Table of Contents

• Session IntroductionZhiyong Lu, Pankaj Agarwal, Atul J. Butte. 1-4 [doi]
• Evaluation of Analytical Methods for Connectivity Map DataJie Cheng, Qing Xie, Vinod Kumar, Mark Hurle, Johannes M. Freudenberg, Lun Yang, Pankaj Agarwal. 5-16 [doi]
• Predictive Systems Biology Approach to Broad-Spectrum, Host-Directed Drug Target Discovery in Infectious DiseasesRamon M. Felciano, Sina Bavari, Daniel R. Richards, Jean-Noel Billaud, Travis Warren, Rekha Panchal, Andreas Krämer. 17-28 [doi]
• A Novel Multi-Modal Drug Repurposing Approach for Identification of Potent ACK1 InhibitorsSharangdhar S. Phatak, Shuxing Zhang. 29-40 [doi]
• Protein-chemical Interaction Prediction via Kernelized Sparse Learning SVMYi Shi, Xinhua Zhang, Xiaoping Liao, Guohui Lin, Dale Schuurmans. 41-52 [doi]
• Drug Target Predictions Based on Heterogeneous Graph InferenceWenhui Wang, Sen Yang, Jing Li. 53-64 [doi]
• Session IntroductionAlexander J. Hartemink, Manolis Kellis, William Stafford Noble, Zhiping Weng. 65-68 [doi]
• A Powerful Statistical Method for Identifying Differentially Methylated Markers in Complex DiseasesSurin Ahn, Tao Wang. 69-79 [doi]
• Using DNase Digestion Data to Accurately Identify Transcription Factor Binding SitesKaixuan Luo, Alexander J. Hartemink. 80-91 [doi]
• Epigenomic Model of Cardiac Enhancers with Application to Genome Wide Association StudiesAvinash Das Sahu, Radhouane Aniba, Yen-Pei Christy Chang, Sridhar Hannenhalli. 92-102 [doi]
• Session IntroductionRachel Karchin, Michael F. Ochs, Joshua M. Stuart, Trey Ideker, Joel S. Bader. 103-110 [doi]
• From Uncertain Protein Interaction Networks to Signaling Pathways Through Intensive Color CodingHaitham Gabr, Alin Dobra, Tamer Kahveci. 111-122 [doi]
• Identifying Master Regulators of Cancer and Their Downstream Targets by Integrating Genomic and Epigenomic FeaturesOlivier Gevaert, Sylvia K. Plevritis. 123-134 [doi]
• Module Cover - A New Approach to Genotype-Phenotype StudiesYoo Ah Kim, Raheleh Salari, Stefan Wuchty, Teresa M. Przytycka. 135-146 [doi]
• Next-Generation Analysis of Cataracts: Determining Knowledge Driven Gene-Gene Interactions Using Biofilter, and Gene-Environment Interactions Using the PhenX ToolkitSarah A. Pendergrass, Shefali S. Verma, Emily Rose Holzinger, Carrie Moore, John R. Wallace, Scott M. Dudek, Wayne Huggins, Terrie Kitchner, Carol Waudby, Richard L. Berg, Catherine A. McCarty, Marylyn D. Ritchie. 147-158 [doi]
• Interpreting Personal Transcriptomes: Personalized Mechanism-Scale Profiling of RNA-seq DataAlan Perez-Rathke, Haiquan Li, Yves A. Lussier. 159-170 [doi]
• Session introductionOliver Stegle, Steven E. Brenner, Quaid Morris, Jennifer Listgarten. 171-174 [doi]
• AMP: Assembly Matching PursuitSurojit Biswas, Vladimir Jojic. 175-187 [doi]
• Insights into Diseases of Human Telomerase from Dynamical ModelingSamuel Coulbourn Flores, Georgeta Zemora, Christina Waldsich. 200-211 [doi]
• Spectral Clustering Strategies for Heterogeneous Disease DataGrace T. Huang, Kathryn I. Cunningham, Panayiotis V. Benos, Chakra Chennubhotla. 212-223 [doi]
• Systematic Identification of Risk Factors for Alzheimer's Disease Through Shared Genetic Architecture and Electronic Medical RecordsLi Li, David Ruau, Rong Chen, Susan C. Weber, Atul J. Butte. 224-235 [doi]
