ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists. - Tomás Helikar; Jim A. Rogers (BMC Syst. Biol., 2009)

The Cell Collective: Toward an open and collaborative approach to systems biology. - Tomás Helikar; Bryan M. Kowal; Sean McClenathan; Mitchell Bruckner; Thaine W. Rowley; Alex Madrahimov; Benjamin Wicks; Manish Shrestha; Kahani Limbu; Jim A. Rogers (BMC Syst. Biol., 2012)

Sensitivity analysis of biological Boolean networks using information fusion based on nonadditive set functions. - Naomi Kochi; Tomás Helikar; Laura Allen; Jim A. Rogers; Zhenyuan Wang; Mihaela Teodora Matache (BMC Syst. Biol., 2014)

Integrating Interactive Computational Modeling in Biology Curricula. - Tomás Helikar; Christine E. Cutucache; Lauren M. Dahlquist; Tyler A. Herek; Joshua J. Larson; Jim A. Rogers (PLoS Comput. Biol., 2015)

Boolean network topologies and the determinative power of nodes. - Bronson W. Wacker; Mihaela T. Velcsov; Jim A. Rogers (J. Complex Networks, 2020)