Discovering Regulated Networks During HIV-1 Latency and Reactivation. - Sourav Bandyopadhyay; Ryan M. Kelley; Trey Ideker (Pacific Symposium on Biocomputing, 2006)

Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood. - Ryan M. Kelley; Hoda Feizi; Trey Ideker (Bioinform., 2008)

Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data. - Sourav Bandyopadhyay; Ryan M. Kelley; Nevan J. Krogan; Trey Ideker (PLoS Comput. Biol., 2008)