Machines vs. Ensembles: Effective MAPK Signaling through Heterogeneous Sets of Protein Complexes. - Ryan Suderman; Eric J. Deeds (PLoS Comput. Biol., 2013)

TRuML: A Translator for Rule-Based Modeling Languages. - Ryan Suderman; William S. Hlavacek (BCB, 2017)

Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor. - Keesha E. Erickson; Oleksii S. Rukhlenko; MD Shahinuzzaman; Kalina P. Slavkova; Yen Ting Lin; Ryan Suderman; Edward C. Stites; Marian Anghel; Richard G. Posner; Dipak Barua; Boris N. Kholodenko; William S. Hlavacek (PLoS Comput. Biol., 2019)