinite Latent Feature Model

Wei Chu, Zoubin Ghahramani, Roland Krause, and David L. Wild; Pacific Symposium on Biocomputing 11:231-242(2006)

High-Accuracy Peak Picking of Proteomics Data Using Wavelet Techniques

Eva Lange, Clemens Gropl, Knut Reinert, Oliver Kohlbacher, and Andreas Hildebrandt; Pacific Symposium on Biocomputing 11:243-254(2006)

Fast De novo Peptide Sequencing and Spectral Alignment via Tree Decomposition

Chunmei Liu, Yinglei Song, Bo Yan, Ying Xu, and Liming Cai; Pacific Symposium on Biocomputing 11:255-266(2006)

Experimental Design of Time Series Data for Learning from Dynamic Bayesian Networks

David Page and Irene M. Ong; Pacific Symposium on Biocomputing 11:267-278(2006)

Finding Diagnostic Biomarkers in Proteomic Spectra

Pallavi N. Pratapa, Edward F. Patz, Jr., Alexander J. Hartemink; Pacific Symposium on Biocomputing 11:279-290(2006)

Gaussian Mixture Modeling of Helix Subclasses: Structure and Sequence Variations

Ashish V. Tendulkar, Babatunde Ogunnaike, and Pramod P. Wangikar; Pacific Symposium on Biocomputing 11:291-302(2006)

An SVM Scorer for More Sensitive and Reliable Peptide Identification via Tandem Mass Spectrometry

Haipeng Wang, Yan Fu, Ruixiang Sun, Simin He, Rong Zeng, and Wen Gao; Pacific Symposium on Biocomputing 11:303-314(2006)

Normalization Regarding Non-Random Missing Values in High-Throughput Mass Spectrometry Data

Pei Wang, Hua Tang, Heidi Zhang, Jeffrey Whiteaker, Amanda G. Paulovich, and Martin Mcintosh ; Pacific Symposium on Biocomputing 11:315-326(2006)

A Point-Process Model for Rapid Identification of Post-Translational Modifications

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)

A New Approach for Alignment of Multiple Proteins

Xu Zhang and Tamer Kahveci; Pacific Symposium on Biocomputing 11:339-350(2006)

Protein Interactions in Disease

Session Introduction

Maricel Kann, Yanay Ofran, Marco Punta, and Predrag Radivojac; Pacific Symposium on Biocomputing 11:351-353(2006)

Discovering Regulated Networks During HIV-1 Latency and Reactivation

Sourav Bandyopadhyay, Ryan Kelley, and Trey Ideker; Pacific Symposium on Biocomputing 11:354-366(2006)

Mining Alzheimer Disease Relevant Proteins from Integrated Protein Interactome Data

Jake Yue Chen, Changyu Shen, and Andrey Y. Sivachenko; Pacific Symposium on Biocomputing 11:367-378(2006)

Accounting for Structural Properties and Nucleotide Co-variations in the Quantitative Prediction of Binding Affinities of Protein-DNA Interactions

Sumedha Gunewardena and Zhaolei Zhang; Pacific Symposium on Biocomputing 11:379-390(2006)

Improving Computational Predictions of Cis- Regulatory Binding Sites

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)

Struct2Net: Integrating Structure into Protein-Protein Interaction Prediction

Rohit Singh, Jinbo Xu, and Bonnie Berger; Pacific Symposium on Biocomputing 11:403-414(2006)

Identifying Interaction Sites in "Recalcitrant" Proteins: Predicted Protein and RNA Binding Sites in Rev Proteins of HIV-1 and EIAV Agree with Experimental Data

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)

Modeling and Simulation with Hybrid Functional Petri Nets of the Role of Interleukin-6 in Human Early Haematopoiesis

Sylvie Troncale, Fariza Tahi, David Campard, Jean-Pierre Vannier, and Janine Guespin; Pacific Symposium on Biocomputing 11:427-438(2006)

Modeling and Analyzing Three-Dimensional Structures of Human Disease Proteins

Yuzhen Ye, Zhanwen Li, and Adam Godzik; Pacific Symposium on Biocomputing 11:439-450(2006)

Design and Analysis of Genetic Studies After the Hapmap Project

Session Introduction

Francisco M. De La Vega, Andrew G. Clark, Andrew Collins, and Kenneth K. Kidd; Pacific Symposium on Biocomputing 11:451-453(2006)

Relaxing Haplotype Block Models for Association Testing

Natalie Castellana, Kedar Dhamdhere, Srinath Sridhar, and Russell Schwartz; Pacific Symposium on Biocomputing 11:454-466(2006)

Effect of the Peroxisome Proliferators-Activated Receptor (PPAR) Gamma 3 Gene on BMI in 1,210 School Students from Morelos, Mexico

Lina Chen, H. Eduardo Velasco Mondragon, Eduardo Lazcano-Ponce, Andrew Collins, and Yin Yao Shugart; Pacific Symposium on Biocomputing 11:467-477(2006)

Transferability of Tag SNPs to Capture Common Genetic Variation in DNA Repair Genes Across Multiple Populations

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)

A Tool for Selecting SNPs for Association Studies Based on Observed Linkage Disequilibrium Patterns

Francisco M. De La Vega, Hadar I. Isaac, and Charles R. Scafe; Pacific Symposium on Biocomputing 11:487-498(2006)

Data Simulation Software for Whole-Genome Association and Other Studies in Human Genetics

Scott M. Dudek, Alison A. Motsinger, Digna R. Velez, Scott M. Williams, and Marylyn D. Ritchie; Pacific Symposium on Biocomputing 11:499-510(2006)

TagSNP Selection Based on Pairwise LD Criteria and Power Analysis in Association Studies

Shyam Gopalakrishnan and Zhaohui S. Qin; Pacific Symposium on Biocomputing 11:511-522(2006)

Efficient Two-Stage Genome-Wide Association Designs Based on False Positive Report Probabilities

Peter Kraft; Pacific Symposium on Biocomputing 11:523-534(2006)

The Whole Genome TagSNP Selection and Transferability Among HapMap Populations

Reedik Magi, Lauris Kaplinski, and Maido Remm; Pacific Symposium on Biocomputing 11:535-543(2006)

Computational Approaches for Pharmacogenomics

Session Introduction

Michelle W. Carrillo, Russell A. Wilke, and Marylyn D. Ritchie; Pacific Symposium on Biocomputing 11:544-546(2006)

Class Prediction from Time Series Gene Expression Profiles Using Dynamical Systems Kernels

Karsten M. Borgwardt, S.V.N. Vishwanathan, and Hans-Peter Kriegel; Pacific Symposium on Biocomputing 11:547-558(2006)

Computational Strategy for Discovering Druggable Gene Networks from Genome-Wide RNA Expression Profiles

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)

A Bivariate Functional Mapping Model for Identifying Haplotypes that Control Drug Response for Systolic and Diastolic Blood Pressures

Min Lin, Rongling Wu, and Julie Johnson; Pacific Symposium on Biocomputing 11:572-583(2006)

Risk Factor Interactions and Genetic Effects Associated with Post-Operative Atrial Fibrillation

Alison A. Motsinger, Brian S. Donahue, Nancy J. Brown, Dan M. Roden, and Marylyn D. Ritchie; Pacific Symposium on Biocomputing 11:584-595(2006)

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 Ruckert, and Stefan Kramer; Pacific Symposium on Biocomputing 11:596-607(2006)