NetPhosYeast: prediction of protein phosphorylation sites in yeast. - Christian R. Ingrell; Martin L. Miller; Ole Nørregaard Jensen; Nikolaj Blom (Bioinform., 2007)

Perturbation Biology: Inferring Signaling Networks in Cellular Systems. - Evan J. Molinelli; Anil Korkut; Weiqing Wang; Martin L. Miller; Nicholas Paul Gauthier; Xiaohong Jing; Poorvi Kaushik; Qin He; Gordon B. Mills; David B. Solit; Christine A. Pratilas; Martin Weigt; et al. (PLoS Comput. Biol., 2013)

MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer. - Nicholas Paul Gauthier; Ed Reznik; Jianjiong Gao; Selçuk Onur Sümer; Nikolaus Schultz; Chris Sander; Martin L. Miller (Nucleic Acids Res., 2016)