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)

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)

The Integration of Biological Pathway Knowledge in Cancer Genomics: A review of existing computational approaches. - Vinay Varadan; Prateek Mittal; Charles J. Vaske; Stephen C. Benz (IEEE Signal Process. Mag., 2012)

Learning subgroup-specific regulatory interactions and regulator independence with PARADIGM. - Andrew J. Sedgewick; Stephen C. Benz; Shahrooz Rabizadeh; Patrick Soon-Shiong; Charles J. Vaske (Bioinform., 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)