Contents

• Computational Drug Repositioning
• Epigenomics
• Identification of Aberrant Pathway and Network Activity from High-Throughput Data
• Personalized Medicine: From Genotypes and Molecular Phenotypes Towards Therapy
• Phylogenomics and Population Genomics: Models, Algorithms, and Analytical Tools
• Post-NGS: Interpretation and Analysis of Next Generation Sequencing Data for Basic and Translational Science
• Text and Data Mining for Biomedical Discovery
• Workshops

Computational drug repositioning

Session Introduction

Zhiyong Lu, Pankaj Agarwal, and Atul Butte; Pacific Symposium on Biocomputing 18:1-4(2013)

Evaluation of Analytical Methods for Connectivity Map Data

Jie Cheng, Qing Xie, Vinod Kumar, Mark Hurle, Johannes M. Freudenberg, Lun Yang, Pankaj Agarwal ; Pacific Symposium on Biocomputing 18:5-16(2013)

Predictive Systems Biology Approach to Broad-Spectrum, Host-Directed Drug Target Discovery in Infectious Diseases

Ramon M. Felciano, Sina Bavari, Daniel R. Richards, Jean-Noel Billaud, Travis Warren, Rekha Panchal, Andreas Kraemer; Pacific Symposium on Biocomputing 18:17-28(2013)

A Novel Multi-Modal Drug Repurposing Approach for Identification of Potent ACK1 Inhibitors

Sharangdhar S. Phatak, Shuxing Zhang; Pacific Symposium on Biocomputing 18:29-40(2013)

Protein-chemical Interaction Prediction via Kernelized Sparse Learning SVM

Yi Shi, Xinhua Zhang, Xiaoping Liao, Guohui Lin, Dale Schuurmans; Pacific Symposium on Biocomputing 18:41-52(2013)

Drug Target Predictions Based on Heterogeneous Graph Inference

Wenhui Wang, Sen Yang, Jing Li; Pacific Symposium on Biocomputing 18:53-64(2013)

Epigenomics

Session Introduction

Alexander J. Hartemink, Manolis Kellis, William Stafford Noble, Zhiping Weng; Pacific Symposium on Biocomputing 18:65-68(2013)

A Powerful Statistical Method for Identifying Differentially Methylated Markers in Complex Diseases

Surin Ahn, Tao Wang; Pacific Symposium on Biocomputing 18:69-79(2013)

Using DNase Digestion Data to Accurately Identify Transcription Factor Binding Sites

Kaixuan Luo, Alexander J. Hartemink; Pacific Symposium on Biocomputing 18:80-91(2013)

Epigenomic Model of Cardiac Enhancers with Application to Genome Wide Association Studies

Avinash Das Sahu, Radhouane Aniba, Yen-Pei Christy Chang, Sridhar Hannenhalli; Pacific Symposium on Biocomputing 18:92-102(2013)

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

Session Introduction

Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, Trey Ideker, Joel S. Bader; Pacific Symposium on Biocomputing 18:103-110(2013)

From Uncertain Protein Interaction Networks to Signaling Pathways Through Intensive Color Coding

Haitham Gabr, Alin Dobra, Tamer Kahveci; Pacific Symposium on Biocomputing 18:111-122(2013)

Identifying Master Regulators of Cancer and Their Downstream Targets by Integrating Genomic and Epigenomic Features

Olivier Gevaert, Sylvia Plevritis; Pacific Symposium on Biocomputing 18:123-134(2013)

Module Cover - A New Approach to Genotype-Phenotype Studies

Yoo-Ah Kim, Raheleh Salari, Stefan Wuchty, Teresa M. Przytycka; Pacific Symposium on Biocomputing 18:135-146(2013)

Next-Generation Analysis of Cataracts: Determining Knowledge Driven Gene-Gene Interactions Using Biofilter, and Gene-Environment Interactions Using the PhenX Toolkit

Sarah A. Pendergrass, Shefali S. Verma, Emily R. Holzinger, Carrie B. Moore, John Wallace, Scott M. Dudek, Wayne Huggins, Terrie Kitchner, Carol Waudby, Richard Berg, Catherine A. McCarty, Marylyn D. Ritchie; Pacific Symposium on Biocomputing 18:147-158(2013)

