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)

Automated visualization of rule-based models. - John A. P. Sekar; José Juan Tapia; James R. Faeder (PLoS Comput. Biol., 2017)

Structured spreadsheets with ObjTables enable data reuse and integration. - Jonathan R. Karr; Wolfram Liebermeister; Arthur P. Goldberg; John A. P. Sekar; Bilal Shaikh (CoRR, 2020)

Exact Parallelization of the Stochastic Simulation Algorithm for Scalable Simulation of Large Biochemical Networks. - Arthur P. Goldberg; John A. P. Sekar; Jonathan R. Karr (CoRR, 2020)