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

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

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

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

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

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

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

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

GenMAPP 2: new features and resources for pathway analysis. - 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 (BMC Bioinform., 2007)

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

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

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

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

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

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

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

The UCSC cancer genomics browser: update 2011. - 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; et al. (Nucleic Acids Res., 2011)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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