A Multi-Scale Approach to Modeling E. coli Chemotaxis. - Eran Agmon; Ryan K. Spangler (Entropy, 2020)

Vivarium: an interface and engine for integrative multiscale modeling in computational biology. - Eran Agmon; Ryan K. Spangler; Christopher J. Skalnik; William Poole; Shayn M. Peirce; Jerry H. Morrison; Markus W. Covert (Bioinform., 2022)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (CoRR, 2022)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (Nucleic Acids Res., 2022)

Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in antibiotic responses. - Christopher J. Skalnik; Sean Y. Cheah; Mica Y. Yang; Mattheus B. Wolff; Ryan K. Spangler; Lee Talman; Jerry H. Morrison; Shayn M. Peirce; Eran Agmon; Markus W. Covert (PLoS Comput. Biol., 2023)