Contents

• CANCER PANOMICS: COMPUTATIONAL METHODS AND INFRASTRUCTURE FOR INTEGRATIVE ANALYSIS OF CANCER HIGH-THROUGHPUT "OMICS" DATA
• CANCER PATHWAYS: AUTOMATIC EXTRACTION, REPRESENTATION, AND REASONING IN THE "BIG DATA" ERA
• CHARACTERIZING THE IMPORTANCE OF ENVIRONMENTAL EXPOSURES, INTERACTIONS BETWEEN THE ENVIRONMENT AND GENETIC ARCHITECTURE, AND GENETIC INTERACTIONS: NEW METHODS FOR UNDERSTANDING THE ETIOLOGY OF COMPLEX TRAITS AND DISEASE
• CROWDSOURCING AND MINING CROWD DATA
• PERSONALIZED MEDICINE: FROM GENOTYPES, MOLECULAR PHENOTYPES AND THE QUANTIFIED SELF, TOWARDS IMPROVED MEDICINE
• Workshops
• Erratum

A Twentieth Anniversary Tribute to PSB

Darla Hewett, Michelle Whirl-Carrillo, Lawrence E. Hunter, Russ B. Altman, Teri E. Klein; Pacific Symposium on Biocomputing 20:1-7(2015)

CANCER PANOMICS: COMPUTATIONAL METHODS AND INFRASTRUCTURE FOR INTEGRATIVE ANALYSIS OF CANCER HIGH-THROUGHPUT "OMICS" DATA

Session Introduction

Soren Brunak, Francisco M. De La Vega, Adam Margolin, Benjamin J. Raphael, Gunnar Raetsch, Joshua M. Stuart; Pacific Symposium on Biocomputing 20:8-9(2015)

Cell Index Database (CELLX): A Web Tool for Cancer Precision Medicine

Keith A. Ching, Kai Wang, Zhengyan Kan, Julio Fernandez, Wenyan Zhong, Jarek Kostrowicki, Tao Xie, Zhou Zhu, Jean-Francois Martini, Maria Koehler, Kim Arndt, Paul Rejto; Pacific Symposium on Biocomputing 20:10-19(2015)

Comparing Nonparametric Bayesian Tree Priors for Clonal Reconstruction of Tumors

Amit G. Deshwar, Shankar Vembu, Quaid Morris; Pacific Symposium on Biocomputing 20:20-31(2015)

Stepwise Group Sparse Regression (SGSR): Gene-Set-Based Pharmacogenomic Predictive Models with Stepwise Selection of Functional Priors

In Sock Jang, Rodrigo Dienstmann, Adam A. Margolin, Justin Guinney; Pacific Symposium on Biocomputing 20:32-43(2015)

Integrative Genome-wide Analysis of the Determinants of RNA Splicing in Kidney Renal Clear Cell Carcinoma

Kjong-Van Lehmann, Andre Kahles, Cyriac Kandoth,William Lee, Nikolaus Schultz, Oliver Stegle, Gunnar Raetsch; Pacific Symposium on Biocomputing 20:44-55(2015)

An Integrated Framework for Reporting Clinically Relevant Biomarkers from Paired Tumor/Normal Genomic and Transcriptomic Sequencing Data In Support of Clinical Trials in Personalized Medicine

Sara Nasser, Ahmet A. Kurdoglu, Tyler Izatt, Jessica Aldrich, Megan L. Russell, Alexis Christoforides, Wiabhav Tembe, Jeffery A. Kiefer, Jason J. Corneveaux, Sara A. Byron, Karen M. Forman, Clarice Zuccaro, Jonathan J. Keats, Patricia M. LoRusso, John D. Carpten, Jeffrey M. Trent, David W. Craig; Pacific Symposium on Biocomputing 20:56-67(2015)

Characteristics of Drug Combination Therapy in Oncology by Analyzing Clinical Trial Data on Clinicaltrials.Gov

Menghua Wu, Marina Sirota, Atul J Butte, Bin Chen; Pacific Symposium on Biocomputing 20:68-79(2015)

