The Yeast Resource Center Public Data Repository. - Michael Riffle; Lars Malmström; Trisha N. Davis (Nucleic Acids Res., 2005)

Transmembrane Topology and Signal Peptide Prediction Using Dynamic Bayesian Networks. - Sheila M. Reynolds; Lukas Käll; Michael Riffle; Jeff A. Bilmes; William Stafford Noble (PLoS Comput. Biol., 2008)

Large-scale prediction of protein-protein interactions from structures. - Martial Hue; Michael Riffle; Jean-Philippe Vert; William Stafford Noble (BMC Bioinform., 2010)

The Yeast Resource Center Public Image Repository: A large database of fluorescence microscopy images. - Michael Riffle; Trisha N. Davis (BMC Bioinform., 2010)

JobCenter: an open source, cross-platform, and distributed job queue management system optimized for scalability and versatility. - Daniel Jaschob; Michael Riffle (Source Code Biol. Medicine, 2012)