Table of Contents

• Frequent Subgraph Mining of Personalized Signaling Pathway Networks Groups Patients with Frequently Dysregulated Disease Pathways and Predicts PrognosisArda Durmaz, Tim A. D. Henderson, Douglas Brubaker, Gürkan Bebek. [doi]
• Scalable Visualization for High-dimensional Single-cell DataJuho Kim, Nate Russell, Jian Peng. [doi]
• Session IntroductionYana Bromberg, Matthew W. Hahn, Predrag Radivojac. 1-2 [doi]
• Identification and Analysis of Bacterial Genomic Metabolic SignaturesNathan Bowerman, Nathan L. Tintle, Matthew DeJongh, Aaron A. Best. 3-14 [doi]
• When should we NOT transfer functional annotation between sequence paralogs?Mengfei Cao, Lenore J. Cowen. 15-26 [doi]
• ProSNet: integrating homology with molecular networks for protein function predictionSheng Wang, Meng Qu, Jian Peng 0001. 27-38 [doi]
• On the power and limits of sequence similarity based clustering of proteins into familiesChristian Wiwie, Richard Röttger. 39-50 [doi]
• Session IntroductionLi Shen, Lee A. D. Cooper. 51-57 [doi]
• Adaptive testing of SNP-brain functional connectivity association via a modular network analysisChen Gao, Junghi Kim, Wei Pan. 58-69 [doi]
• Exploring Brain Transcriptomic Patterns: A Topological Analysis Using Spatial Expression NetworksZhana Kuncheva, Michelle L. Krishnan, Giovanni Montana. 70-81 [doi]
• Integrative Analysis for Lung Adenocarcinoma Predicts Morphological Features Associated with Genetic VariationsChao Wang, Hai Su, Lin Yang, Kun Huang. 82-93 [doi]
• Identification of Discriminative Imaging Proteomics Associations in Alzheimer's Disease via a Novel Sparse Correlation Model>Jingwen Yan, Shannon L. Risacher, Kwangsik Nho, Andrew J. Saykin, Li Shen. 94-104 [doi]
• Enforcing Co-expression in Multimodal Regression FrameworkPascal Zille, Vince D. Calhoun, Yu-Ping Wang. 96-107 [doi]
• Session IntroductionKonrad J. Karczewski, Nicholas P. Tatonetti, Chirag J. Patel, Arjun K. Manrai, C. Titus Brown, John P. A. Ioannidis. 117-119 [doi]
• Exploring the Reproducibility of Probabilistic Causal Molecular Network Models>Ariella Cohain, Aparna A. Divaraniya, Kuixi Zhu, Joseph R. Scarpa, Andrew Kasarskis, Jun Zhu, Rui Chang, Joel T. Dudley, Eric E. Schadt. 120-131 [doi]
• Reproducible Drug Repurposing: When Similarity Does Not SufficeEmre Guney. 132-143 [doi]
• Empowering Multi-Cohort Gene Expression Analysis to Increase ReproducibilityWinston A. Haynes, Francesco Vallania, Charles Liu, Erika Bongen, Aurelie Tomczak, Marta Andres-Terrè, Shane Lofgren, Andrew Tam, Cole A. Deisseroth, Matthew D. Li, Timothy E. Sweeney, Purvesh Khatri. 144-153 [doi]
• Rabix: An Open-Source Workflow Executor Supporting Recomputability and Interoperability of Workflow DescriptionsGaurav Kaushik, Sinisa Ivkovic, Janko Simonovic, Nebojsa Tijanic, Brandi Davis-Dusenbery, Deniz Kural. 154-165 [doi]
• Data Sharing and Reproducible Clinical Genetic Testing: Successes and ChallengesShan Yang, Melissa S. Cline, Can Zhang, Benedict Paten, Stephen E. Lincoln. 166-176 [doi]
• Session IntroductionAnna Okula Basile, Anurag Verma, Marta Byrska-Bishop, Sarah P. Pendergrass, Christian Darabos, H. Lester Kirchner. 177-183 [doi]
• Learning Attributes of Disease Progression from Trajectories of Sparse Lab ValuesVibhu Agarwal, Nigam H. Shah. 184-194 [doi]
• Computer Aided Image Segmentation and Classification for Viable and Non-Viable Tumor Identification in OsteosarcomaHarish Babu Arunachalam, Rashika Mishra, Bogdan Armaselu, Ovidiu Daescu, Maria Martinez, Patrick Leavey, Dinesh Rakheja, Kevin Cederberg, Anita Sengupta, Molly Ni'suilleabhain. 195-206 [doi]
• Missing Data Imputation in the Electronic Health Record Using Deeply Learned AutoencodersBrett K. Beaulieu-Jones, Jason H. Moore, et al.. 207-218 [doi]
• A Deep Learning Approach for Cancer Detection and Relevant Gene IdentificationPadideh Danaee, Reza Ghaeini, David Hendrix. 219-229 [doi]
