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22. PSB 2017: Kohala Coast, Hawaii, USA
- Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Marylyn D. Ritchie, Teri E. Klein:
Biocomputing 2017: Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA, January 3-7, 2017. 2017
Computational Approaches to Understanding the Evolution of Molecular Function
- Yana Bromberg, Matthew W. Hahn, Predrag Radivojac:
Session Introduction. 1-2 - Nathan Bowerman, Nathan L. Tintle, Matthew DeJongh, Aaron A. Best:
Identification and Analysis of Bacterial Genomic Metabolic Signatures. 3-14 - Mengfei Cao, Lenore J. Cowen:
When should we NOT transfer functional annotation between sequence paralogs? 15-26 - Sheng Wang, Meng Qu, Jian Peng:
ProSNet: integrating homology with molecular networks for protein function prediction. 27-38 - Christian Wiwie, Richard Röttger:
On the power and limits of sequence similarity based clustering of proteins into families. 39-50
Imaging Genomics
- Li Shen, Lee A. D. Cooper:
Session Introduction. 51-57 - Chen Gao, Junghi Kim, Wei Pan:
Adaptive testing of SNP-brain functional connectivity association via a modular network analysis. 58-69 - Zhana Kuncheva, Michelle L. Krishnan, Giovanni Montana:
Exploring Brain Transcriptomic Patterns: A Topological Analysis Using Spatial Expression Networks. 70-81 - Chao Wang, Hai Su, Lin Yang, Kun Huang:
Integrative Analysis for Lung Adenocarcinoma Predicts Morphological Features Associated with Genetic Variations. 82-93 - Jingwen Yan, Shannon L. Risacher, Kwangsik Nho, Andrew J. Saykin, Li Shen:
Identification of Discriminative Imaging Proteomics Associations in Alzheimer's Disease via a Novel Sparse Correlation Model>. 94-104 - Pascal Zille, Vince D. Calhoun, Yu-Ping Wang:
Enforcing Co-expression in Multimodal Regression Framework. 96-107
Methods to Ensure the Reproducibility of Biomedical Research
- Konrad J. Karczewski, Nicholas P. Tatonetti, Chirag J. Patel, Arjun K. Manrai, C. Titus Brown, John P. A. Ioannidis:
Session Introduction. 117-119 - Ariella Cohain, Aparna A. Divaraniya, Kuixi Zhu, Joseph R. Scarpa, Andrew Kasarskis, Jun Zhu, Rui Chang, Joel T. Dudley, Eric E. Schadt:
Exploring the Reproducibility of Probabilistic Causal Molecular Network Models>. 120-131 - Emre Guney:
Reproducible Drug Repurposing: When Similarity Does Not Suffice. 132-143 - Winston 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:
Empowering Multi-Cohort Gene Expression Analysis to Increase Reproducibility. 144-153 - Gaurav Kaushik, Sinisa Ivkovic, Janko Simonovic, Nebojsa Tijanic, Brandi Davis-Dusenbery, Deniz Kural:
Rabix: An Open-Source Workflow Executor Supporting Recomputability and Interoperability of Workflow Descriptions. 154-165 - Shan Yang, Melissa S. Cline, Can Zhang, Benedict Paten, Stephen E. Lincoln:
Data Sharing and Reproducible Clinical Genetic Testing: Successes and Challenges. 166-176
Patterns in Biomedical Data - How do we find them?
