PSB 2011 Online Proceedings

 PSB 2011

PSB Proceedings for All Years

Contents

Preface

Computational Methods Integrating Diverse Biological and Clinical Data for Translational Science

Session Introduction
Gurkan Bebek, Mehmet Koyutuk, Mark Chance, Nathan D. Price; Pacific Symposium On Biocomputing 16:1-3(2011)
Towards Integrative Gene Prioritization in Alzheimer's Disease
Jang Lee, Graciela Gonzalez; Pacific Symposium On Biocomputing 16:4-13(2011)
Systems Biology Analyses of Gene Expression and Genome Wide Association Study Data in Obstructive Sleep Apnea
Yu Liu, Sanjay R. Patel, Rod K. Nibbe, Sean Maxwell, Salim A. Chowdhury, Mehmet Koyuturk, Xiaofeng Zhu, Emma Larkin, Sarah Buxbaum, Naresh Punjabi, Sina Gharib, Susan Redline, Mark R. Chance; Pacific Symposium On Biocomputing 16:14-25(2011)
Finding Most Likely Haplotypes in General Pedigrees Through Parallel Search with Dynamic Load Balancing
Lars Otten, Rina Dechter; Pacific Symposium On Biocomputing 16:26-37(2011)
Dynamic, Multi-Level Network Models of Clinical Trials
Marco D. Sorani, Geoffrey T. Manley, J. Claude Hemphill, Sergio E. Baranzini; Pacific Symposium On Biocomputing 16:38-49(2011)
Mining Functionally Relevant Gene Sets for Analyzing Physiologically Novel Clinical Expression Data
Sevin Turcan, Xintao Wei, Jill Maron, Douglas E. Vetter, Donna K. Slonim; Pacific Symposium On Biocomputing 16:50-61(2011)
Genotype Phenotype Mapping in Rna Viruses - Disjunctive Normal Form Learning
Chuang Wu, Andrew S. Walsh, Roni Rosenfeld; Pacific Symposium On Biocomputing 16:62-73(2011)

Genome-Wide Association Mapping and Rare Alleles: From Population Genomics to Personalized Medicine

Session introduction
Francisco M. De La Vega, Carlos D. Bustamante, Suzanne M. Leal; Pacific Symposium On Biocomputing 16:74-75(2011)
An Application and Empirical Comparison of Statistical Analysis Methods for Associating Rare Variants to a Complex Phenotype
Vikas Bansal, Ondrej Libiger, Ali Torkamani, Nicholas J. Schork; Pacific Symposium On Biocomputing 16:76-87(2011)
Haplotype Phasing By Multi-Assembly of Shared Haplotypes: Phase-Dependent Interactions Between Rare Variants
Bjarni V. Halldorsson, Derek Aguiar, Sorin Istrail; Pacific Symposium On Biocomputing 16:88-99(2011)
An Evaluation of Power to Detect Low-Frequency Variant Associations Using Allele-Matching Tests that Account for Uncertainty
Eleftheria Zeggini, Jennifer L. Asimit; Pacific Symposium On Biocomputing 16:100-105(2011)
Penalized Regression for Genome-Wide Association Screening of Sequence Data
Hua Zhou, David Alexander, Mary Sehl, Janet Sinsheimer, Kenneth Lange; Pacific Symposium on Biocomputing 16:106-117(2011)

Microbiome Studies: Understanding How the Dominant Form of Life Affects Us

Session introduction
James Foster, Jason Moore; Pacific Symposium on Biocomputing 16:118-120(2011)
Estimating the Number of Species with Catchall
John Bunge; Pacific Symposium on Biocomputing 16:121-130(2011)
A Framework for Analysis of Metagenomic Sequencing Data
A. Murat Eren, Michael J. Ferris, Christopher M. Taylor; Pacific Symposium on Biocomputing 16:131-141(2011)
Visualization and Statistical Comparisons of Microbial Communities Using R Packages on Phylochip Data
S. Holmes, A. Alekseyenko, A. Timme, T. Nelson, P.J. Pasricha, A. Spormann; Pacific Symposium on Biocomputing 16:142-153(2011)
Human Microbiome Visualization Using 3d Technology
Jason H. Moore, Richard Cowper-Sal.Lari, Douglas Hill, Patricia Hibberd, Juliette Madan; Pacific Symposium on Biocomputing 16:154-164(2011)
Comparing Bacterial Communities Inferred from 16s Rrna Gene Sequencing and Shotgun Metagenomics
Neethu Shah, Haixu Tang, Thomas G. Doak, Yuzhen Ye; Pacific Symposium on Biocomputing 16:165-176(2011)

