PSB 2012 Online Proceedings

 PSB 2012

PSB Proceedings for All Years

Contents

Preface

Identification of Aberrant Pathway and Network Activity from High-Throughput Data

Session Introduction
Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, and Joel S. Bader; Pacific Symposium on Biocomputing 17:1-6(2012)
SSLPred : Predicting Synthetic Sickness Lethality
Nirmalya Bandyopadhyay, Sanjay Ranka, and Tamer Kahveci ; Pacific Symposium on Biocomputing 17:7-18(2012)
Predicting the Effects of Copy-Number Variation in Double and Triple Mutant Combinations
Gregory W. Carter, Michelle Hays, Song Li, and Timothy Galitski ; Pacific Symposium on Biocomputing 17:19-30(2012)
Integrative Network Analysis to Identify Aberrant Pathway Networks in Ovarian Cancer
Li Chen, Jianhua Xuan, Jinghua Gu, Yue Wang, Li Chen, Zhen Zhang, Tian-Li Wang, and Ie-Ming Shih; Pacific Symposium on Biocomputing 17:31-42(2012)
Role of Synthetic Genetic Interactions in Understanding Functional Interactions Among Pathways
Shahin Mohammadi, Giorgos Kollias, and Ananth Grama; Pacific Symposium on Biocomputing 17:43-54(2012)
Discovery of Mutated Subnetworks Associated with Clinical Data in Cancer
Fabio Vandin, Patrick Clay, Eli Upfal, and Benjamin J. Raphael; Pacific Symposium on Biocomputing 17:55-66(2012)

Intrinsically Disordered Proteins: Analysis, Prediction, Simulation, and Biology

Session introduction
Jianhan Chen, Jianlin Cheng, and A. Keith Dunker; Pacific Symposium on Biocomputing 17:67-69(2012)
Quasi-Anharmonic Analysis Reveals Intermediate States in the Nuclear Co-Activator Receptor Binding Domain Ensemble
Virginia M. Burger, Arvind Ramanathan, Andrej J. Savol, Christopher B. Stanley, Pratul K. Agarwal, and Chakra S. Chennubhotla; Pacific Symposium on Biocomputing 17:70-81(2012)
Efficient Construction of Disordered Protein Ensembles in a Bayesian Framework with Optimal Selection of Conformations
Charles K. Fisher, Orly Ullman, and Collin M. Stultz ; Pacific Symposium on Biocomputing 17:82-93(2012)
Correlation Between Posttranslational Modification and Intrinsic Disorder in Protein
Jianjiong Gao and Dong Xu; Pacific Symposium on Biocomputing 17:94-103(2012)
Intrinsic Disorder Within and Flanking the DNA-Binding Domains of Human Transcription Factors
Xin Guo, Martha L. Bulyk, and Alexander J. Hartemink; Pacific Symposium on Biocomputing 17:104-115(2012)
Intrinsic Protein Disorder and Protein-Protein Interactions
Wei-Lun Hsu, Christopher Oldfield, Jingwei Meng, Fei Huang, Bin Xue, Vladimir N. Uversky, Pedro Romero, and A. Keith Dunker; Pacific Symposium on Biocomputing 17:116-127(2012)
Subclassifying Disordered Proteins by the CH-CDF Plot Method
Fei Huang, Christopher Oldfield, Jingwei Meng, Wei-lun Hsu, Bin Xue, Vladimir N. Uversky, Pedro Romero, and A. Keith Dunker; Pacific Symposium on Biocomputing 17:128-139(2012)
Coevolved Residues and the Functional Association for Intrinsically Disordered Proteins
Chan-Seok Jeong and Dongsup Kim; Pacific Symposium on Biocomputing 17:140-151(2012)
Cryptic Disorder: An Order-Disorder Transformation Regulates the Function of Nucleophosmin
Diana M. Mitrea and Richard W. Kriwacki; Pacific Symposium on Biocomputing 17:152-163(2012)
Functional Annotation of Intrinsically Disordered Domains by Their Amino Acid Content Using IDD Navigator
Ashwini Patil, Shunsuke Teraguchi, Huy Dinh, Kenta Nakai, and Daron M Standley; Pacific Symposium on Biocomputing 17:164-175(2012)
On the Complementarity of the Consensus-Based Disorder Prediction
Zhenling Peng and Lukasz Kurgan; Pacific Symposium on Biocomputing 17:176-187(2012)
Modulating Protein-DNA Interactions by Post-Translational Modifications at Disordered Regions
Dana Vuzman, Yonit Hoffman, and Yaakov Levy; Pacific Symposium on Biocomputing 17:188-199(2012)

Microbiome Studies: Analytical Tools and Techniques

Session introduction
James A. Foster, Jason H. Moore, Jack Gilbert, and John Bunge; Pacific Symposium on Biocomputing 17:200-202(2012)
Estimating Population Diversity with Unreliable Low Frequency Counts
John Bunge, Dankmar Boehning, Heather Allen, and James A. Foster; Pacific Symposium on Biocomputing 17:203-212(2012)
Comparisons of Distance Methods for Combining Covariates and Abundances in Microbiome Studies
Julia Fukuyama, Paul J. Mcmurdie, Les Dethlefsen, David A. Relman, and Susan Holmes; Pacific Symposium on Biocomputing 17:213-224(2012)
Proteotyping of Microbial Communities by Optimization of Tandem Mass Spectrometry Data Interpretation
Alys Hugo, Douglas J. Baxter, William R. Cannon, Ananth Kalyanaraman, Gaurav Kulkarni, and Stephen J. Callister; Pacific Symposium on Biocomputing 17:225-234(2012)
phyloseq: A Bioconductor Package for Handling and Analysis of High-Throughput Phylogenetic Sequence Data
Paul J. McMurdie and Susan Holmes; Pacific Symposium on Biocomputing 17:235-246(2012)
SEPP: SATe -Enabled Phylogenetic Placement
Siavash Mirarab, Nam Nguyen, and Tandy Warno; Pacific Symposium on Biocomputing 17:247-258(2012)
Artificial Functional Difference Between Microbial Communities Caused by Length Difference of Sequencing Reads
Quan Zhang, Thomas G. Doak, and Yuzhen Ye; Pacific Symposium on Biocomputing 17:259-270(2012)
MetaDomain: A Profile HMM-Based Protein Domain Classification Tool for Short Sequences
Yuan Zhang and Yanni Sun; Pacific Symposium on Biocomputing 17:271-282(2012)

