PSB 2016 Online Proceedings

PSB 2016
CC BY: PSB 2016 proceedings are published as Open Access chapters by World Scientific Publishing Company and distributed under the terms of the Creative Commons Attribution (CC BY) 4.0 License.

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Session Introduction
Kelly Regan, Zachary Abrams, Michael Sharpnack, Arunima Srivastava, Kun Huang, Nigam Shah, Philip R.O. Payne; Pacific Symposium on Biocomputing 21:1-8(2016)
An Integrated Network Approach to Identifying Biological Pathways and Environmental Exposure Interactions in Complex Diseases
Christian Darabos, Jingya Qiu, Jason H. Moore; Pacific Symposium on Biocomputing 21:9-20(2016)
Computing Therapy for Precision Medicine: Collaborative Filtering Integrates and Predicts Multi-entity Interactions
Sam Regenbogen, Angela D. Wilkins, Olivier Lichtarge; Pacific Symposium on Biocomputing 21:21-32(2016)
Knowledge-Assisted Approach to Identify Pathways with Differential Dependencies
Gil Speyer, Jeff Kiefer, Harshil Dhruv, Michael Berens, Seungchan Kim; Pacific Symposium on Biocomputing 21:33-44(2016)
Integrating Genetic and Structural Data on Human Protein Kinome in Network-Based Modeling of Kinase Sensitivities and Resistance to Targeted and Personalized Anticancer Drugs
Gennady M. Verkhivker; Pacific Symposium on Biocomputing 21:45-56(2016)
Phenome-Wide Interaction Study (PheWIS) in Aids Clinical Trials Group Data (ACTG)
Shefali S. Verma, Alex T. Frase, Anurag Verma, Sarah A. Pendergrass, Shaun Mahony, David W. Haas, Marylyn D. Ritchie; Pacific Symposium on Biocomputing 21:57-68(2016)
A Framework for Attribute-Based Community Detection with Applications to Integrated Functional Genomics
Han Yu, Rachael Hageman Blair; Pacific Symposium on Biocomputing 21:69-80(2016)
Collective Pairwise Classification for Multi-Way Analysis of Disease and Drug Data
Marinka Zitnik, Blaz Zupan; Pacific Symposium on Biocomputing 21:81-92(2016)


Session Introduction
Melissa A. Haendel, Maricel G. Kann, Nicole L. Washington; Pacific Symposium on Biocomputing 21:93-95(2016)
Testing Population-Specific Quantitative Trait Associations for Clinical Outcome Relevance in a Biorepository Linked to Electronic Health Records: LPA and Myocardial Infarction in African Americans
Logan Dumitrescu, Kirsten E. Diggins, Robert Goodloe, Dana C. Crawford; Pacific Symposium on Biocomputing 21:96-107(2016)
Diagnosis-Guided Method for Identifying Multi-Modality Neuroimaging Biomarkers Associated with Genetic Risk Factors in Alzheimer’s Disease
Xiaoke Hao, Jingwen Yan, Xiaohui Yao, Shannon L. Risacher, Andrew J. Saykin, Daoqiang Zhang, Li Shen, for the ADNI; Pacific Symposium on Biocomputing 21:108-119(2016)
Metabolomics Differential Correlation Network Analysis of Osteoarthritis
Ting Hu, Weidong Zhang, Zhaozhi Fan, Guang Sun, Sergei Likhodi, Edward Randell, Guangju Zhai; Pacific Symposium on Biocomputing 21:120-131(2016)
Investigating the Importance of Anatomical Homology for Cross-Species Phenotype Comparisons Using Semantic Similarity
Prashanti Manda, Christopher J. Mungall, James P. Balhoff, Hilmar Lapp, Todd J. Vision; Pacific Symposium on Biocomputing 21:132-143(2016)
Discovering Patient Phenotypes Using Generalized Low Rank Models
Alejandro Schuler, Vincent Liu, Joe Wan, Alison Callahan, Madeleine Udell, David E. Stark, Nigam H. Shah; Pacific Symposium on Biocomputing 21:144-155(2016)
Inference of Personalized Drug Targets via Network Propagation
Ortal Shnaps, Eyal Perry, Dana Silverbush, Roded Sharan; Pacific Symposium on Biocomputing 21:156-167(2016)
Integrating Clinical Laboratory Measures and ICD-9 Code Diagnoses in Phenome-Wide Association Studies
Anurag Verma, Joseph B. Leader, Shefali S. Verma, Alex Frase, John Wallace, Scott Dudek, Daniel R. Lavage, Cristopher V. Van Hout, Frederick E. Dewey, John Penn, Alex Lopez, John D. Overton, David J. Carey, David H. Ledbetter, H. Lester Kirchner, Marylyn D. Ritchie, Sarah A. Pendergrass; Pacific Symposium on Biocomputing 21:168-179(2016)