- Anna Okula Basile, Anurag Verma, Marta Byrska-Bishop, Sarah A. Pendergrass, Christian Darabos, H. Lester Kirchner:
Session Introduction. 177-183 - Vibhu Agarwal, Nigam H. Shah:
Learning Attributes of Disease Progression from Trajectories of Sparse Lab Values. 184-194 - Harish Babu Arunachalam, Rashika Mishra, Bogdan Armaselu, Ovidiu Daescu, Maria Martinez, Patrick Leavey, Dinesh Rakheja, Kevin Cederberg, Anita Sengupta, Molly Ni'suilleabhain:
Computer Aided Image Segmentation and Classification for Viable and Non-Viable Tumor Identification in Osteosarcoma. 195-206 - Brett K. Beaulieu-Jones, Jason H. Moore, et al.:
Missing Data Imputation in the Electronic Health Record Using Deeply Learned Autoencoders. 207-218 - Padideh Danaee, Reza Ghaeini, David Hendrix:
A Deep Learning Approach for Cancer Detection and Relevant Gene Identification. 219-229 - Brittany M. Hollister, Nicole A. Restrepo, Eric Farber-Eger, Dana C. Crawford, Melinda C. Aldrich, Amy Non:
Development and Performance of Text-Mining Algorithms to Extract Socioeconomic Status from De-Identified Electronic Health Records. 230-241 - Jacob 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 Ida Chen, Kent D. Taylor, Stephen S. Rich, Lynne E. Wagenknecht, Barry I. Freedman, Donald W. Bowden:
Genome-Wide Interaction with Selected Type 2 Diabetes Loci Reveals Novel Loci for Type 2 Diabetes in African Americans. 242-253 - Jack Lanchantin, Ritambhara Singh, Beilun Wang, Yanjun Qi:
Deep Motif Dashboard: Visualizing and Understanding Genomic Sequences Using Deep Neural Networks. 254-265 - Madeleine Scott, Francesco Vallania, Purvesh Khatri:
Meta-Analysis of Continuous Phenotypes Identifies a Gene Signature that Correlates with COPD Disease Status. 266-275 - Khader Shameer, Kipp W. Johnson, Alexandre Yahi, Riccardo Miotto, Li Li, Doran Ricks, Jebakumar Jebakaran, Patricia H. Kovatch, Partho P. Sengupta, Annetine Gelijns, Alan Moskovitz, Bruce Darrow, David L. Reich, Andrew Kasarskis, Nicholas P. Tatonetti, Deborah F. Pinney, Joel T. Dudley:
Predictive Modeling of Hospital Readmission Rates Using Electronic Medical Record-Wide Machine Learning: A Case-Study Using Mount Sinai Heart Failure Cohort. 276-287 - Ana Stanescu, Gaurav Pandey:
Learning Parsimonious Ensembles for Unbalanced Computational Genomics Problems. 288-299 - Nicole L. Tignor, Pei Wang, Nicholas Genes, Linda Rogers, Steven G. Hershman, Erick R. Scott, Micol Zweig, Yu-Feng Yvonne Chan, Eric E. Schadt:
Methods for Clustering Time Series Data Acquired from Mobile Health Apps. 300-323 - Modest von Korff, Tobias Fink, Thomas Sander:
A New Relevance Estimator for the Compilation and Visualization of Disease Patterns and Potential Drug Targets. 312-323 - Kathleen Whiting, Larry Y. Liu, Mehmet Koyutürk, Gunnur Karakurt:
Network Map of Adverse Health Effects Among Victims of Intimate Partner Violence. 324-335 - Stephen J. Wilson, Angela D. Wilkins, Chih-Hsu Lin, Rhonald C. Lua, Olivier Lichtarge:
Discovery of Functional and Disease Pathways by Community Detection in Protein-Protein Interaction Networks. 336-347
Precision Medicine: Data and Discovery for Improved Health and Therapy
- Alexander A. Morgan, Dana C. Crawford, Joshua C. Denny, Sean D. Mooney, Bruce J. Aronow, Steven E. Brenner:
Session Introduction. 348-355 - Christopher R. Bauer, Daniel R. Lavage, John Snyder, Joseph B. Leader, J. Matthew Mahoney, Sarah A. Pendergrass:
Opening the Door to the Large Scale Use of Clinical Lab Measures for Association Testing: Exploring Different Methods for Defining Phenotypes. 356-367 - Andrew Beck, Alexander Luedtke, Keli Liu, Nathan L. Tintle:
A Powerful Method for Including Genotype Uncertainty in Tests of Hardy-Weinberg Equilibrium. 368-379 - Mette Beck, David Westergaard, Leif Groop, Søren Brunak:
Temporal Order of Disease Pairs Affects Subsequent Disease Trajectories: The Case of Diabetes and Sleep Apnea. 380-389 - Diana Diaz, Michele Donato, Tin Nguyen, Sorin Draghici:
MicroRNA-Augmented Pathways (mirAP) and Their Applications to Pathway Analysis and Disease Subtyping. 390-401 - Arda Durmaz, Tim A. D. Henderson, Douglas Brubaker, Gürkan Bebek:
Frequent Subgraph Mining of Personalized Signaling Pathway Networks Groups Patients with Frequently Dysregulated Disease Pathways and Predicts Prognosis. - Jonathan Gallion, Angela D. Wilkins, Olivier Lichtarge:
