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21. PSB 2016: Kohala Coast, Hawaii, USA
- Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein, Marylyn D. Ritchie:
Biocomputing 2016: Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA, January 4-8, 2016. 2016
Discovery of Molecularly Targeted Therapies
- Kelly Regan, Zachary B. Abrams, Michael F. Sharpnack, Arunima Srivastava, Kun Huang, Nigam Shah, Philip R. O. Payne:
Session Introduction. 1-8 - Christian Darabos, Jingya Qiu, Jason H. Moore:
An Integrated Network Approach to Identifying Biological Pathways and Environmental Exposure Interactions in Complex Diseases. 9-20 - Sam Regenbogen, Angela D. Wilkins, Olivier Lichtarge:
Computing Therapy for Precision Medicine: Collaborative Filtering Integrates and Predicts Multi-entity Interactions. 21-32 - Gil Speyer, Jeff Kiefer, Harshil Dhruv, Michael E. Berens, Seungchan Kim:
Knowledge-Assisted Approach to Identify Pathways with Differential Dependencies. 33-44 - Gennady M. Verkhivker:
Integrating Genetic and Structural Data on Human Protein Kinome in Network-Based Modeling of Kinase Sensitivities and Resistance to Targeted and Personalized Anticancer Drugs. 45-56 - Shefali S. Verma, Alex T. Frase, Anurag Verma, Sarah A. Pendergrass, Shaun Mahony, David W. Haas, Marylyn D. Ritchie:
Phenome-Wide Interaction Study (PheWIS) in Aids Clinical Trials Group Data (ACTG). 57-68 - Han Yu, Rachael Hageman Blair:
A Framework for Attribute-Based Community Detection with Applications to Integrated Functional Genomics. 69-80 - Marinka Zitnik, Blaz Zupan:
Collective Pairwise Classification for Multi-Way Analysis of Disease and Drug Data. 81-92
Innovative Approaches to Combining Genotype, Phenotype, Epigenetic, and Exposure Data for Precision Diagnostics
- Melissa A. Haendel, Maricel G. Kann, Nicole L. Washington:
Session Introduction. 93-95 - Logan Dumitrescu, Kirsten E. Diggins, Robert J. Goodloe, Dana C. Crawford:
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. 96-107 - Xiaoke Hao, Jingwen Yan, Xiaohui Yao, Shannon L. Risacher, Andrew J. Saykin, Daoqiang Zhang, Li Shen:
Diagnosis-Guided Method for Identifying Multi-Modality Neuroimaging Biomarkers Associated with Genetic Risk Factors in Alzheimer's Disease. 108-119 - Ting Hu, Weidong Zhang, Zhaozhi Fan, Guang Sun, Sergei Likhodi, Edward Randell, Guangju Zhai:
Metabolomics Differential Correlation Network Analysis of Osteoarthritis. 120-131 - Prashanti Manda, Christopher J. Mungall, James P. Balhoff, Hilmar Lapp, Todd J. Vision:
Investigating the Importance of Anatomical Homology for Cross-Species Phenotype Comparisons Using Semantic Similarity. 132-143 - Alejandro Schuler, Vincent X. Liu, Joe Wan, Alison Callahan, Madeleine Udell
, David E. Stark, Nigam H. Shah:
Discovering Patient Phenotypes Using Generalized Low Rank Models. 144-155 - Ortal Shnaps, Eyal Perry, Dana Silverbush, Roded Sharan:
Inference of Personalized Drug Targets via Network Propagation. 156-167 - Anurag Verma, Joseph B. Leader, Shefali S. Verma, Alex T. Frase, John R. Wallace, Scott M. Dudek, Daniel R. Lavage, Cristopher V. Van Hout, Frederick E. Dewey, John Penn, Alexander E. Lopez, John D. Overton, David J. Carey, David H. Ledbetter, H. Lester Kirchner, Marylyn D. Ritchie, Sarah A. Pendergrass:
Integrating Clinical Laboratory Measures and ICD-9 Code Diagnoses in Phenome-Wide Association Studies. 168-179