• Session introductionLuay Nakhleh, Noah Rosenberg, Tandy Warnow. 247-249 [doi]
• Inferring Optimal Species Trees Under Gene Duplication and LossMd. Shamsuzzoha Bayzid, Siavash Mirarab, Tandy Warnow. 250-261 [doi]
• Evaluating Variations on the STAR Algorithm for Relative Efficiency and Sample Sizes Needed to Reconstruct Species TreesJames H. Degnan. 262-272 [doi]
• The Behavior of Admixed Populations in Neighbor-Joining Inference of Population TreesNaama M. Kopelman, Lewi Stone, Olivier Gascuel, Noah A. Rosenberg. 273-284 [doi]
• Maximum Likelihood Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Tree of 68 EukaryotesYu Lin, Fei Hu, Jijun Tang, Bernard M. E. Moret. 285-296 [doi]
• An Analytical Comparison of Multilocus Methods Under the Multispecies Coalescent: The Three-Taxon CaseSébastien Roch. 297-306 [doi]
• Session introductionGürkan Bebek, Mehmet Koyutürk, Thomas LaFramboise, Benjamin J. Raphael, Mark R. Chance. 307-309 [doi]
• LSHPlace: Fast Phylogenetic Placement Using Locality-Sensitive HashingDaniel G. Brown 0001, Jakub Truszkowski. 310-319 [doi]
• ChIPModule: Systematic Discovery of Transcription Factors and Their Cofactors from ChIP-seq DataJun Ding, Xiaohui Cai, Ying Wang, Haiyan Hu, Xiaoman Shawn Li. 320-331 [doi]
• Using BioBin to Explore Rare Variant Population StratificationCarrie Moore, John R. Wallace, Alex T. Frase, Sarah A. Pendergrass, Marylyn D. Ritchie. 332-343 [doi]
• Detecting Highly Differentiated Copy-Number Variants from Pooled Population SequencingDaniel R. Schrider, David J. Begun, Matthew W. Hahn. 344-355 [doi]
• MetaSeq: Privacy Preserving Meta-Analysis of Sequencing-Based Association StudiesAngad Pal Singh, Samreen Zafer, Itsik Pe'er. 356-367 [doi]
• Session introductionGraciela Gonzalez, Kevin Bretonnel Cohen, Casey S. Greene, Udo Hahn, Maricel G. Kann, Robert Leaman, Nigam Shah, Jieping Ye. 368-372 [doi]
• ATHENA: A Tool for Meta-Dimensional Analysis Applied to Genotypes and Gene Expression Data to Predict HDL Cholesterol LevelsEmily Rose Holzinger, Scott M. Dudek, Alex T. Frase, Ronald M. Krauss, Marisa Wong Medina, Marylyn D. Ritchie. 385-396 [doi]
• Statistical Epistasis Networks Reduce the Computational Complexity of Searching Three-Locus Genetic ModelsTing Hu, Angeline S. Andrew, Margaret R. Karagas, Jason H. Moore. 397-408 [doi]
• Evaluation of Linear Classifiers on Articles Containing Pharmacokinetic Evidence of Drug-Drug InteractionsArtemy Kolchinsky, Anália Lourenço, Lang Li, Luis Mateus Rocha. 409-420 [doi]
• Detection of Protein Catalytic Sites in the Biomedical LiteratureKarin Verspoor, Andrew MacKinlay, Judith D. Cohn, Michael E. Wall. 433-444 [doi]
• Modeling cell heterogeneity: from single-cell variations to mixed cells populationsEric Batchelor, Maricel G. Kann, Teresa M. Przytycka, Benjamin J. Raphael, Damian Wójtowicz. 445-450 [doi]
• Computational Biology in the Cloud: Methods and New Insights from Computing at ScalePeter M. Kasson. 451-453 [doi]
• Computational Challenges of Mass PhenotypingLawrence Hunter. 454-455 [doi]
• The Future of Genome-Based MedicineQuaid Morris, Steven E. Brenner, Jennifer Listgarten, Oliver Stegle. 456-458 [doi]