Contents

• COMPUTATIONAL APPROACHES TO UNDERSTANDING THE EVOLUTION OF MOLECULAR FUNCTION
• IMAGING GENOMICS
• METHODS TO ENSURE THE REPRODUCIBILITY OF BIOMEDICAL RESEARCH
• PATTERNS IN BIOMEDICAL DATA-HOW DO WE FIND THEM?
• PRECISION MEDICINE: DATA AND DISCOVERY FOR IMPROVED HEALTH AND THERAPY
• SINGLE-CELL ANALYSIS AND MODELLING OF CELL POPULATION HETEROGENEITY
• WORKSHOPS

COMPUTATIONAL APPROACHES TO UNDERSTANDING THE EVOLUTION OF MOLECULAR FUNCTION

Session Introduction

Yana Bromberg, Matthew W. Hahn, Predrag Radivojac; Pacific Symposium on Biocomputing 22:1-2(2017)

Identification and Analysis of Bacterial Genomic Metabolic Signatures

Nathan Bowerman, Nathan Tintle, Matthew DeJongh, Aaron A. Best; Pacific Symposium on Biocomputing 22:3-14(2017)

When should we NOT transfer functional annotation between sequence paralogs?

Mengfei Cao, Lenore J. Cowen; Pacific Symposium on Biocomputing 22:15-26(2017)

ProSNet: integrating homology with molecular networks for protein function prediction

Sheng Wang, Meng Qu, Jian Peng; Pacific Symposium on Biocomputing 22:27-38(2017)

On the power and limits of sequence similarity based clustering of proteins into families

Christian Wiwie, Richard Röttger; Pacific Symposium on Biocomputing 22:39-50(2017)

IMAGING GENOMICS

Session Introduction

Li Shen, Lee A.D. Cooper; Pacific Symposium on Biocomputing 22:51-57(2017)

Adaptive testing of SNP-brain functional connectivity association via a modular network analysis

Chen Gao, Junghi Kim, Wei Pan; Pacific Symposium on Biocomputing 22:58-69(2017)

Exploring Brain Transcriptomic Patterns: A Topological Analysis Using Spatial Expression Networks

Zhana Kuncheva, Michelle L. Krishnan, Giovanni Montana; Pacific Symposium on Biocomputing 22:70-81(2017)

Integrative Analysis for Lung Adenocarcinoma Predicts Morphological Features Associated with Genetic Variations

Chao Wang, Hai Su, Lin Yang, Kun Huang; Pacific Symposium on Biocomputing 22:82-93(2017)

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; Pacific Symposium on Biocomputing 22:94-104(2017)

Enforcing Co-expression in Multimodal Regression Framework

Pascal Zille, Vince D. Calhoun, Yu-Ping Wang ; Pacific Symposium on Biocomputing 22:96-107(2017)

METHODS TO ENSURE THE REPRODUCIBILITY OF BIOMEDICAL RESEARCH

Session Introduction

Konrad J. Karczewski, Nicholas P. Tatonetti, Chirag J. Patel, Arjun K. Manrai, C. Titus Brown, John P.A. Ioannidis; Pacific Symposium on Biocomputing 22:117-119(2017)

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; Pacific Symposium on Biocomputing 22:120-131(2017)

Reproducible Drug Repurposing: When Similarity Does Not Suffice

Emre Guney; Pacific Symposium on Biocomputing 22:132-143(2017)

Empowering Multi-Cohort Gene Expression Analysis to Increase Reproducibility

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, and Purvesh Khatri; Pacific Symposium on Biocomputing 22:144-153(2017)

Rabix: An Open-Source Workflow Executor Supporting Recomputability and Interoperability of Workflow Descriptions

Gaurav Kaushik, Sinisa Ivkovic, Janko Simonovic, Nebojsa Tijanic, Brandi Davis-Dusenbery, Deniz Kural; Pacific Symposium on Biocomputing 22:154-165(2017)

Data Sharing and Reproducible Clinical Genetic Testing: Successes and Challenges

Shan Yang, Melissa Cline, Can Zhang, Benedict Paten and Stephen E. Lincoln; Pacific Symposium on Biocomputing 22:166-176(2017)

PATTERNS IN BIOMEDICAL DATA-HOW DO WE FIND THEM?