• Development and Performance of Text-Mining Algorithms to Extract Socioeconomic Status from De-Identified Electronic Health RecordsBrittany M. Hollister, Nicole A. Restrepo, Eric Farber-Eger, Dana C. Crawford, Melinda C. Aldrich, Amy Non. 230-241 [doi]
• Genome-Wide Interaction with Selected Type 2 Diabetes Loci Reveals Novel Loci for Type 2 Diabetes in African AmericansJacob M. Keaton, Jacklyn N. Hellwege, Maggie C. Y. Ng, Nicholette D. Palmer, James S. Pankow, Myriam Fornage, James G. Wilson, Adolfo Correa, Laura Rasmussen-Torvik, Jerome I. Rotter, Yii-Der I. Chen, Kent D. Taylor, Stephen S. Rich, Lynne E. Wagenknecht, Barry I. Freedman, Donald W. Bowden. 242-253 [doi]
• Deep Motif Dashboard: Visualizing and Understanding Genomic Sequences Using Deep Neural NetworksJack Lanchantin, Ritambhara Singh, Beilun Wang, Yanjun Qi. 254-265 [doi]
• Meta-Analysis of Continuous Phenotypes Identifies a Gene Signature that Correlates with COPD Disease StatusMadeleine Scott, Francesco Vallania, Purvesh Khatri. 266-275 [doi]
• Predictive Modeling of Hospital Readmission Rates Using Electronic Medical Record-Wide Machine Learning: A Case-Study Using Mount Sinai Heart Failure CohortKhader Shameer, Kipp W. Johnson, Alexandre Yahi, Riccardo Miotto, Li Li, Doran Ricks, Jebakumar Jebakaran, Patricia A. Kovatch, Partho P. Sengupta, Annetine Gelijns, Alan Moskovitz, Bruce Darrow, David L. Reich, Andrew Kasarskis, Nicholas P. Tatonetti, Deborah F. Pinney, Joel T. Dudley. 276-287 [doi]
• Learning Parsimonious Ensembles for Unbalanced Computational Genomics ProblemsAna Stanescu, Gaurav Pandey. 288-299 [doi]
• Methods for Clustering Time Series Data Acquired from Mobile Health AppsNicole L. Tignor, Pei Wang, Nicholas Genes, Linda Rogers, Steven G. Hershman, Erick R. Scott, Micol Zweig, Yu-Feng Yvonne Chan, Eric E. Schadt. 300-323 [doi]
• A New Relevance Estimator for the Compilation and Visualization of Disease Patterns and Potential Drug TargetsModest von Korff, Tobias Fink, Thomas Sander. 312-323 [doi]
• Network Map of Adverse Health Effects Among Victims of Intimate Partner ViolenceKathleen Whiting, Larry Y. Liu, Mehmet Koyutürk, Gunnur Karakurt. 324-335 [doi]
• Discovery of Functional and Disease Pathways by Community Detection in Protein-Protein Interaction NetworksStephen J. Wilson, Angela D. Wilkins, Chih-Hsu Lin, Rhonald C. Lua, Olivier Lichtarge. 336-347 [doi]
• Session IntroductionAlexander A. Morgan, Dana C. Crawford, Joshua C. Denny, Sean D. Mooney, Bruce J. Aronow, Steven E. Brenner. 348-355 [doi]
• Opening the Door to the Large Scale Use of Clinical Lab Measures for Association Testing: Exploring Different Methods for Defining PhenotypesChristopher R. Bauer, Daniel R. Lavage, John Snyder, Joseph B. Leader, J. Matthew Mahoney, Sarah A. Pendergrass. 356-367 [doi]
• A Powerful Method for Including Genotype Uncertainty in Tests of Hardy-Weinberg EquilibriumAndrew Beck, Alexander Luedtke, Keli Liu, Nathan L. Tintle. 368-379 [doi]
• Temporal Order of Disease Pairs Affects Subsequent Disease Trajectories: The Case of Diabetes and Sleep ApneaMette Beck, David Westergaard, Leif Groop, Søren Brunak. 380-389 [doi]
• MicroRNA-Augmented Pathways (mirAP) and Their Applications to Pathway Analysis and Disease SubtypingDiana Diaz, Michele Donato, Tin Nguyen, Sorin Draghici. 390-401 [doi]
• Human Kinases Display Mutational Hotspots at Cognate Positions Within CancerJonathan Gallion, Angela D. Wilkins, Olivier Lichtarge. 414-425 [doi]
• MUSE: A Multi-locus Sampling-based Epistasis Algorithm for Quantitative Genetic Trait PredictionDan He, Laxmi Parida. 426-437 [doi]
• ceRNA Search Method Identified a MET-activated Subgroup Among EGFR DNA Amplified Lung Adenocarcinoma PatientsHalla Kabat, Leo Tunkle, Inhan Lee. 438-448 [doi]
• Improved Performance of Gene Set Analysis on Genome-Wide Transcriptomics Data when Using Gene Activity State EstimatesThomas Kamp, Micah Adams, Craig Disselkoen, Nathan L. Tintle. 449-460 [doi]