Mehtods to Enhance the Reproducibility of Precision Medicine
- Arjun K. Manrai, Chirag J. Patel, Nils Gehlenborg, Nicholas P. Tatonetti, John P. A. Ioannidis, Isaac S. Kohane:
Session Introduction. 180-182 - Benjamin J. Callahan, Diana Proctor, David A. Relman, Julia Fukuyama, Susan P. Holmes:
Reproducible Research Workflow in R for the Analysis of Personalized Human Microbiome Data. 183-194 - Jonathan H. Chen, Mary K. Goldstein, Steven M. Asch, Russ B. Altman:
Dynamically Evolving Clinical Practices and Implications for Predicting Medical Decisions. 195-206 - Amanda Koire, Panagiotis Katsonis, Olivier Lichtarge:
Repurposing Germline Exomes of the Cancer Genome Atlas Demands a Cautious Approach and Sample-Specific Variant Filtering. 207-218 - Handong Mao, Chunhua Weng:
Identification of Questionable Exclusion Criteria in Mental Disorder Clinical Trials Using a Medical Encyclopedia. 219-230 - Arjun K. Manrai, Brice L. Wang, Chirag J. Patel, Isaac S. Kohane:
Reproducible and Shareable Quantifications of Pathogenicity. 231-242
Precision Medicine: Data and Discovery for Improved Health and Therapy
- Alexander A. Morgan, Sean D. Mooney, Bruce J. Aronow, Steven E. Brenner:
Session Introduction. 243-248 - Anna Okula Basile, John R. Wallace, Peggy L. Peissig, Catherine A. McCarty, Murray H. Brilliant, Marylyn D. Ritchie:
Knowledge Driven Binning and PheWAS Analysis in Marshfield Personalized Medicine Research Project Using BioBin. 249-260 - Victor Bellon, Véronique Stoven, Chloé-Agathe Azencott:
Multitask Feature Selection with Task Descriptors. 261-272 - Elias Chaibub Neto, Brian M. Bot, Thanneer M. Perumal, Larsson Omberg, Justin Guinney, Mike Kellen, Arno Klein, Stephen H. Friend, Andrew D. Trister:
Personalized Hypothesis Tests for Detecting Medication Response in Parkinson Disease Patients Using iPhone Sensor Data. 273-284 - Jessica Cooke Bailey, Sarah Wilson, Kristin Brown-Gentry, Robert J. Goodloe, Dana C. Crawford:
Kidney Disease Genetics and the Importance of Diversity in Precision Medicine. 285-296 - Alex M. Fichtenholtz, Nicholas D. Camarda, Eric K. Neumann:
Predicting Significance of Unknown Variants in Glial Tumors Through Sub-Class Enrichment. 297-308 - Nophar Geifman, Atul J. Butte:
Do Cancer Clinical Trial Populations Truly Represent Cancer Patients? A Comparison of Open Clinical Trials to the Cancer Genome Atlas. 309-320 - Vladimir Gligorijevic, Noël Malod-Dognin, Natasa Przulj:
Patient-Specific Data Fusion for Cancer Stratification and Personalised Treatment. 321-332 - Maulik R. Kamdar, Michelle J. Wu:
PRISM: A Data-Driven Platform for Monitoring Mental Health. 333-344 - Sahand Khakabimamaghani, Martin Ester:
Bayesian Biclustering for Patient Stratification. 345-356 - Dokyoon Kim, Anastasia Lucas, Joseph Glessner, Shefali S. Verma, Yukiko Bradford, Ruowang Li, Alex T. Frase, Hakon Hakonarson, Peggy L. Peissig, Murray H. Brilliant, Marylyn D. Ritchie:
Biofilter as a Functional Annotation Pipeline for Common and Rare Copy Number Burden. 357-368 - Sarah M. Laper, Nicole A. Restrepo, Dana C. Crawford:
The Challenges in Using Electronic Health Records for Pharmacogenomics and Precision Medicine Research. 369-380 - Yong Fuga Li, Fuxiao Xin, Russ B. Altman:
Separating the Causes and Consequences in Disease Transcriptome. 381-392 - Subhajit Sengupta, Tianjian Zhou, Peter Müller, Yuan Ji:
A Bayesian Nonparametric Model for Reconstructing Tumor Subclones Based on Mutation Pairs. 393-404 - Artem Sokolov, Evan O. Paull, Joshua M. Stuart:
One-Class Detection of Cell States in Tumor Subtypes. 405-416 - Nattaphon Thanintorn, Juexin Wang, Ilker Ersoy, Zainab Al-Taie, Yuexu Jiang, Duolin Wang, Megha Verma, Trupti Joshi, Richard D. Hammer, Dong Xu, Dmitriy Shin:
RDF Sketch Maps - Knowledge Complexity Reduction for Precision Medicine Analytics. 417-428
Regulatory RNA
- Drena Dobbs, Steven E. Brenner, Vasant G. Honavar, Robert L. Jernigan, Alain Laederach, Quaid Morris:
Session Introduction. 429-432 - Wanja Kassuhn, Uwe Ohler, Philipp Drewe:
Cseq-Simulator: A Data Simulator for CLIP-Seq Experiments. 433-444 - Usha Muppirala, Benjamin A. Lewis, Carla M. Mann, Drena Dobbs:
A Motif-Based Method for Predicting Interfacial Residues in Both the RNA and Protein Components of Protein-RNA Complexes. 445-455 - Lourdes Peña Castillo, Marc Gruell, Martin E. Mulligan, Andrew S. Lang:
Detection of Bacterial Small Transcripts from RNA-Seq Data: A Comparative Assessment. 456-467
Social Media Mining for Public Health Monitoring and Surveillance
- Michael J. Paul, Abeed Sarker, John S. Brownstein, Azadeh Nikfarjam, Matthew Scotch, Karen L. Smith, Graciela Gonzalez-Hernandez:
Session Introduction. 468-479 - Yin Aphinyanaphongs, Armine Lulejian, Duncan Penfold-Brown, Richard Bonneau, Paul Krebs:
Text Classification for Automatic Detection of E-Cigarette Use and Use for Smoking Cessation from Twitter: A Feasibility Pilot. 480-491 - Rion Brattig Correia, Lang Li, Luis M. Rocha:
Monitoring Potential Drug Interactions and Reactions via Network Analysis of Instagram User Timelines. 492-503 - Bahadorreza Ofoghi, Meghan Mann, Karin Verspoor:
Towards Early Discovery of Salient Health Threats: A Social Media Emotion Classification Technique. 504-515 - H. Andrew Schwartz, Maarten Sap, Margaret L. Kern, Johannes C. Eichstaedt, Adam Kapelner, Megha Agrawal, Eduardo Blanco, Lukasz Dziurzynski, Gregory J. Park, David Stillwell, Michal Kosinski, Martin E. P. Seligman, Lyle H. Ungar:
Predicting Individual Well-Being Through the Language of Social Media. 516-527 - Ryan Sullivan, Abeed Sarker, Karen O'Connor, Amanda Goodin, Mark Karlsrud, Graciela Gonzalez:
Finding Potentially Unsafe Nutritional Supplements from User Reviews with Topic Modeling. 528-539 - Ingmar Weber, Palakorn Achananuparp:
Insights from Machine-Learned Diet Success Prediction. 540-551
Workshops
- Jessica D. Tenenbaum, Subha Madhavan, Robert R. Freimuth, Joshua C. Denny, Lewis J. Frey:
Translational Bioinformatics 101. 552-556 - Casey S. Greene, James A. Foster, Bruce A. Stanton, Deborah A. Hogan, Yana Bromberg:
Computational Approaches to Study Microbes and Microbiomes. 557-565 - Steven E. Brenner, Stephen Kingsmore, Sean D. Mooney, Robert Nussbaum, Jennifer Puck:
Use of Genome Data in Newborns as a Starting Point for Life-Long Precision Medicine. 568-575 - Eric K. Neumann, Svetlana Lockwood, Bala Krishnamoorthy, David I. Spivak:
Workshop on Topology and Abstract Algebra for Biomedicine. 576-580 - Abeed Sarker, Azadeh Nikfarjam, Graciela Gonzalez-Hernandez:
Social Media Mining Shared Task Workshop. 581-592
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