Session Introduction

Anna Okula Basile, Anurag Verma, Marta Byrska-Bishop, Sarah P. Pendergrass, Christian Darabos, H. Lester Kirchner; Pacific Symposium on Biocomputing 22:177-183(2017)

Learning Attributes of Disease Progression from Trajectories of Sparse Lab Values

Vibhu Agarwal, Nigam H. Shah; Pacific Symposium on Biocomputing 22:184-194(2017)

Computer Aided Image Segmentation and Classification for Viable and Non-Viable Tumor Identification in Osteosarcoma

Harish Babu Arunachalam, Rashika Mishra, Bogdan Armaselu, Ovidiu Daescu, Maria Martinez, Patrick Leavey, Dinesh Rakheja, Kevin Cederberg, Anita Sengupta, Molly Ni'suilleabhain; Pacific Symposium on Biocomputing 22:195-206(2017)

Missing Data Imputation in the Electronic Health Record Using Deeply Learned Autoencoders

Brett K. Beaulieu-Jones, Jason H. Moore, The Pooled Resource Open-Access ALS Clinical Trials Consortium; Pacific Symposium on Biocomputing 22:207-218(2017)

A Deep Learning Approach for Cancer Detection and Relevant Gene Identification

Padideh Danaee, Reza Ghaeini, David Hendrix; Pacific Symposium on Biocomputing 22:219-229(2017)

Development and Performance of Text-Mining Algorithms to Extract Socioeconomic Status from De-Identified Electronic Health Records

Brittany M. Hollister, Nicole A. Restrepo, Eric Farber-Eger, Dana C. Crawford, Melinda C. Aldrich, Amy Non; Pacific Symposium on Biocomputing 22:230-241(2017)

Genome-Wide Interaction with Selected Type 2 Diabetes Loci Reveals Novel Loci for Type 2 Diabetes in African Americans

Jacob M. Keaton, Jacklyn N. Hellwege, Maggie C. Y. Ng, Nicholette D. Palmer, James S. Pankow, Myriam Fornage, James G. Wilson, Adolfo Correa, Laura J. Rasmussen-Torvik, Jerome I. Rotter, Yii-Der I. Chen, Kent D. Taylor, Stephen S. Rich, Lynne E. Wagenknecht, Barry I. Freedman, Donald W. Bowden; Pacific Symposium on Biocomputing 22:242-253(2017)

Deep Motif Dashboard: Visualizing and Understanding Genomic Sequences Using Deep Neural Networks

Jack Lanchantin, Ritambhara Singh, Beilun Wang, Yanjun Qi; Pacific Symposium on Biocomputing 22:254-265(2017)

Meta-Analysis of Continuous Phenotypes Identifies a Gene Signature that Correlates with COPD Disease Status

Madeleine Scott, Francesco Vallania, and Purvesh Khatri; Pacific Symposium on Biocomputing 22:266-275(2017)

Predictive Modeling of Hospital Readmission Rates Using Electronic Medical Record-Wide Machine Learning: A Case-Study Using Mount Sinai Heart Failure Cohort

Khader Shameer, Kipp W. Johnson, Alexandre Yahi, Riccardo Miotto, Li Li, Doran Ricks, Jebakumar Jebakaran, Patricia Kovatch, Partho P. Sengupta, Annetine Gelijns, Alan Moskovitz, Bruce Darrow, David L. Reich, Andrew Kasarskis, Nicholas P. Tatonetti, Sean Pinney, Joel T. Dudley; Pacific Symposium on Biocomputing 22:276-287(2017)

Learning Parsimonious Ensembles for Unbalanced Computational Genomics Problems

Ana Stanescu, Gaurav Pandey; Pacific Symposium on Biocomputing 22:288-299(2017)

Methods for Clustering Time Series Data Acquired from Mobile Health Apps

Nicole Tignor, Pei Wang, Nicholas Genes, Linda Rogers, Steven G. Hershman, Erick R. Scott, Micol Zweig, Yu-Feng Yvonne Chan, Eric E. Schadt; Pacific Symposium on Biocomputing 22:300-323(2017)

A New Relevance Estimator for the Compilation and Visualization of Disease Patterns and Potential Drug Targets

Modest von Korff, Tobias Fink, Thomas Sander; Pacific Symposium on Biocomputing 22:312-323(2017)

Network Map of Adverse Health Effects Among Victims of Intimate Partner Violence

Kathleen Whiting, Larry Y. Liu, Mehmet Koyuturk, Gunnur Karakurt; Pacific Symposium on Biocomputing 22:324-335(2017)