CANCER PATHWAYS: AUTOMATIC EXTRACTION, REPRESENTATION, AND REASONING IN THE "BIG DATA" ERA

Session Introduction

Graciela Gonzalez, Chitta Baral, Jeff Kiefer, Suengchan Kim, Jieping Ye; Pacific Symposium on Biocomputing 20:80-83(2015)

Identifying Mutation Specific Cancer Pathways Using a Structurally Resolved Protein Interaction Network

H. Billur Engin, Matan Hofree, Hannah Carter; Pacific Symposium on Biocomputing 20:84-95(2015)

Binning Somatic Mutations Based on Biological Knowledge for Predicting Survival: An Application in Renal Cell Carcinoma

Dokyoon Kim, Ruowang Li, Scott M. Dudek, John R. Wallace, Marylyn D. Ritchie; Pacific Symposium on Biocomputing 20:96-107(2015)

Topological Features in Cancer Gene Expression Data>

Svetlana Lockwood, Bala Krishnamoorthy; Pacific Symposium on Biocomputing 20:108-119(2015)

Distant Supervision for Cancer Pathway Extraction from Text

Hoifung Poon, Kristina Toutanova, Chris Quirk; Pacific Symposium on Biocomputing 20:120-131(2015)

Unsupervised Feature Construction and Knowledge Extraction from Genome-Wide Assays of Breast Cancer with Denoising Autoencoders

Jie Tan, Matthew Ung, Chao Cheng, Casey S. Greene; Pacific Symposium on Biocomputing 20:132-143(2015)

Automated Gene Expression Pattern Annotation in the Mouse Brain

Tao Yang, Xinlin Zhao, Binbin Lin, Tao Zeng, Shuiwang Ji, Jieping Ye; Pacific Symposium on Biocomputing 20:144-155(2015)

CHARACTERIZING THE IMPORTANCE OF ENVIRONMENTAL EXPOSURES, INTERACTIONS BETWEEN THE ENVIRONMENT AND GENETIC ARCHITECTURE, AND GENETIC INTERACTIONS: NEW METHODS FOR UNDERSTANDING THE ETIOLOGY OF COMPLEX TRAITS AND DISEASE

Session Introduction

Molly Hall, Shefali Setia Verma, Dennis P. Wall, Jason H. Moore, Brendan Keating, Daniel B. Campbell, Gregory Gibson, Folkert W. Asselbergs, Sarah A. Pendergrass; Pacific Symposium on Biocomputing 20:156-160(2015)

Measures of Exposure Impact Genetic Association Studies: An Example in Vitamin K Levels and VKORC1

Dana C. Crawford, Kristin Brown-Gentry, Mark J. Rieder; Pacific Symposium on Biocomputing 20:161-170(2015)

A Bipartite Network Approach to Inferring Interactions Between Environmental Exposures and Human Diseases

Christian Darabos, Emily D. Grussing, Maria E. Cricco, Kenzie A. Clark, Jason H. Moore; Pacific Symposium on Biocomputing 20:171-182(2015)

A Screening-Testing Approach for Detecting Gene-Environment Interactions Using Sequential Penalized and Unpenalized Multiple Logistic Regression

H. Robert Frost, Angeline S. Andrew, Margaret R. Karagas, Jason H. Moore; Pacific Symposium on Biocomputing 20:183-194(2015)

Variable Selection Method for the Identification of Epistatic Models

Emily Rose Holzinger, Silke Szymczak, Abhijit Dasgupta, James Malley, Qing Li, Joan E. Bailey-Wilson; Pacific Symposium on Biocomputing 20:195-206(2015)

Genome-Wide Genetic Interaction Analysis of Glaucoma Using Expert Knowledge Derived from Human Phenotype Networks

Ting Hu, Christian Darabos, Maria E. Cricco, Emily Kong, Jason H. Moore; Pacific Symposium on Biocomputing 20:207-218(2015)

Identification of Gene-Gene and Gene-Environment Interactions Within the Fibrinogen Gene Cluster for Fibrinogen Levels in Three Ethnically Diverse Populations

