Table of Contents

• Session IntroductionSøren Brunak, Francisco M. de la Vega, Gunnar Rätsch, Joshua M. Stuart. 1-2 [doi]
• Tumor Haplotype Assembly Algorithms for Cancer GenomicsDerek Aguiar, Wendy S. W. Wong, Sorin Istrail. 3-14 [doi]
• Extracting Significant Sample-Specific Cancer Mutations Using Their Protein InteractionsLiviu Badea. 15-26 [doi]
• The Stream Algorithm: Computationally Efficient Ridge-Regression via Bayesian Model Averaging, and Applications to Pharmacogenomic Prediction of Cancer Cell Line SensitivityElias Chaibub Neto, In Sock Jang, Stephen H. Friend, Adam A. Margolin. 27-38 [doi]
• Sharing Information to Reconstruct Patient-Specific Pathways in Heterogeneous DiseasesAnthony Gitter, Alfredo Braunstein, Andrea Pagnani, Carlo Baldassi, Christian Borgs, Jennifer T. Chayes, Riccardo Zecchina, Ernest Fraenkel. 39-50 [doi]
• Detecting Statistical Interaction Between Somatic Mutational Events and Germline Variation from Next-Generation Sequence DataHao Hu, Chad D. Huff. 51-62 [doi]
• Systematic Assessment of Analytical Methods for Drug Sensitivity Prediction from Cancer Cell Line DataIn Sock Jang, Elias Chaibub Neto, Justin Guinney, Stephen H. Friend, Adam A. Margolin. 63-74 [doi]
• Integrative Analysis of Two Cell Lines Derived from a Non-Small-Lung Cancer Patient - A Panomics ApproachOleg Mayba, Florian Gnad, Michael Peyton, Fan Zhang, Kimberly Walter, Pan Du, Melanie A. Huntley, Zhaoshi Jiang, Jinfeng Liu, Peter M. Haverty, Robert Gentleman, Ruiqiang Li, John D. Minna, Yingrui Li, David S. Shames, Zemin Zhang. 75-86 [doi]
• An Integrated Approach To Blood-Based Cancer Diagnosis And Biomarker DiscoveryMartin Renqiang Min, Salim A. Chowdhury, Yanjun Qi, Alex Stewart, Rachel Ostroff. 87-98 [doi]
• Multiplex Meta-Analysis of Medulloblastoma Expression Studies with External ControlsAlexander A. Morgan, Matthew D. Li, Achal S. Achrol, Purvesh Khatri, Samuel H. Cheshier. 99-109 [doi]
• Session IntroductionS. Joshua Swamidass, Zhiyong Lu, Pankaj Agarwal, Atul J. Butte. 110-113 [doi]
• Challenges in Secondary Analysis of High Throughput Screening DataAurora S. Blucher, Shannon K. McWeeney. 114-124 [doi]
• Drug Intervention Response Predictions with Paradigm (DIRPP) Identifies Drug Resistant Cancer Cell Lines and Pathway Mechanisms of ResistanceDouglas Brubaker, Analisa Difeo, YanWen Chen, Taylor Pearl, Kaide Zhai, Gürkan Bebek, Mark R. Chance, Jill S. Barnholtz-Sloan. 125-135 [doi]
• Anti-Infectious Drug Repurposing Using an Integrated Chemical Genomics and Structural Systems Biology ApproachClara Ng, Ruth Hauptman, Yinliang Zhang, Philip E. Bourne, Lei Xie. 136-147 [doi]
• Prediction of Off-Target Drug Effects Through Data FusionEmmanuel R. Yera, Ann E. Cleves, Ajay N. Jain. 160-171 [doi]
• Exploring the Pharmacogenomics Knowledge Base (PharmGKB) for Repositioning Breast Cancer Drugs by Leveraging Web Ontology Language (OWL) and Cheminformatics ApproachesQian Zhu, Cui Tao, Feichen Shen, Christopher G. Chute. 172-182 [doi]
• Session introductionAnna L. Tyler, Dana C. Crawford, Sarah A. Pendergrass. 183-187 [doi]
• Using the Bipartite Human Phenotype Network to Reveal Pleiotropy and Epistasis Beyond the GeneChristian Darabos, Samantha H. Harmon, Jason H. Moore. 188-199 [doi]
• Dissection of Complex Gene Expression Using the Combined Analysis of Pleiotropy and EpistasisVivek M. Philip, Anna L. Tyler, Gregory W. Carter. 200-211 [doi]