Human Kinases Display Mutational Hotspots at Cognate Positions Within Cancer. 414-425 - Dan He, Laxmi Parida:
MUSE: A Multi-locus Sampling-based Epistasis Algorithm for Quantitative Genetic Trait Prediction. 426-437 - Halla Kabat, Leo Tunkle, Inhan Lee:
ceRNA Search Method Identified a MET-activated Subgroup Among EGFR DNA Amplified Lung Adenocarcinoma Patients. 438-448 - Thomas Kamp, Micah Adams, Craig Disselkoen, Nathan L. Tintle:
Improved Performance of Gene Set Analysis on Genome-Wide Transcriptomics Data when Using Gene Activity State Estimates. 449-460 - Pei Fen Kuan, Junyan Song, Shuyao He:
methylDMV: Simultaneous Detection of Differential DNA Methylation and Variability with Confounder Adjustment. 461-472 - Meng Ma, Changchang Wang, Benjamin S. Glicksberg, Eric E. Schadt, Shuyu Dan Li, Rong Chen:
Identify Cancer Driver Genes Through Shared Mendelian Disease Pathogenic Variants and Cancer Somatic Mutations. 473-484 - André Schultz, Sanket Mehta, Chenyue W. Hu, Fieke W. Hoff, Terzah M. Horton, Steven M. Kornblau, Amina A. Qutub:
Identifying Cancer Specific Metabolic Signatures Using Constraint-Based Models. 485-496 - Gil Speyer, Divya Mahendra, Hai J. Tran, Jeff Kiefer, Stuart L. Schreiber, Paul A. Clemons, Harshil Dhruv, Michael E. Berens, Seungchan Kim:
Differential Pathway Dependency Discovery Associated with Drug Response across Cancer Cell Lines. 497-508 - Jeffrey A. Thompson, Carmen J. Marsit:
A Methylation-to-Expression Feature Model for Generating Accurate Prognostic Risk Scores and Identifying Disease Targets in Clear Cell Kidney Cancer. 509-520 - Guhan Ram Venkataraman, Chloe O'Connell, Fumiko Egawa, Dorna Kashef Haghighi, Dennis P. Wall:
De Novo Mutations in Autism Implicate the Synaptic Elimination Network. 521-532 - Shefali 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:
Identifying Genetic Associations with Variability in Metabolic Health and Blood Count Laboratory Values: Diving into the Quantitative Traits by Leveraging Longitudinal Data from an EHR. 533-544 - Laura K. Wiley, Jacob P. VanHouten, David Samuels, Melinda Aldrich, Dan M. Roden, Josh F. Peterson, Joshua C. Denny:
Strategies for Equitable Pharmacogenomic-Guided Warfarin Dosing Among European and African American Individuals in a Clinical Population. 545-556
Single-Cell Analysis and Modelling of Cell Population Heterogeneity
- Nikolay Samusik, Nima Aghaeepour, Sean Bendall:
Session Introduction. 557-563 - Brian D. Aevermann, Jamison M. McCorrison, Pratap Venepally, Rebecca D. Hodge, Trygve E. Bakken, Jeremy A. Miller, Mark Novotny, Danny N. Tran, Francisco Diez-Fuertes, Lena Christiansen, Fan Zhang, Frank Steemers, Roger S. Lasken, Ed S. Lein, Nicholas J. Schork, Richard H. Scheuermann:
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 Neocortex. 564-575 - Pablo Cordero, Joshua M. Stuart:
Tracing Co-Regulatory Network Dynamics in Noisy, Single-Cell Transcriptome Trajectories. 576-587 - Kristin I. Fread, William D. Strickland, Garry P. Nolan, Eli R. Zunder:
An Updated Debarcoding Tool for Mass Cytometry with Cell Type-Specific and Cell Sample-Specific Stringency Adjustment. 588-598 - Travis S. Johnson, Zachary B. Abrams, Yan Zhang, Kun Huang:
Mapping Neuronal Cell Types Using Integrative Multi-Species Modeling of Human and Mouse Single Cell RNA Sequencing. 599-610 - Kimberly R. Kanigel Winner, James C. Costello:
A Spatiotemporal Model to Simulate Chemotherapy Regimens for Heterogeneous Bladder Cancer Metastases to the Lung. 611-622 - Juho Kim, Nate Russell, Jian Peng:
Scalable Visualization for High-dimensional Single-cell Data.
Workshops
- Kun-Hsing Yu, Steven N. Hart, Rachel L. Goldfeder, Qiangfeng Cliff Zhang, Stephen C. J. Parker, Michael Snyder:
Harnessing Big Data for Precision Medicine: Infrastructures and Applications. 635-639 - Lana X. Garmire, Stephen V. Gliske, Quynh C. Nguyen, Jonathan H. Chen, Shamim Nemati, John D. Van Horn, Jason H. Moore, Carol Shreffler, Michelle Dunn:
The Training of Next Generation Data Scientists in Biomedicine. 640-645 - Jason 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:
No-Boundary Thinking in Bioinformatics. 646-648 - Philip R. O. Payne, Kun Huang, Nigam H. Shah, Jessica D. Tenenbaum:
Open Data for Discovery Science. 649-652
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