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)

GetBonNie for building, analyzing and sharing rule-based models. - Bin Hu 025; G. Matthew Fricke; James R. Faeder; Richard G. Posner; William S. Hlavacek (Bioinform., 2009)

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)

BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments. - Brandon R. Thomas; Lily A. Chylek; Joshua Colvin; Suman Sirimulla; Andrew H. A. Clayton; William S. Hlavacek; Richard G. Posner (Bioinform., 2016)

AutoDock VinaXB: implementation of XBSF, new empirical halogen bond scoring function, into AutoDock Vina. - Mathew R. Koebel; Grant Schmadeke; Richard G. Posner; Suman Sirimulla (J. Cheminformatics, 2016)

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)

Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit. - Jacob Neumann; Yen Ting Lin; Abhishek Mallela; Ely F. Miller; Joshua Colvin; Abell T. Duprat; Ye Chen; William S. Hlavacek; Richard G. Posner (Bioinform., 2022)