Discovery of Functional and Disease Pathways by Community Detection in Protein-Protein Interaction Networks

Stephen J. Wilson, Angela D. Wilkins, Chih-Hsu Lin, Rhonald C. Lua, Olivier Lichtarge; Pacific Symposium on Biocomputing 22:336-347(2017)

PRECISION MEDICINE: DATA AND DISCOVERY FOR IMPROVED HEALTH AND THERAPY

Session Introduction

Alexander A. Morgan, Dana C. Crawford, Josh C. Denny, Sean D. Mooney, Bruce J. Aronow, Steven E. Brenner; Pacific Symposium on Biocomputing 22:348-355(2017)

Opening the Door to the Large Scale Use of Clinical Lab Measures for Association Testing: Exploring Different Methods for Defining Phenotypes

Christopher R. Bauer, Daniel Lavage, John Snyder, Joseph Leader, J. Matthew Mahoney, Sarah A. Pendergrass; Pacific Symposium on Biocomputing 22:356-367(2017)

A Powerful Method for Including Genotype Uncertainty in Tests of Hardy-Weinberg Equilibrium

Andrew Beck, Alexander Luedtke, Keli Liu, Nathan Tintle; Pacific Symposium on Biocomputing 22:368-379(2017)

Temporal Order of Disease Pairs Affects Subsequent Disease Trajectories: The Case of Diabetes and Sleep Apnea

Mette Beck, David Westergaard, Leif Groop and Soren Brunak; Pacific Symposium on Biocomputing 22:380-389(2017)

MicroRNA-Augmented Pathways (mirAP) and Their Applications to Pathway Analysis and Disease Subtyping

Diana Diaz, Michele Donato, Tin Nguyen, Sorin Draghici; Pacific Symposium on Biocomputing 22:390-401(2017)

Frequent Subgraph Mining of Personalized Signaling Pathway Networks Groups Patients with Frequently Dysregulated Disease Pathways and Predicts Prognosis

Arda Durmaz, Tim A.D. Henderson, Douglas Brubaker, Gurkan Bebek; Pacific Symposium on Biocomputing 22:402-(2017)

Human Kinases Display Mutational Hotspots at Cognate Positions Within Cancer

Jonathan Gallion, Angela D. Wilkins, Olivier Lichtarge; Pacific Symposium on Biocomputing 22:414-425(2017)

MUSE: A Multi-locus Sampling-based Epistasis Algorithm for Quantitative Genetic Trait Prediction

Dan He, Laxmi Parida; Pacific Symposium on Biocomputing 22:426-437(2017)

ceRNA Search Method Identified a MET-activated Subgroup Among EGFR DNA Amplified Lung Adenocarcinoma Patients

Halla Kabat, Leo Tunkle, Inhan Lee; Pacific Symposium on Biocomputing 22:438-448(2017)

Improved Performance of Gene Set Analysis on Genome-Wide Transcriptomics Data when Using Gene Activity State Estimates

Thomas Kamp, Micah Adams, Craig Disselkoen, Nathan Tintle; Pacific Symposium on Biocomputing 22:449-460(2017)

methylDMV: Simultaneous Detection of Differential DNA Methylation and Variability with Confounder Adjustment

Pei Fen Kuan, Junyan Song, Shuyao He; Pacific Symposium on Biocomputing 22:461-472(2017)

Identify Cancer Driver Genes Through Shared Mendelian Disease Pathogenic Variants and Cancer Somatic Mutations

Meng Ma, Changchang Wang, Benjamin Glicksberg, Eric Schadt, Shuyu D. Li, Rong Chen; Pacific Symposium on Biocomputing 22:473-484(2017)

Identifying Cancer Specific Metabolic Signatures Using Constraint-Based Models

André Schultz, Sanket Mehta, Chenyue W. Hu, Fieke W Hoff, Terzah M. Horton, Steven M. Kornblau, Amina A. Qutub; Pacific Symposium on Biocomputing 22:485-496(2017)

Differential Pathway Dependency Discovery Associated with Drug Response across Cancer Cell Lines

Gil Speyer, Divya Mahendra, Hai J. Tran, Jeff Kiefer, Stuart L. Schreiber, Paul A. Clemons, Harshil Dhruv, Michael Berens, Seungchan Kim; Pacific Symposium on Biocomputing 22:497-508(2017)