Modeling Host-Pathogen Interactions: Computational Biology And Bioinformatics For Infectious Disease Research

Session introduction
Jason E. Mcdermott, Pascal Braun, Richard Bonneau, and Daniel R. Hyduke; Pacific Symposium on Biocomputing 17:283-286(2012)
Structural Models for Host-Pathogen Protein-Protein Interactions: Assessing Coverage and Bias
Eric A. Franzosa and Yu Xia; Pacific Symposium on Biocomputing 17:287-298(2012)
Identification of Cell Cycle-Regulated, Putative Hyphal Genes in Candida Albicans
Raluca Gordan, Saumyadipta Pyne, and Martha L. Bulyk; Pacific Symposium on Biocomputing 17:299-310(2012)
Determining Confidence of Predicted Interactions Between HIV-1 and Human Proteins Using Conformal Method
Ilia Nouretdinov, Alex Gammerman, Yanjun Qi, and Judith Klein-Seetharaman; Pacific Symposium on Biocomputing 17:311-322(2012)

Personalized Medicine: From Genotypes and Molecular Phenotypes Towards Computed Therapy

Session introduction
Oliver Stegle, Frederick P. Roth, Quaid Morris, and Jennifer Listgarten; Pacific Symposium on Biocomputing 17:323-326(2012)
Finding Genome-Transcriptome-Phenome Associations with Structured Association Mapping and Visualization in GenAMap
Ross E. Curtis, Junming Yin, Peter Kinnaird, and Eric P. Xing; Pacific Symposium on Biocomputing 17:327-338(2012)
Interpretome: A Freely Available, Modular, and Secure Personal Genome Interpretation Engine
Konrad J. Karczewski, Robert P. Tirrell, Pablo Cordero, Nicholas P. Tatonetti, Joel T. Dudley, Keyan Salari, Michael Snyder, Russ B. Altman, and Stuart K. Kim; Pacific Symposium on Biocomputing 17:339-350(2012)
A Kinase Inhibition Map Approach for Tumor Sensitivity Prediction and Combination Therapy Design for Targeted Drugs
Ranadip Pal and Noah Berlow; Pacific Symposium on Biocomputing 17:351-362(2012)
Mixture Model for Sub-Phenotyping in GWAS
David Warde-Farley, Michael Brudno, Quaid Morris, and Anna Goldenberg; Pacific Symposium on Biocomputing 17:363-374(2012)

Text and Knowledge Mining for Pharmacogenomics: Genotypephenotype-Drug Relationships

Session introduction
Kevin Bretonnel Cohen, Yael Garten, Nigham Shah, and Udo Hahn; Pacific Symposium on Biocomputing 17:375(2012)
The Extraction of Pharmacogenetic and Pharmacogenomic Relations - A Case Study Using PharmGKB
Ekaterina Buyko, Elena Beisswanger, and Udo Hahn; Pacific Symposium on Biocomputing 17:376-387(2012)
Linking PharmGKB to Phenotype Studies and Animal Models of Disease for Drug Repurposing
Robert Hoehndorf, Anika Oellrich, Dietrich Rebholz-Schuhmann, Paul Schofield, and Georgios V. Gkoutos ; Pacific Symposium on Biocomputing 17:388-399(2012)
Integrating VA's NDF-RT Drug Terminology with PharmGKB: Preliminary Results
Jyotishman Pathak, Laura C. Weiss, Matthew J. Durski, Qian Zhu, Robert R. Freimuth, and Christopher G. Chute; Pacific Symposium on Biocomputing 17:400-409(2012)
Discovery and Explanation of Drug-Drug Interactions via Text Mining
Bethany Percha, Yael Garten, and Russ B. Altman; Pacific Symposium on Biocomputing 17:410-421(2012)
Ranking Gene-Drug Relationships in Biomedical Literature Using Latent Dirichlet Allocation
Yonghui Wu, Mei Liu, W. Jim Zheng, Zhongming Zhao, and Hua Xu; Pacific Symposium on Biocomputing 17:422-433(2012)

Workshops

The Structure and Function of Chromatin and Chromosomes
William Stafford Noble, C. Anthony Blau, Job Dekker, Zhi-Jun Duan, and Yi Mao; Pacific Symposium on Biocomputing 17:434-440(2012)
Law, Bioethics and the Current Status of Ownership, Privacy, Informed Consent in the Genomic Age
Greg Hampikian and Eric M. Meslin; Pacific Symposium on Biocomputing 17:441(2012)
Systems Pharmacogenomics-Bridging the Gap
Marylyn Ritchie, Nancy Cox, Cheng Cheng, Scott Weiss, Teri Klein and Russ Altman; Pacific Symposium on Biocomputing 17:442(2012)
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