Compartmental Rule-based Modeling of Biochemical Systems. - Leonard A. Harris; Justin S. Hogg; James R. Faeder (WSC, 2009)

Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems. - Justin S. Hogg; Leonard A. Harris; Lori J. Stover; Niketh S. Nair; James R. Faeder (PLoS Comput. Biol., 2014)

Energy-based modeling in BioNetGen. - John A. P. Sekar; Justin S. Hogg; James R. Faeder (BIBM, 2016)

BioNetGen 2.2: advances in rule-based modeling. - Leonard A. Harris; Justin S. Hogg; José Juan Tapia; John A. P. Sekar; Sanjana Gupta; Ilya Korsunsky; Arshi Arora; Dipak Barua; Robert P. Sheehan; James R. Faeder (Bioinform., 2016)

Evaluation of Parallel Tempering to Accelerate Bayesian Parameter Estimation in Systems Biology. - Sanjana Gupta; Liam Hainsworth; Justin S. Hogg; Robin Lee; James R. Faeder (PDP, 2018)