Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs. - John C. Obenauer; Lewis C. Cantley; Michael B. Yaffe (Nucleic Acids Res., 2003)

NetworKIN: a resource for exploring cellular phosphorylation networks. - Rune Linding; Lars Juhl Jensen; Adrian Pasculescu; Marina Olhovsky; Karen Colwill; Peer Bork; Michael B. Yaffe; Tony Pawson (Nucleic Acids Res., 2008)

MCAM: Multiple Clustering Analysis Methodology for Deriving Hypotheses and Insights from High-Throughput Proteomic Datasets. - Kristen M. Naegle; Roy E. Welsch; Michael B. Yaffe; Forest M. White; Douglas A. Lauffenburger (PLoS Comput. Biol., 2011)