Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. - Sorin Draghici; Purvesh Khatri; Pratik Bhavsar; Abhik Shah; Stephen A. Krawetz; Michael A. Tainsky (Nucleic Acids Res., 2003)

Using mechanistic Bayesian networks to identify downstream targets of the Sonic Hedgehog pathway. - Abhik Shah; Toyoaki Tenzen; Andrew P. McMahon; Peter J. Woolf (BMC Bioinform., 2009)

Python Environment for Bayesian Learning: Inferring the Structure of Bayesian Networks from Knowledge and Data. - Abhik Shah; Peter J. Woolf (J. Mach. Learn. Res., 2009)