Interpreting Personal Transcriptomes: Personalized Mechanism-Scale Profiling of RNA-seq Data

Alan Perez-Rathke, Haiquan Li, Yves A. Lussier; Pacific Symposium on Biocomputing 18:159-170(2013)

Personalized medicine: from genotypes and molecular phenotypes towards therapy

Session introduction

Oliver Stegle, Steven E. Brenner, Quaid Morris, Jennifer Listgarten; Pacific Symposium on Biocomputing 18:171-174(2013)

AMP: Assembly Matching Pursuit

Surojit Biswas, Vladimir Jojic; Pacific Symposium on Biocomputing 18:175-187(2013)

Characterization of the Metabochip in Diverse Populations from the International HapMap Project in the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) Project

Dana C. Crawford, Robert Goodloe, Kristin Brown-Gentry, Sarah Wilson, Jamie Roberson, Niloufar B. Gillani, Marylyn D. Ritchie, Holli H. Dilks, William S. Bush ; Pacific Symposium on Biocomputing 18:188-199(2013)

Insights into Diseases of Human Telomerase from Dynamical Modeling

Samuel Coulbourn Flores, Georgeta Zemora, Christina Waldsich; Pacific Symposium on Biocomputing 18:200-211(2013)

Spectral Clustering Strategies for Heterogeneous Disease Data

Grace T. Huang, Kathryn I. Cunningham, Panayiotis V. Benos, Chakra S. Chennubhotla; Pacific Symposium on Biocomputing 18:212-223(2013)

Systematic Identification of Risk Factors for Alzheimer's Disease Through Shared Genetic Architecture and Electronic Medical Records

Li Li, David Ruau, Rong Chen, Susan Weber, Atul J. Butte; Pacific Symposium on Biocomputing 18:224-235(2013)

A Correlated Meta-Analysis Strategy for Data Mining “Omic” Scans

Michael A. Province, Ingrid B. Borecki; Pacific Symposium on Biocomputing 18:236-246(2013)

Phylogenomics and Population Genomics: Models, Algorithms, and Analytical Tools

Session introduction

Luay Nakhleh, Noah Rosenberg, Tandy Warnow; Pacific Symposium on Biocomputing 18:247-249(2013)

Inferring Optimal Species Trees Under Gene Duplication and Loss

M.S. Bayzid, Siavash Mirarab, Tandy Warnow; Pacific Symposium on Biocomputing 18:250-261(2013)

Evaluating Variations on the STAR Algorithm for Relative Efficiency and Sample Sizes Needed to Reconstruct Species Trees

James H. Degnan; Pacific Symposium on Biocomputing 18:262-272(2013)

The Behavior of Admixed Populations in Neighbor-Joining Inference of Population Trees

Naama M. Kopelman, Lewi Stone, Olivier Gascuel, Noah A. Rosenberg; Pacific Symposium on Biocomputing 18:273-284(2013)

Maximum Likelihood Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Tree of 68 Eukaryotes

Yu Lin, Fei Hu, Jijun Tang, Bernard M.E. Moret; Pacific Symposium on Biocomputing 18:285-296(2013)

An Analytical Comparison of Multilocus Methods Under the Multispecies Coalescent: The Three-Taxon Case

Sebastien Roch; Pacific Symposium on Biocomputing 18:297-306(2013)

Post-NGS: Interpretation and Analysis of Next Generation Sequencing Data for Basic and Translational Science

Session introduction

Gurkan Bebek, Mehmet Koyuturk, Thomas LaFramboise, Benjamin J. Raphael, Mark R. Chance; Pacific Symposium on Biocomputing 18:307-309(2013)

LSHPlace: Fast Phylogenetic Placement Using Locality-Sensitive Hashing

Daniel G. Brown, Jakub Truszkowski; Pacific Symposium on Biocomputing 18:310-319(2013)

ChIPModule: Systematic Discovery of Transcription Factors and Their Cofactors from ChIP-seq Data