• PATH-SCAN: A Reporting Tool for Identifying Clinically Actionable VariantsRoxana Daneshjou, Zachary Zappala, Kimberly R. Kukurba, Sean M. Boyle, Kelly E. Ormond, Teri E. Klein, Michael Snyder, Carlos D. Bustamante, Russ B. Altman, Stephen B. Montgomery. 229-240 [doi]
• Session introductionJennifer Listgarten, Oliver Stegle, Quaid Morris, Steven E. Brenner, Leopold Parts. 247-249 [doi]
• Utilization of an EMR-Biorepository to Identify the Genetic Predictors of Calcineurin-Inhibitor Toxicity in Heart Transplant RecipientsMatthew Oetjens, William S. Bush, Kelly A. Birdwell, Holli H. Dilks, Erica A. Bowton, Joshua C. Denny, Russell A. Wilke, Dan M. Roden, Dana C. Crawford. 253-264 [doi]
• Imputation-based Assessment of Next Generation Rare Exome Variant ArraysAlicia R. Martin, Gerard Tse, Carlos D. Bustamante, Eimear E. Kenny. 262-272 [doi]
• Robust Reverse Engineering of Dynamic Gene Networks Under Sample Size HeterogeneityAnkur P. Parikh, Wei Wu, Eric P. Xing. 265-276 [doi]
• Variant Priorization and Analysis Incorporating Problematic Regions of the GenomeAnil Patwardhan, Michael Clark, Alex Morgan, Stephen A. Chervitz, Mark Pratt, Gábor T. Bartha, Gemma Chandratillake, Sarah Garcia, Nan Leng, Richard Chen. 277-287 [doi]
• Bags of Words Models of Epitope Sets: HIV Viral Load Regression with Counting GridsAlessandro Perina, Pietro Lovato, Nebojsa Jojic. 288-300 [doi]
• Joint Association Discovery and Diagnosis of Alzheimer's Disease by Supervised Heterogeneous Multiview LearningShandian Zhe, Zenglin Xu, Yuan Qi, Peng Yu. 300-311 [doi]
• Session introductionGraciela Gonzalez, Kevin Bretonnel Cohen, Robert Leaman, Casey S. Greene, Nigam Shah, Maricel G. Kann, Jieping Ye. 312-315 [doi]
• Vector Quantization Kernels for the Classification of Protein Sequences and StructuresWyatt T. Clark, Predrag Radivojac. 316-327 [doi]
• Combining Heterogenous Data for Prediction of Disease Related and PharmacogenesChristopher S. Funk, Lawrence E. Hunter, K. Bretonnel Cohen. 328-339 [doi]
• A Novel Profile Biomarker Diagnosis for Mass Spectral ProteomicsHenry Han. 340-351 [doi]
• Towards Pathway Curation Through Literature Mining - A Case Study Using PharmGKBK. E. Ravikumar, Kavishwar B. Wagholikar, Hongfang Liu. 352-363 [doi]
• Sparse Generalized Functional Linear Model for Predicting Remission Status of Depression PatientsYashu Liu, Zhi Nie, Jiayu Zhou, Michael Farnum, Vaibhav A. Narayan, Gayle Wiittenberg, Jieping Ye. 364-375 [doi]
• Development of a Data-Mining Algorithm to Identify Ages at Reproductive Milestones in Electronic Medical RecordsJennifer Malinowski, Eric Farber-Eger, Dana C. Crawford. 376-387 [doi]
• An Efficient Algorithm to Integrate Network and Attribute Data for Gene Function PredictionShankar Vembu, Quaid Morris. 388-399 [doi]
• Matrix Factorization-Based Data Fusion for Gene Function Prediction in Baker's Yeast and Slime MoldMarinka Zitnik, Blaz Zupan. 400-411 [doi]
• Applications of Bioinformatics to Non-Coding RNAs in the Era of Next-Generation SequencingChao Cheng, Jason H. Moore, Casey S. Greene. 412-416 [doi]
• Building the Next Generation of Quantitative BiologistsKristine A. Pattin, Anna C. Greene, Russ B. Altman, Lawrence E. Hunter, David A. Ross, James A. Foster, Jason H. Moore. 417-421 [doi]
• Uncovering the Etiology of Autism Spectrum Disorders: Genomics, Bioinformatics, Environment, Data Collection and Exploration, and Future PossibilitiesSarah A. Pendergrass, Santhosh Girirajan, Scott B. Selleck. 422-426 [doi]