Simulation of large-scale rule-based models. - Joshua Colvin; Michael I. Monine; James R. Faeder; William S. Hlavacek; Daniel D. Von Hoff; Richard G. Posner (Bioinform., 2009)

Clustering Context-Specific Gene Regulatory Networks. - Archana Ramesh; Robert P. Trevino; Daniel D. Von Hoff; Seungchan Kim (Pacific Symposium on Biocomputing, 2010)

RuleMonkey: software for stochastic simulation of rule-based models. - Joshua Colvin; Michael I. Monine; Ryan N. Gutenkunst; William S. Hlavacek; Daniel D. Von Hoff; Richard G. Posner (BMC Bioinform., 2010)

Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling. - Matthew S. Creamer; Edward C. Stites; Meraj Aziz; James A. Cahill; Chin Wee Tan; Michael E. Berens; Haiyong Han; Kimberly J. Bussey; Daniel D. Von Hoff; William S. Hlavacek; Richard G. Posner (BMC Syst. Biol., 2012)