Session Introduction
Arjun K. Manrai, Chirag J. Patel, Nils Gehlenborg, Nicholas P. Tatonetti, John P.A. Ioannidis, Isaac S. Kohane; Pacific Symposium on Biocomputing 21:180-182(2016)
Reproducible Research Workflow in R for the Analysis of Personalized Human Microbiome Data
Benjamin Callahan, Diana Proctor, David Relman, Julia Fukuyama, Susan Holmes; Pacific Symposium on Biocomputing 21:183-194(2016)
Dynamically Evolving Clinical Practices and Implications for Predicting Medical Decisions
Jonathan H. Chen, Mary K. Goldstein, Steven M. Asch, Russ B. Altman; Pacific Symposium on Biocomputing 21:195-206(2016)
Repurposing Germline Exomes of the Cancer Genome Atlas Demands a Cautious Approach and Sample-Specific Variant Filtering
Amanda Koire, Panagiotis Katsonis, Olivier Lichtarge; Pacific Symposium on Biocomputing 21:207-218(2016)
Identification of Questionable Exclusion Criteria in Mental Disorder Clinical Trials Using a Medical Encyclopedia
Handong Ma, Chunhua Weng; Pacific Symposium on Biocomputing 21:219-230(2016)
Reproducible and Shareable Quantifications of Pathogenicity
Arjun K. Manrai, Brice L. Wang, Chirag J. Patel, Isaac S. Kohane; Pacific Symposium on Biocomputing 21:231-242(2016)


Session Introduction
Alexander A. Morgan, Sean D. Mooney, Bruce J. Aronow, Steven E. Brenner; Pacific Symposium on Biocomputing 21:243-248(2016)
Knowledge Driven Binning and PheWAS Analysis in Marshfield Personalized Medicine Research Project Using BioBin
Anna O. Basile, John R. Wallace, Peggy Peissig, Catherine A. McCarty, Murray Brilliant, Marylyn D. Ritchie; Pacific Symposium on Biocomputing 21:249-260(2016)
Multitask Feature Selection with Task Descriptors
Victor Bellon, Veronique Stoven, Chloe-Agathe Azencott; Pacific Symposium on Biocomputing 21:261-272(2016)
Personalized Hypothesis Tests for Detecting Medication Response in Parkinson Disease Patients Using iPhone Sensor Data
Elias Chaibub Neto, Brian M. Bot, Thanneer Perumal, Larsson Omberg, Justin Guinney, Mike Kellen, Arno Klein, Stephen H. Friend, Andrew D. Trister; Pacific Symposium on Biocomputing 21:273-284(2016)
Kidney Disease Genetics and the Importance of Diversity in Precision Medicine
Jessica N. Cooke Bailey, Sarah Wilson, Kristin Brown-Gentry, Robert Goodloe, Dana C. Crawford; Pacific Symposium on Biocomputing 21:285-296(2016)
Predicting Significance of Unknown Variants in Glial Tumors Through Sub-Class Enrichment
Alex M. Fichtenholtz, Nicholas D. Camarda, Eric K. Neumann; Pacific Symposium on Biocomputing 21:297-308(2016)
Do Cancer Clinical Trial Populations Truly Represent Cancer Patients? A Comparison of Open Clinical Trials to the Cancer Genome Atlas
Nophar Geifman, Atul J. Butte; Pacific Symposium on Biocomputing 21:309-320(2016)
Patient-Specific Data Fusion for Cancer Stratification and Personalised Treatment
Vladimir Gligorijevic, Noel Malod-Dognin, Natasa Przulj; Pacific Symposium on Biocomputing 21:321-332(2016)
PRISM: A Data-Driven Platform for Monitoring Mental Health
Maulik R. Kamdar, Michelle J. Wu; Pacific Symposium on Biocomputing 21:333-344(2016)
Bayesian Biclustering for Patient Stratification
Sahand Khakabimamaghani, Martin Ester; Pacific Symposium on Biocomputing 21:345-356(2016)
Biofilter as a Functional Annotation Pipeline for Common and Rare Copy Number Burden
Dokyoon Kim, Anastasia Lucas, Joseph Glessner, Shefali S. Verma, Yuki Bradford, Ruowang Li, Alex T. Frase, Hakon Hakonarson, Peggy Peissig, Murray Brilliant, Marylyn D. Ritchie; Pacific Symposium on Biocomputing 21:357-368(2016)
The Challenges in Using Electronic Health Records for Pharmacogenomics and Precision Medicine Research
Sarah M. Laper, Nicole A. Restrepo, Dana C. Crawford; Pacific Symposium on Biocomputing 21:369-380(2016)
Separating the Causes and Consequences in Disease Transcriptome
Yong Fuga Li, Fuxiao Xin, and Russ B. Altman; Pacific Symposium on Biocomputing 21:381-392(2016)
A Bayesian Nonparametric Model for Reconstructing Tumor Subclones Based on Mutation Pairs
Subhajit Sengupta, Tianjian Zhou, Peter Mueller, Yuan Ji; Pacific Symposium on Biocomputing 21:393-404(2016)
One-Class Detection of Cell States in Tumor Subtypes
Artem Sokolov, Evan O. Paull, Joshua M. Stuart; Pacific Symposium on Biocomputing 21:405-416(2016)
RDF Sketch Maps - Knowledge Complexity Reduction for Precision Medicine Analytics
Nattapon Thanintorn, Juexin Wang, Ilker Ersoy, Zainab Al-Taie, Yuexu Jiang, Duolin Wang, Megha Verma, Trupti Joshi, Richard Hammer, Dong Xu, Dmitriy Shin; Pacific Symposium on Biocomputing 21:417-428(2016)


