TCGA Kidney Cancers. - Weinstein, John N.; Collisson, Eric A.; Mills, Gordon B.; Shaw, Kenna R. Mills; Ozenberger, Brad A.; Ellrott, Kyle; Shmulevich, Ilya; Sander, Chris; Stuart, Joshua M. (UCI Machine Learning Repository, 2023)

Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge. - Uzunangelov, Vladislav; Wong, Christopher K.; Stuart, Joshua M. (PLoS Comput. Biol., 2021)

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. - Rheinbay, Esther; Nielsen, Morten Muhlig; Abascal, Federico; Wala, Jeremiah; Shapira, Ofer; Tiao, Grace; Hornshøj, Henrik; Hess, Julian M.; Juul, Randi Istrup; Lin, Ziao; Feuerbach, Lars; Sabarinathan, Radhakrishnan; et al. (Nat., 2020)

Using Transcriptional Signatures to Find Cancer Drivers with LURE. - Haan, David; Tao, Ruikang; Friedl, Verena; Anastopoulos, Ioannis N.; Wong, Christopher K.; Weinstein, Alana S.; Stuart, Joshua M. (2020)

PLATYPUS: A Multiple-View Learning Predictive Framework for Cancer Drug Sensitivity Prediction. - Graim, Kiley; Friedl, Verena; Houlahan, Kathleen E.; Stuart, Joshua M. (2019)

Germline contamination and leakage in whole genome somatic single nucleotide variant detection. - Sendorek, Dorota H.; Caloian, Cristian; Ellrott, Kyle; Bare, J. Christopher; Yamaguchi, Takafumi N.; Ewing, Adam D.; Houlahan, Kathleen E.; Norman, Thea C.; Margolin, Adam A.; Stuart, Joshua M.; Boutros, Paul C. (BMC Bioinform., 2018)

Valection: design optimization for validation and verification studies. - Cooper, Christopher I; Yao, Delia; Sendorek, Dorota H.; Yamaguchi, Takafumi N.; P'ng, Christine; Houlahan, Kathleen E.; Caloian, Cristian; Fraser, Michael; Ellrott, Kyle; Margolin, Adam A.; Bristow, Robert G.; Stuart, Joshua M.; et al. (BMC Bioinform., 2018)

Tracing Co-Regulatory Network Dynamics in Noisy, Single-Cell Transcriptome Trajectories. - Cordero, Pablo; Stuart, Joshua M. (2017)

Pathway-Based Genomics Prediction using Generalized Elastic Net. - Sokolov, Artem; Carlin, Daniel E.; Paull, Evan O.; Baertsch, Robert; Stuart, Joshua M. (PLoS Comput. Biol., 2016)

One-Class Detection of Cell States in Tumor Subtypes. - Sokolov, Artem; Paull, Evan O.; Stuart, Joshua M. (2016)

The NIH BD2K center for big data in translational genomics. - Paten, Benedict; Diekhans, Mark; Druker, Brian J.; Friend, Stephen H.; Guinney, Justin; Gassner, Nadine; Guttman, Mitchell; Kent, W. James; Mantey, Patrick; Margolin, Adam A.; Massie, Matt; Novak, Adam M.; et al. (J. Am. Medical Informatics Assoc., 2015)

Session Introduction. - Brunak, Søren; Vega, Francisco M. de la; Margolin, Adam A.; Raphael, Benjamin J.; Rätsch, Gunnar; Stuart, Joshua M. (2015)

Session Introduction. - Brunak, Søren; Vega, Francisco M. de la; Rätsch, Gunnar; Stuart, Joshua M. (2014)

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE). - Paull, Evan O.; Carlin, Daniel E.; Niepel, Mario; Sorger, Peter K.; Haussler, David; Stuart, Joshua M. (Bioinform., 2013)

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

The UCSC Interaction Browser: multidimensional data views in pathway context. - Wong, Christopher K.; Vaske, Charles J.; Ng, Sam; Sanborn, J. Zachary; Benz, Stephen C.; Haussler, David; Stuart, Joshua M. (Nucleic Acids Res., 2013)

Session Introduction. - Karchin, Rachel; Ochs, Michael F.; Stuart, Joshua M.; Ideker, Trey; Bader, Joel S. (2013)

PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis. - Ng, Sam; Collisson, Eric A.; Sokolov, Artem; Goldstein, Theodore; Gonzalez-Perez, Abel; López-Bigas, Núria; Benz, Christopher; Haussler, David; Stuart, Joshua M. (Bioinform., 2012)

Session Introduction. - Karchin, Rachel; Ochs, Michael F.; Stuart, Joshua M.; Bader, Joel S. (2012)

The UCSC cancer genomics browser: update 2011. - Sanborn, J. Zachary; Benz, Stephen C.; Craft, Brian; Szeto, Christopher; Kober, Kord M.; Meyer, Laurence R.; Vaske, Charles J.; Goldman, Mary; Smith, Kayla E.; Kuhn, Robert M.; Karolchik, Donna; Kent, W. James; et al. (Nucleic Acids Res., 2011)

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. - Vaske, Charles J.; Benz, Stephen C.; Sanborn, J. Zachary; Earl, Dent; Szeto, Christopher; Zhu, Jingchun; Haussler, David; Stuart, Joshua M. (Bioinform., 2010)

Core stemness mechanisms revealed through homology. - Koeva, Martina; Forsberg, E. Camilla; Stuart, Joshua M. (BMC Bioinform., 2009)

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

Inferring Disease-Related Pathways Using A Probabilistic Epistasis Model. - Kanabar, Pinal N.; Vaske, Charles J.; Yeang, Chen-Hsiang; Yildiz, Fitnat H.; Stuart, Joshua M. (2009)

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

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

A search engine to identify pathway genes from expression data on multiple organisms. - Chen, Chunnuan; Weirauch, Matthew T.; Powell, Corey; Zambon, Alexander C.; Stuart, Joshua M. (BMC Syst. Biol., 2007)

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

Recommending Pathway Genes Using a Compendium of Clustering Solutions. - Ng, David M.; Woehrmann, Marcos H.; Stuart, Joshua M. (2007)

A Novel Quartet-Based Method for Phylogenetic Inference. - Powell, Corey; Stuart, Joshua M. (2005)

Biological Pathway Prediction from Multiple Data Sources Using Iterative Bayesian Updating. - Powell, Corey; Stuart, Joshua M. (2005)

Discovering Functional Transcription Factor Binding from Superimposed Gene Networks. - Weirauch, Matthew T.; Stuart, Joshua M. (2005)

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

Ontology Development for a Pharmacogenetics Knowledge Base. - Oliver, Diane E.; Rubin, Daniel L.; Stuart, Joshua M.; Hewett, Micheal; Klein, Teri E.; Altman, Russ B. (2002)

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

Learning the Grammar of Dance. - Stuart, Joshua M.; Bradley, Elizabeth (1998)