Janina M. Jeff, Kristin Brown-Gentry, Dana C. Crawford; Pacific Symposium on Biocomputing 20:219-230(2015)

Development of Exposome Correlations Globes to Map Out Environment-Wide Associations

Chirag J. Patel, Arjun K. Manrai; Pacific Symposium on Biocomputing 20:231-242(2015)

Mitochondrial Variation and the Risk of Age-Related Macular Degeneration Across Diverse Populations

Nicole A. Restrepo, Sabrina L. Mitchell, Robert J. Goodloe, Deborah G. Murdock, Jonathan L. Haines, Dana C. Crawford; Pacific Symposium on Biocomputing 20:243-254(2015)

iPINBPA: An Integrative Network-Based Functional Module Discovery Tool for Genome-Wide Association Studies

Lili Wang, Parvin Mousavi, Sergio E. Baranzini; Pacific Symposium on Biocomputing 20:255-266(2015)

CROWDSOURCING AND MINING CROWD DATA

Session Introduction

Robert Leaman, Benjamin M. Good, Andrew I. Su, Zhiyong Lu; Pacific Symposium on Biocomputing 20:267-269(2015)

Reputation-Based Collaborative Network Biology

The sbv IMPROVER project team (in alphabetical order): Jean Binder, Stephanie Boue, Anselmo Di Fabio, R. Brett Fields, William Hayes, Julia Hoeng, Jennifer S. Park, Manuel C. Peitsch; Pacific Symposium on Biocomputing 20:270-281(2015)

Microtask Crowdsourcing for Disease Mention Annotation in PubMed Abstracts

Benjamin M. Good, Max Nanis, Chunlei Wu, Andrew I. Su; Pacific Symposium on Biocomputing 20:282-293(2015)

Crowdsourcing Image Annotation for Nucleus Detection and Segmentation in Computational Pathology: Evaluating Experts, Automated Methods, and the Crowd

Humayun Irshad, Laleh Montaser-Kouhsari, Gail Waltz, Octavian Bucur, Jonathan A. Nowak, Fei Dong, Nicholas W. Knoblauch, Andrew H. Beck; Pacific Symposium on Biocomputing 20:294-305(2015)

Analyzing Search Behavior of Healthcare Professionals for Drug Safety Surveillance

David J. Odgers, Rave Harpaz, Alison Callahan, Gregor Stiglic, Nigam H. Shah; Pacific Symposium on Biocomputing 20:306-317(2015)

Refining Literature Curated Protein Interactions Using Expert Opinions

Oznur Tastan, Yanjun Qi, Jaime G. Carbonell, Judith Klein-Seetharaman; Pacific Symposium on Biocomputing 20:318-329(2015)

Crowdsourcing RNA Structural Alignments with an Online Computer Game

Jérôme Waldispühl, Arthur Kam, Paul P. Gardner; Pacific Symposium on Biocomputing 20:330-341(2015)

PERSONALIZED MEDICINE: FROM GENOTYPES, MOLECULAR PHENOTYPES AND THE QUANTIFIED SELF, TOWARDS IMPROVED MEDICINE

Session introduction

Joel T. Dudley, Jennifer Listgarten, Oliver Stegle, Steven E. Brenner, Leopold Parts; Pacific Symposium on Biocomputing 20:342-346(2015)

KLEAT: Cleavage Site Analysis of Transcriptomes

Inanc Birol, Anthony Raymond, Readman Chiu, Ka Ming Nip, Shaun D. Jackman, Maayan Kreitzman, T. Roderick Docking, Catherine A. Ennis, A. Gordon Robertson, Aly Karsan; Pacific Symposium on Biocomputing 20:347-358(2015)

Causal Inference in Biology Networks with Integrated Belief Propagation

Rui Chang, Jonathan R. Karr, Eric E. Schadt; Pacific Symposium on Biocomputing 20:359-370(2015)

Machine Learning from Concept to Clinic: Reliable Detection of BRAF V600E DNA Mutations in Thyroid Nodules Using High-Dimensional RNA Expression Data