A Methylation-to-Expression Feature Model for Generating Accurate Prognostic Risk Scores and Identifying Disease Targets in Clear Cell Kidney Cancer

Jeffrey A. Thompson, Carmen J. Marsit; Pacific Symposium on Biocomputing 22:509-520(2017)

De Novo Mutations in Autism Implicate the Synaptic Elimination Network

Guhan Ram Venkataraman, Chloe O'Connell, Fumiko Egawa, Dorna Kashef-Haghighi, Dennis Paul Wall; Pacific Symposium on Biocomputing 22:521-532(2017)

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

Shefali S. Verma, Anastasia M. Lucas, Daniel R. Lavage, Joseph B. Leader, Raghu Metpally, Sarathbabu Krishnamurthy, Frederick Dewey, Ingrid Borecki, Alexander Lopez, John Overton, John Penn, Jeffrey Reid, Sarah A. Pendergrass, Gerda Breitwieser, Marylyn D. Ritchie; Pacific Symposium on Biocomputing 22:533-544(2017)

Strategies for Equitable Pharmacogenomic-Guided Warfarin Dosing Among European and African American Individuals in a Clinical Population

Laura Wiley, Jacob VanHouten, David Samuels, Melinda Aldrich, Dan Roden, Josh Peterson, Joshua Denny; Pacific Symposium on Biocomputing 22:545-556(2017)

SINGLE-CELL ANALYSIS AND MODELLING OF CELL POPULATION HETEROGENEITY

Session Introduction

Nikolay Samusik, Nima Aghaeepour, Sean Bendall; Pacific Symposium on Biocomputing 22:557-563(2017)

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

Brian Aevermann, Jamison 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 Schork, Richard H. Scheuermann; Pacific Symposium on Biocomputing 22:564-575(2017)

Tracing Co-Regulatory Network Dynamics in Noisy, Single-Cell Transcriptome Trajectories

Pablo Cordero, Joshua M. Stuart; Pacific Symposium on Biocomputing 22:576-587(2017)

An Updated Debarcoding Tool for Mass Cytometry with Cell Type-Specific and Cell Sample-Specific Stringency Adjustment

Kristin I. Fread, William D. Strickland, Garry P. Nolan, Eli R. Zunder; Pacific Symposium on Biocomputing 22:588-598(2017)

Mapping Neuronal Cell Types Using Integrative Multi-Species Modeling of Human and Mouse Single Cell RNA Sequencing

Travis Johnson, Zachary Abrams, Yan Zhang, Kun Huang; Pacific Symposium on Biocomputing 22:599-610(2017)

A Spatiotemporal Model to Simulate Chemotherapy Regimens for Heterogeneous Bladder Cancer Metastases to the Lung

Kimberly R. Kanigel Winner, James C. Costello; Pacific Symposium on Biocomputing 22:611-622(2017)

Scalable Visualization for High-dimensional Single-cell Data

Juho Kim, Nate Russell, Jian Peng; Pacific Symposium on Biocomputing 22:623-(2017)

WORKSHOPS

Harnessing Big Data for Precision Medicine: Infrastructures and Applications

Kun-Hsing Yu, Steven N. Hart, Rachel Goldfeder, Qiangfeng Cliff Zhang, Stephen C. J. Parker, Michael Snyder; Pacific Symposium on Biocomputing 22:635-639(2017)

The Training of Next Generation Data Scientists in Biomedicine

Lana Garmire, Stephen Gliske, Quynh C Nguyen, Jonathan H. Chen, Shamim Nemati, John D. Van Horn, Jason H. Moore, Carol Shreffler, Michelle Dunn; Pacific Symposium on Biocomputing 22:640-645(2017)

No-Boundary Thinking in Bioinformatics

Jason H. Moore, Steven F. Jennings, Casey S. Greene, Lawrence E. Hunter, Andy D. Perkins, Clarlynda Williams-Devane, Donald C. Wunsch, Zhongming Zhao, Xiuzhen Huang; Pacific Symposium on Biocomputing 22:646-648(2017)

Open Data for Discovery Science

Philip R.O. Payne, Kun Huang, Nigam H. Shah, Jessica Tenenbaum; Pacific Symposium on Biocomputing 22:649-652(2017)

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Updated: December 1, 2016