Session Introduction
Drena Dobbs, Steven E. Brenner, Vasant G. Honavar, Robert L. Jernigan, Alain Laederach, Quaid Morris; Pacific Symposium on Biocomputing 21:429-432(2016)
Cseq-Simulator: A Data Simulator for CLIP-Seq Experiments
Wanja Kassuhn, Uwe Ohler, Philipp Drewe; Pacific Symposium on Biocomputing 21:433-444(2016)
A Motif-Based Method for Predicting Interfacial Residues in Both the RNA and Protein Components of Protein-RNA Complexes
Usha K. Muppirala, Benjamin A. Lewis, Carla M. Mann, Drena Dobbs; Pacific Symposium on Biocomputing 21:445-455(2016)
Detection of Bacterial Small Transcripts from RNA-Seq Data: A Comparative Assessment
Lourdes Pena-Castillo, Marc Gruell, Martin E. Mulligan, Andrew S. Lang; Pacific Symposium on Biocomputing 21:456-467(2016)


Session Introduction
Michael J. Paul, Abeed Sarker, John S. Brownstein, Azadeh Nikfarjam, Matthew Scotch, Karen L. Smith, Graciela Gonzalez; Pacific Symposium on Biocomputing 21:468-479(2016)
Text Classification for Automatic Detection of E-Cigarette Use and Use for Smoking Cessation from Twitter: A Feasibility Pilot
Yin Aphinyanaphongs, Armine Lulejian, Duncan Penfold Brown, Richard Bonneau, Paul Krebs; Pacific Symposium on Biocomputing 21:480-491(2016)
Monitoring Potential Drug Interactions and Reactions via Network Analysis of Instagram User Timelines
Rion Brattig Correia, Lang Li, Luis M. Rocha; Pacific Symposium on Biocomputing 21:492-503(2016)
Towards Early Discovery of Salient Health Threats: A Social Media Emotion Classification Technique
Bahadorreza Ofoghi, Meghan Mann, Karin Verspoor; Pacific Symposium on Biocomputing 21:504-515(2016)
Predicting Individual Well-Being Through the Language of Social Media
H. Andrew Schwartz, Maarten Sap, Margaret L. Kern, Johannes C. Eichstaedt, Adam Kapelner, Megha Agrawal, Eduardo Blanco, Lukasz Dziurzynski, Gregory Park, David Stillwell, Michal Kosinski, Martin E.P. Seligman, Lyle H. Ungar; Pacific Symposium on Biocomputing 21:516-527(2016)
Finding Potentially Unsafe Nutritional Supplements from User Reviews with Topic Modeling
Ryan Sullivan, Abeed Sarker, Karen O'Connor, Amanda Goodin, Mark Karlsrud, Graciela Gonzalez; Pacific Symposium on Biocomputing 21:528-539(2016)
Insights from Machine-Learned Diet Success Prediction
Ingmar Weber, Palakorn Achananuparp; Pacific Symposium on Biocomputing 21:540-551(2016)


Translational Bioinformatics 101
Jessica D. Tenenbaum, Subha Madhavan, Robert R. Freimuth, Joshua C. Denny, Lewis Frey; Pacific Symposium on Biocomputing 21:552-556(2016)
Computational Approaches to Study Microbes and Microbiomes
Casey S. Greene, James A. Foster, Bruce A. Stanton, Deborah A. Hogan, Yana Bromberg; Pacific Symposium on Biocomputing 21:557-565(2016)
Use of Genome Data in Newborns as a Starting Point for Life-Long Precision Medicine
Steven E. Brenner, Stephen Kingsmore, Sean D. Mooney, Robert Nussbaum, Jennifer Puck; Pacific Symposium on Biocomputing 21:568-575(2016)
Workshop on Topology and Abstract Algebra for Biomedicine
Eric K. Neumann, Svetlana Lockwood, Bala Krishnamoorthy, David Spivak; Pacific Symposium on Biocomputing 21:576-580(2016)
Social Media Mining Shared Task Workshop
Abeed Sarker, Azadeh Nikfarjam, Graciela Gonzalez; Pacific Symposium on Biocomputing 21:581-592(2016)
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