The p53HMM algorithm: using profile hidden markov models to detect p53-responsive genes. - Todd Riley; Xin Yu; Eduardo D. Sontag; Arnold Levine (BMC Bioinform., 2009)

ModEx: A text mining system for extracting mode of regulation of transcription factor-gene regulatory interaction. - Saman Farahmand; Todd Riley; Kourosh Zarringhalam (J. Biomed. Informatics, 2020)