James Diggans, Su Yeon Kim, Zhanzhi Hu, Daniel Pankratz, Mei Wong, Jessica Reynolds, Ed Tom, Moraima Pagan, Robert Monroe, Juan Rosai, Virginia A. Livolsi, Richard B. Lanman, Richard T. Kloos, P. Sean Walsh, Giulia C. Kennedy; Pacific Symposium on Biocomputing 20:371-382(2015)

A Systematic Assessment of Linking Gene Expression with Genetic Variants for Prioritizing Candidate Targets

Hua Fan-Minogue, Bin Chen, Weronika Sikora-Wohlfeld, Marina Sirota, Atul J. Butte; Pacific Symposium on Biocomputing 20:383-394(2015)

Drug-induced mRNA Signatures Are Enriched for the Minority of Genes that Are Highly Heritable

Tianxiang Gao, Petter Brodin, Mark M Davis, Vladimir Jojic; Pacific Symposium on Biocomputing 20:395-406(2015)

An Integrative Pipeline for Multi-Modal Discovery of Disease Relationships

Benjamin S. Glicksberg, Li Li, Wei-Yi Cheng, Khader Shameer, Jo\0x0308rg Hakenberg, Rafael Castellanos, Meng Ma, Lisong Shi, Hardik Shah, Joel T. Dudley, Rong Chen; Pacific Symposium on Biocomputing 20:407-418(2015)

PEAX: Interactive Visual Analysis and Exploration of Complex Clinical Phenotype and Gene Expression Association

Michael A. Hinterberg, David P. Kao, Michael R. Bristow, Lawrence E. Hunter, J. David Port, Carsten Goerg; Pacific Symposium on Biocomputing 20:419-430(2015)

T-ReCS: Stable Selection of Dynamically Formed Groups of Features with Application to Prediction of Clinical Outcomes

Grace T. Huang, Ioannis Tsamardinos, Vineet Raghu, Naftali Kaminski, Panayiotis V. Benos; Pacific Symposium on Biocomputing 20:431-442(2015)

Meta-Analysis of Differential Gene Co-Expression: Application to Lupus

Sumit B. Makashir, Leah C. Kottyan, Matthew T. Weirauch; Pacific Symposium on Biocomputing 20:443-454(2015)

Melancholic Depression Prediction by Identifying Representative Features in Metabolic and Microarray Profiles with Missing Values

Zhi Nie, Tao Yang, Yashu Liu, Binbin Lin, Qingyang Li, Vaibhav A Narayan, Gayle Wittenberg, Jieping Ye; Pacific Symposium on Biocomputing 20:455-466(2015)

BayClone: Bayesian Nonparametric Inference of Tumor Subclones Using NGS Data

Subhajit Sengupta, Jin Wang, Juhee Lee, Peter Mueller, Kamalakar Gulukota, Arunava Banerjee, Yuan Ji; Pacific Symposium on Biocomputing 20:467-478(2015)

Workshops

Human Evolutionary Genomics and the Search for the Genes that Made Us Human

James M. Sikela; Pacific Symposium on Biocomputing 20:479-481(2015)

Discovery Informatics in Biological and Biomedical Sciences: Research Challenges and Opportunities

Vasant Honavar; Pacific Symposium on Biocomputing 20:482(2015)

Inviting the Public: The Impact on Informatics Arising from Emerging Global Health Research Paradigms

Richard Gayle, Mark Minie, Erik Nilsson; Pacific Symposium on Biocomputing 20:483-487(2015)

Training the Next Generation of Quantitative Biologists in the Era of Big Data

Kristine A. Pattin, Anna C. Greene, Russ B. Altman, Kevin B. Cohen, Elizabeth Wethington, Carsten Goerg, Lawrence E. Hunter, Spencer V. Muse, Predrag Radivojac, Jason H. Moore; Pacific Symposium on Biocomputing 20:488-492(2015)

Erratum

ERRATUM: Next-Generation Analysis of Cataracts: Determining Knowledge Driven Gene-Gene Interactions Using Biofilter, and Gene-Environment Interactions Using the PhenX Toolkit

Pacific Symposium on Biocomputing 20:493-505(2015)

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Updated: October 21, 2014