Joshua M. Stuart

Mary Goldman, Brian Craft, Teresa Swatloski, Kyle Ellrott, Melissa S. Cline, Mark Diekhans, Singer Ma, Chris Wilks, Joshua M. Stuart, David Haussler, Jingchun Zhu: The UCSC Cancer Genomics Browser: update 2013. Nucleic Acids Research 41(Database-Issue): 949-954 (2013)

Sam Ng, Eric A. Collisson, Artem Sokolov, Theodore Goldstein, Abel Gonzalez-Perez, Nuria Lopez-Bigas, Christopher Benz, David Haussler, Joshua M. Stuart: PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis. Bioinformatics 28(18): 640-646 (2012)

J. Zachary Sanborn, Stephen C. Benz, Brian Craft, Christopher Szeto, Kord M. Kober, Laurence R. Meyer, Charles J. Vaske, Mary Goldman, Kayla E. Smith, Robert M. Kuhn, Donna Karolchik, W. James Kent, Joshua M. Stuart, David Haussler, Jingchun Zhu: The UCSC cancer genomics browser: update 2011. Nucleic Acids Research 39(Database-Issue): 951-959 (2011)

Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, Joshua M. Stuart: Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics [ISMB] 26(12): 237-245 (2010)

Martina Koeva, E. Camilla Forsberg, Joshua M. Stuart: Core stemness mechanisms revealed through homology. BMC Bioinformatics 10(S-13): 0 (2009)

Charles J. Vaske, Carrie House, Truong Luu, Bryan Frank, Chen-Hsiang Yeang, Norman H. Lee, Joshua M. Stuart: A Factor Graph Nested Effects Model To Identify Networks from Genetic Perturbations. PLoS Computational Biology 5(1) (2009)

P. N. Kanabar, Charles J. Vaske, Chen-Hsiang Yeang, F. H. Yildiz, Joshua M. Stuart: Inferring Disease-Related Pathways Using A Probabilistic Epistasis Model. Pacific Symposium on Biocomputing 2009: 480-491

Matthew T. Weirauch, Christopher K. Wong, Alexandra B. Byrne, Joshua M. Stuart: Information-based methods for predicting gene function from systematic gene knock-downs. BMC Bioinformatics 9 (2008)

Nathan Salomonis, Kristina Hanspers, Alexander C. Zambon, Karen Vranizan, Steven C. Lawlor, Kam D. Dahlquist, Scott Doniger, Joshua M. Stuart, Bruce R. Conklin, Alexander R. Pico: GenMAPP 2: new features and resources for pathway analysis. BMC Bioinformatics 8 (2007)

Zhenjun Hu, David M. Ng, Takuji Yamada, Chunnuan Chen, Shuichi Kawashima, Joe Mellor, Bolan Linghu, Minoru Kanehisa, Joshua M. Stuart, Charles DeLisi: VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Research 35(Web-Server-Issue): 625-632 (2007)

David M. Ng, Marcos H. Woehrmann, Joshua M. Stuart: Recommending Pathway Genes Using a Compendium of Clustering Solutions. Pacific Symposium on Biocomputing 2007: 379-390

Corey Powell, Joshua M. Stuart: A Novel Quartet-Based Method for Phylogenetic Inference. CSB Workshops 2005: 59-60

Corey Powell, Joshua M. Stuart: Biological Pathway Prediction from Multiple Data Sources Using Iterative Bayesian Updating. CSB Workshops 2005: 159-160

Matthew T. Weirauch, Joshua M. Stuart: Discovering Functional Transcription Factor Binding from Superimposed Gene Networks. CSB Workshops 2005: 178-179

Micheal Hewett, Diane E. Oliver, Daniel L. Rubin, Katrina L. Easton, Joshua M. Stuart, Russ B. Altman, Teri E. Klein: PharmGKB: the Pharmacogenetics Knowledge Base. Nucleic Acids Research 30(1): 163-165 (2002)

Diane E. Oliver, Daniel L. Rubin, Joshua M. Stuart, Micheal Hewett, Teri E. Klein, Russ B. Altman: Ontology Development for a Pharmacogenetics Knowledge Base. Pacific Symposium on Biocomputing 2002: 65-76

Soumya Raychaudhuri, Joshua M. Stuart, Xuemin Liu, Peter M. Small, Russ B. Altman: Pattern Recognition of Genomic Features with Microarrays: Site Typing of Mycobacterium Tuberculosis Strains. ISMB 2000: 286-295

Joshua M. Stuart, Elizabeth Bradley: Learning the Grammar of Dance. ICML 1998: 547-555