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ORCID20. PSB 2015: Kohala Coast, Hawaii, USA
- Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein, Marylyn D. Ritchie:
Biocomputing 2015: Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA, January 4-8, 2015. 2015 - Darla Hewett, Michelle Whirl Carrillo, Lawrence E. Hunter, Russ B. Altman, Teri E. Klein:
A Twentieth Anniversary Tribute to PSB. 1-7
Cancer Panomics: Computational Methods and Infrastructure for Integrative Analysis of Cancer High-throughput "OMICS" Data
- Søren Brunak, Francisco M. de la Vega, Adam A. Margolin, Benjamin J. Raphael, Gunnar Rätsch, Joshua M. Stuart:
Session Introduction. 8-9 - Keith A. Ching, Kai Wang, Zhengyan Kan, Julio Fernández, Wenyan Zhong, Jarek Kostrowicki, Tao Xie, Zhou Zhu, Jean-François Martin, Maria Koehler, Kim Arndt, Paul A. Rejto:
Cell Index Database (CELLX): A Web Tool for Cancer Precision Medicine. 10-19 - Amit G. Deshwar, Shankar Vembu, Quaid Morris:
Comparing Nonparametric Bayesian Tree Priors for Clonal Reconstruction of Tumors. 20-31 - In Sock Jang, Rodrigo Dienstmann, Adam A. Margolin, Justin Guinney:
Stepwise Group Sparse Regression (SGSR): Gene-Set-Based Pharmacogenomic Predictive Models with Stepwise Selection of Functional Priors. 32-43 - Kjong-Van Lehmann, André Kahles, Cyriac Kandoth, William Lee, Nikolaus Schultz, Oliver Stegle, Gunnar Rätsch:
Integrative Genome-wide Analysis of the Determinants of RNA Splicing in Kidney Renal Clear Cell Carcinoma. 44-55 - Sara Nasser, Ahmet A. Kurdolgu, Tyler Izatt, Jessica Aldrich, Megan L. Russell, Alexis Christoforides, Waibhav Tembe, Jeffery A. Keifer, 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:
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. 56-67 - Menghua Wu, Marina Sirota, Atul J. Butte, Bin Chen:
Characteristics of Drug Combination Therapy in Oncology by Analyzing Clinical Trial Data on Clinicaltrials.Gov. 68-79
Cancer Pathways: Automatic Extraction, Representation, and Reasoning in the "Big Data" Era
- Graciela Gonzalez, Chitta Baral, Jeff Kiefer, Suengchan Kim, Jieping Ye:
Session Introduction. 80-83 - Billur Engin, Matan Hofree, Hannah Carter:
Identifying Mutation Specific Cancer Pathways Using a Structurally Resolved Protein Interaction Network. 84-95 - Dokyoon Kim, Ruowang Li, Scott M. Dudek, John R. Wallace, Marylyn D. Ritchie:
Binning Somatic Mutations Based on Biological Knowledge for Predicting Survival: An Application in Renal Cell Carcinoma. 96-107 - Svetlana Lockwood, Bala Krishnamoorthy:
Topological Features in Cancer Gene Expression Data>. 108-119 - Hoifung Poon, Kristina Toutanova, Chris Quirk:
Distant Supervision for Cancer Pathway Extraction from Text. 120-131 - Jie Tan, Matthew Ung, Chao Cheng, Casey S. Greene:
Unsupervised Feature Construction and Knowledge Extraction from Genome-Wide Assays of Breast Cancer with Denoising Autoencoders. 132-143 - Tao Yang, Xinlin Zhao, Binbin Lin, Tao Zeng, Shuiwang Ji, Jieping Ye:
Automated Gene Expression Pattern Annotation in the Mouse Brain. 144-155
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
- Molly A. Hall, Shefali S. Verma, Dennis P. Wall, Jason H. Moore, Brendan Keating, Daniel B. Campbell, Gregory Gibson, Folkert W. Asselbergs, Sarah A. Pendergrass:
Session Introduction. 156-160 - Dana C. Crawford, Kristin Brown-Gentry, Mark J. Rieder:
Measures of Exposure Impact Genetic Association Studies: An Example in Vitamin K Levels and VKORC1. 161-170 - Christian Darabos, Emily D. Grussing, Maria E. Cricco, Kenzie A. Clark, Jason H. Moore:
A Bipartite Network Approach to Inferring Interactions Between Environmental Exposures and Human Diseases. 171-182 - Emily Rose Holzinger, Silke Szymczak, Abhijit Dasgupta, James D. Malley, Qing Li, Joan E. Bailey-Wilson:
Variable Selection Method for the Identification of Epistatic Models. 195-206 - Ting Hu, Christian Darabos, Maria E. Cricco, Emily Kong, Jason H. Moore:
Genome-Wide Genetic Interaction Analysis of Glaucoma Using Expert Knowledge Derived from Human Phenotype Networks. 207-218 - Janina M. Jeff, Kristin Brown-Gentry, Dana C. Crawford:
Identification of Gene-Gene and Gene-Environment Interactions Within the Fibrinogen Gene Cluster for Fibrinogen Levels in Three Ethnically Diverse Populations. 219-230 - Chirag J. Patel, Arjun K. Manrai:
Development of Exposome Correlations Globes to Map Out Environment-Wide Associations. 231-242 - Nicole A. Restrepo, Sabrina L. Mitchell, Robert J. Goodloe, Deborah G. Murdock, Jonathan L. Haines, Dana C. Crawford:
Mitochondrial Variation and the Risk of Age-Related Macular Degeneration Across Diverse Populations. 243-254 - Lili Wang, Parvin Mousavi, Sergio Baranzini:
iPINBPA: An Integrative Network-Based Functional Module Discovery Tool for Genome-Wide Association Studies. 255-266
Crowdsourcing and Mining Crowd Data
- Robert Leaman, Benjamin M. Good, Andrew I. Su, Zhiyong Lu:
Session Introduction. 267-269 - Jean Binder, Stéphanie Boué, Anselmo Di Fabio, Brett Fields, William Hayes, Julia Hoeng, Jennifer Park, Manuel C. Peitsch:
Reputation-Based Collaborative Network Biology. 270-281 - Benjamin M. Good, Max Nanis, Chunlei Wu, Andrew I. Su:
Microtask Crowdsourcing for Disease Mention Annotation in PubMed Abstracts. 282-293 - David J. Odgers, Rave Harpaz, Alison Callahan, Gregor Stiglic, Nigam H. Shah:
Analyzing Search Behavior of Healthcare Professionals for Drug Safety Surveillance. 306-317 - Öznur Tastan, Yanjun Qi, Jaime G. Carbonell, Judith Klein-Seetharaman:
Refining Literature Curated Protein Interactions Using Expert Opinions. 318-329 - Jérôme Waldispühl, Arthur Kam, Paul P. Gardner:
Crowdsourcing RNA Structural Alignments with an Online Computer Game. 330-341
Personalized Medicine: From Genotypes, Molecular Phenotypes and Phenotypes and the Quantified Self, Towards Improved Medicine
- Joel T. Dudley, Jennifer Listgarten, Oliver Stegle, Steven E. Brenner, Leopold Parts:
Session introduction. 342-346 - Inanç Birol, Anthony Raymond, Readman Chiu, Ka Ming Nip, Shaun D. Jackman, Maayan Kreitzman, T. Roderick Docking, Catherine A. Ennis, A. Gordon Robertson, Aly Karsan:
KLEAT: Cleavage Site Analysis of Transcriptomes. 347-358 - Rui Chang, Jonathan R. Karr, Eric E. Schadt:
Causal Inference in Biology Networks with Integrated Belief Propagation. 359-370 - James Diggans, Su Yeon Kim, Zhanzhi Hu, Daniel G. Pankratz, Mei G. Wong, Jessica Reynolds, Ed Y. Tom, Moraima Pagan, Robert J. Monroe, Juan Rosai, Virginia A. Livolsi, Richard B. Lanman, Richard T. Kloos, P. Sean Walsh, Giulia C. Kennedy:
Machine Learning from Concept to Clinic: Reliable Detection of BRAF V600E DNA Mutations in Thyroid Nodules Using High-Dimensional RNA Expression Data. 371-382 - Hua Fan-Minogue, Bin Chen, Weronika Sikora-Wohlfeld, Marina Sirota, Atul J. Butte:
A Systematic Assessment of Linking Gene Expression with Genetic Variants for Prioritizing Candidate Targets. 383-394 - Tianxiang Gao, Petter Brodin, Mark M. Davis, Vladimir Jojic:
Drug-induced mRNA Signatures Are Enriched for the Minority of Genes that Are Highly Heritable. 395-406 - Benjamin S. Glicksberg, Li Li, Wei-Yi Cheng, Khader Shameer, Jörg Hakenberg, Rafael Castellanos, Meng Ma, Lisong Shi, Hardik Shah, Joel T. Dudley, Rong Chen:
An Integrative Pipeline for Multi-Modal Discovery of Disease Relationships. 407-418 - Michael A. Hinterberg, David P. Kao, Michael R. Bristow, Lawrence E. Hunter, J. David Port, Carsten Görg:
PEAX: Interactive Visual Analysis and Exploration of Complex Clinical Phenotype and Gene Expression Association. 419-430 - Grace T. Huang, Ioannis Tsamardinos, Vineet K. Raghu, Naftali Kaminski, Panayiotis V. Benos:
T-ReCS: Stable Selection of Dynamically Formed Groups of Features with Application to Prediction of Clinical Outcomes. 431-442 - Sumit B. Makashir, Leah C. Kottyan, Matthew T. Weirauch:
Meta-Analysis of Differential Gene Co-Expression: Application to Lupus. 443-454 - Zhi Nie, Tao Yang, Yashu Liu, Binbin Lin, Qingyang Li, Vaibhav A. Narayan, Gayle M. Wittenberg, Jieping Ye:
Melancholic Depression Prediction by Identifying Representative Features in Metabolic and Microarray Profiles with Missing Values. 455-466 - Subhajit Sengupta, Jing Wang, Juhee Lee, Peter Müller, Kamalakar Gulukota, Arunava Banerjee, Yuan Ji:
BayClone: Bayesian Nonparametric Inference of Tumor Subclones Using NGS Data. 467-478
Workshops
- James M. Sikela:
Human Evolutionary Genomics and the Search for the Genes that Made Us Human. 479-481 - Vasant G. Honavar:
Discovery Informatics in Biological and Biomedical Sciences: Research Challenges and Opportunities. 482 - Richard Gayle, Mark E. Minie, Erik J. Nilsson:
Inviting the Public: The Impact on Informatics Arising from Emerging Global Health Research Paradigms. 483-487 - Kristine A. Pattin, Anna C. Greene, Russ B. Altman, Kevin Bretonnel Cohen, Elizabeth Wethington, Carsten Görg, Lawrence E. Hunter, Spencer V. Muse, Predrag Radivojac, Jason H. Moore:
Training the Next Generation of Quantitative Biologists in the Era of Big Data. 488-492
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