• methylDMV: Simultaneous Detection of Differential DNA Methylation and Variability with Confounder AdjustmentPei Fen Kuan, Junyan Song, Shuyao He. 461-472 [doi]
• Identify Cancer Driver Genes Through Shared Mendelian Disease Pathogenic Variants and Cancer Somatic MutationsMeng Ma, Changchang Wang, Benjamin S. Glicksberg, Eric E. Schadt, Shuyu Dan Li, Rong Chen. 473-484 [doi]
• Identifying Cancer Specific Metabolic Signatures Using Constraint-Based ModelsAndré Schultz, Sanket Mehta, Chenyue W. Hu, Fieke W. Hoff, Terzah M. Horton, Steven M. Kornblau, Amina A. Qutub. 485-496 [doi]
• Differential Pathway Dependency Discovery Associated with Drug Response across Cancer Cell LinesGil Speyer, Divya Mahendra, Hai J. Tran, Jeff Kiefer, Stuart L. Schreiber, Paul A. Clemons, Harshil Dhruv, Michael E. Berens, Seungchan Kim. 497-508 [doi]
• A Methylation-to-Expression Feature Model for Generating Accurate Prognostic Risk Scores and Identifying Disease Targets in Clear Cell Kidney CancerJeffrey A. Thompson, Carmen J. Marsit. 509-520 [doi]
• De Novo Mutations in Autism Implicate the Synaptic Elimination NetworkGuhan Ram Venkataraman, Chloe O'Connell, Fumiko Egawa, Dorna Kashef Haghighi, Dennis P. Wall. 521-532 [doi]
• Identifying Genetic Associations with Variability in Metabolic Health and Blood Count Laboratory Values: Diving into the Quantitative Traits by Leveraging Longitudinal Data from an EHRShefali S. Verma, Anastasia Lucas, Daniel R. Lavage, Joseph B. Leader, Raghu Metpally, Sarathbabu Krishnamurthy, Frederick E. Dewey, Ingrid B. Borecki, Alexander E. Lopez, John D. Overton, John Penn, Jeffrey G. Reid, Sarah A. Pendergrass, Gerda Breitwieser, Marylyn D. Ritchie. 533-544 [doi]
• Strategies for Equitable Pharmacogenomic-Guided Warfarin Dosing Among European and African American Individuals in a Clinical PopulationLaura K. Wiley, Jacob P. VanHouten, David Samuels, Melinda Aldrich, Dan M. Roden, Josh F. Peterson, Joshua C. Denny. 545-556 [doi]
• Session IntroductionNikolay Samusik, Nima Aghaeepour, Sean Bendall. 557-563 [doi]
• Production of a Preliminary Quality Control Pipeline for Single Nuclei RNA-Seq and Its Application in the Analysis of Cell Type Diversity of Post-Mortem Human Brain NeocortexBrian D. Aevermann, Jamison M. McCorrison, Pratap Venepally, Rebecca Hodge, Trygve Bakken, Jeremy Miller, Mark Novotny, Danny N. Tran, Francisco Diez-Fuertes, Lena Christiansen, Fan Zhang, Frank Steemers, Roger S. Lasken, Ed Lein, Nicholas J. Schork, Richard H. Scheuermann. 564-575 [doi]
• Tracing Co-Regulatory Network Dynamics in Noisy, Single-Cell Transcriptome TrajectoriesPablo Cordero, Joshua M. Stuart. 576-587 [doi]
• An Updated Debarcoding Tool for Mass Cytometry with Cell Type-Specific and Cell Sample-Specific Stringency AdjustmentKristin I. Fread, William D. Strickland, Garry P. Nolan, Eli R. Zunder. 588-598 [doi]
• Mapping Neuronal Cell Types Using Integrative Multi-Species Modeling of Human and Mouse Single Cell RNA SequencingTravis Johnson, Zachary B. Abrams, Yan Zhang, Kun Huang. 599-610 [doi]
• A Spatiotemporal Model to Simulate Chemotherapy Regimens for Heterogeneous Bladder Cancer Metastases to the LungKimberly R. Kanigel Winner, James C. Costello. 611-622 [doi]
• Harnessing Big Data for Precision Medicine: Infrastructures and ApplicationsKun-Hsing Yu, Steven N. Hart, Rachel L. Goldfeder, Qiangfeng Cliff Zhang, Stephen C. J. Parker, Michael Snyder. 635-639 [doi]
• The Training of Next Generation Data Scientists in BiomedicineLana X. Garmire, Stephen V. Gliske, Quynh C. Nguyen, Jonathan H. Chen, Shamim Nemati, John D. Van Horn, Jason H. Moore, Carol Shreffler, Michelle Dunn. 640-645 [doi]
• No-Boundary Thinking in BioinformaticsJason H. Moore, Steven F. Jennings, Casey S. Greene, Lawrence E. Hunter, Andy D. Perkins, ClarLynda R. Williams-DeVane, Donald C. Wunsch, Zhongming Zhao, Xiuzhen Huang. 646-648 [doi]
• Open Data for Discovery SciencePhilip R. O. Payne, Kun Huang, Nigam H. Shah, Jessica D. Tenenbaum. 649-652 [doi]