Jun Ding, Xiaohui Cai, Ying Wang, Haiyan Hu, Xiaoman Li; Pacific Symposium on Biocomputing 18:320-331(2013)

Using BioBin to Explore Rare Variant Population Stratification

Carrie B. Moore, John R. Wallace, Alex T. Frase, Sarah A. Pendergrass, Marylyn D. Ritchie; Pacific Symposium on Biocomputing 18:332-343(2013)

Detecting Highly Differentiated Copy-Number Variants from Pooled Population Sequencing

Daniel R. Schrider, David J. Begun, Matthew W. Hahn; Pacific Symposium on Biocomputing 18:344-355(2013)

MetaSeq: Privacy Preserving Meta-Analysis of Sequencing-Based Association Studies

Angad Pal Singh, Samreen Zafer, Itsik Pe'er; Pacific Symposium on Biocomputing 18:356-367(2013)

Text and Data Mining for Biomedical Discovery

Session introduction

Graciela H. Gonzalez, Kevin Bretonnel Cohen, Casey Greene, Udo Hahn, Maricel G. Kann, Robert Leaman, Nigam Shah, Jieping Ye; Pacific Symposium on Biocomputing 18:368-372(2013)

Enabling High-Throughput Genotype-Phenotype Associations in the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) Project as Part of the Population Architecture Using Genomics and Epidemiology (PAGE) Study

William S. Bush, Jonathan Boston, Sarah A. Pendergrass, Logan Dumitrescu, Robert Goodloe, Kristin Brown-Gentry, Sarah Wilson, Bob McClellan Jr., Eric Torstenson, Melissa A. Basford, Kylee L. Spencer, Marylyn D. Ritchie, Dana C. Crawford; Pacific Symposium on Biocomputing 18:373-384(2013)

ATHENA: A Tool for Meta-Dimensional Analysis Applied to Genotypes and Gene Expression Data to Predict HDL Cholesterol Levels

Emily R Holzinger, Scott M. Dudek, Alex T. Frase, Ronald M. Krauss, Marisa W. Medina, Marylyn D. Ritchie; Pacific Symposium on Biocomputing 18:385-396(2013)

Statistical Epistasis Networks Reduce the Computational Complexity of Searching Three-Locus Genetic Models

Ting Hu, Angeline S. Andrew, Margaret R. Karagas, Jason H. Moore; Pacific Symposium on Biocomputing 18:397-408(2013)

Evaluation of Linear Classifiers on Articles Containing Pharmacokinetic Evidence of Drug-Drug Interactions

Artemy Kolchinsky, Analia Lourenco, Lang Li, Luis M. Rocha; Pacific Symposium on Biocomputing 18:409-420(2013)

Incorporating Expert Terminology and Disease Risk Factors into Consumer Health Vocabularies

Michael Seedorff, Kevin J. Peterson, Laurie A. Nelsen, Cristian Cocos, Jennifer B. McCormick, Christopher G. Chute, Jyotishman Pathak; Pacific Symposium on Biocomputing 18:421-432(2013)

Detection of Protein Catalytic Sites in the Biomedical Literature

Karin Verspoor, Andrew MacKinlay, Judith D. Cohn, Michael E. Wall; Pacific Symposium on Biocomputing 18:433-444(2013)

Workshops

Modeling cell heterogeneity: from single-cell variations to mixed cells populations

Eric Batchelor, Maricel G. Kann, Teresa M. Przytycka, Benjamin J. Raphael, and Damian Wojtowicz; Pacific Symposium on Biocomputing 18:445-450(2013)

Computational Biology in the Cloud: Methods and New Insights from Computing at Scale

Peter M. Kasson; Pacific Symposium on Biocomputing 18:451-453(2013)

Computational Challenges of Mass Phenotyping

Lawrence Hunter; Pacific Symposium on Biocomputing 18:454-455(2013)

The Future of Genome-Based Medicine

Quaid Morris, Steven E. Brenner, Jennifer Listgarten, Oliver Stegle; Pacific Symposium on Biocomputing 18:456-458(2013)

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Updated: October 19, 2012