Multi-Scale Modelling of Biosystems: From Molecular to Mesoscale

Session introduction
Julie Bernauer, Samuel Flores, Xuhui Huang, Seokmin Shin, Ruhong Zhou; Pacific Symposium on Biocomputing 16:177-180(2011)
Computational Generation inhibitor-Bound Conformers of P38 Map Kinase and Comparison with Experiments
Ahmet Bakan, Ivet Bahar; Pacific Symposium on Biocomputing 16:181-192(2011)
Molecular Dynamics Simulations of the Full Triple Helical Region of Collagen Type I Provide An Atomic Scale View of the Protein's Regional Heterogeneity
Dale L Bodian, Randall J Radmer, Sean Holbert, Teri E Klein; Pacific Symposium on Biocomputing 16:193-204(2011)
Structural insights into Pre-Translocation Ribosome Motions
Samuel Coulbourn Flores, Russ B. Altman; Pacific Symposium on Biocomputing 16:205-216(2011)
New Conformational Search Method Using Genetic Algorithm and Knot Theory for Proteins
Yoshitake Sakae, tomoyuki Hiroyasu, Mitsunori Miki, Yuko Okamoto; Pacific Symposium on Biocomputing 16:217-228(2011)

Personal Genomics

Session introduction
Can Alkan, Emidio Capriotti, Eleazar Eskin, Fereydoun Hormozdiari, Maricel G. Kann; Pacific Symposium on Biocomputing 16:229-230(2011)
The Reference Human Genome Demonstrates High Risk of Type 1 Diabetes and Other Disorders
Rong Chen, Atul J. Butte; Pacific Symposium on Biocomputing 16:231-242(2011)
Matching Cancer Genomes to Established Cell Lines for Personalized Oncology
Joel T. Dudley, Rong Chen, Atul J. Butte; Pacific Symposium on Biocomputing 16:243-252(2011)
Use of Biological Knowledge to Inform The Analysis of Gene-Gene Interactions Involved in Modulating Virologic Failure with Efavirenz-Containing Treatment Regimens in Art-Naive Actg Clinical Trials Participants
Benjamin J. Grady, Eric C. Torstenson, Paul J. Mclaren, Paul W. De Bakker, David W. Haas, Gregory K. Robbins, Roy M. Gulick, Richard Haubrich, Heather Ribaudo, Marylyn D. Ritchie; Pacific Symposium on Biocomputing 16:253-264(2011)
Visual integration of Results from a Large Dna Biobank (Biovu) Using Synthesis-View
Sarah Pendergrass, Scott M. Dudek, Dan M. Roden, Dana C. Crawford, Marylyn D. Ritchie; Pacific Symposium on Biocomputing 16:265-275(2011)
Multivariate Analysis of Regulatory Snps: Empowering Personal Genomics by Considering Cis-Epistasis and Heterogeneity
Stephen D. Turner, William S. Bush; Pacific Symposium on Biocomputing 16:276-287(2011)
Haplotype inference from Single Short Sequence Reads Using a Population Genealogical History Model
Jin Zhang, Yufeng Wu; Pacific Symposium on Biocomputing 16:288-299(2011)

Reverse Engineering and Synthesis of Biomolecular Systems

Session introduction
Gil Alterovitz, Silvio Cavalcanti, Taro M. Muso, Marco F. Ramoni, May Wang; Pacific Symposium on Biocomputing 16:300-301(2011)
Binary Counting with Chemical Reactions
Aleksandra Kharam, Hua Jiang, Marc Riedel; Pacific Symposium on Biocomputing 16:302-313(2011)
Defining the Players in Higher-Order Networks: Predictive Modeling for Reverse Engineering Functional Influence Networks
Jason E. McDermott, Michelle Archuleta, Susan L. Stevens, Mary P. Stenzel-Poore, Antonio Sanfilippo; Pacific Symposium on Biocomputing 16:314-325(2011)
Rate-Independent Constructs for Chemical Computation
Philip Senum, Marc Riedel; Pacific Symposium on Biocomputing 16:326-337(2011)
Towards Real-Time Control of Gene Expression: Controlling the Hog Signaling Cascade
Jannis Uhlendorf, Samuel Bottani, Francois Fages, Pascal Hersen, Gregory Batt; Pacific Symposium on Biocomputing 16:338-349(2011)
Identifying Targets for intervention by Analyzing Basins of Attraction
Michael P. Verdicchio, Seungchan Kim; Pacific Symposium on Biocomputing 16:350-361(2011)

Mining the Pharmacogenomics Literature

Workshop introduction
Kevin Bretonnel Cohen, Yael Garten, Udo Hahn, Nigam H. Shah; Pacific Symposium on Biocomputing 16:362-363(2011)

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

Workshop introduction
Michael Ochs, Rachel Karchin, Habtom Ressom, Robert Gentleman; Pacific Symposium on Biocomputing 16:364-368(2011)

Validation and Modeling of Electron Cryo-Microscopy Structures of Biological Nanomachines

Workshop introduction
Steven Ludtke, Catherine Lawson, Gerard Kleywegt, Helen Berman, Wah Chiu; Pacific Symposium on Biocomputing 16:369(2011)
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