Selected Publications

  1. Skalnik, C.J., Cheah, S.Y., Yang, M.Y., Wolff, M.B., Spangler, R.K., Talman, L., Morrison, J.H., Peirce, S.M., Agmon, E., and Covert, M.W. (2023). Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in antibiotic responses. PLOS Computational Biology. Available here

  2. Johnson, G.T., Agmon, E., Akamatsu, M., Lundberg, E., Lyons, B., Ouyang, W., Quintero-Carmona, O.A., Riel-Mehan, M., Rafelski, S., & Horwitz, R. (2023). Building the next generation of virtual cells to understand cellular biology. Biophysical Journal. Available here

  3. Shaikh, Bilal, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew et al. (2022). BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic acids research. Available here

  4. Agmon, E., Spangler, R.K., Skalnik, C.J., Poole, W., Morrison, J.H., Peirce, S.M., and Covert, M.W. (2022). Vivarium: an interface and engine for integrative multi-scale modeling in computational biology. Bioinformatics. Available here

  5. Covert, M.W., Gillies, T. E., Kudo, T., & Agmon, E. (2021). A forecast for large-scale, predictive biology: Lessons from meteorology. Cell systems. Available here

  6. Agmon, E., and Spangler, R.K. (2020). A multi-scale approach to modeling E. coli chemotaxis. Entropy. Available here

  7. Macklin, D.N., Ruggero, N.A., Carrera, J., Choi, H., Horst, T.A., Mason, J.C., Sun, G., Agmon, E., DeFelice, M.M., Maayan, I., Lane, K., Spangler, R.K., Gillies, T.E., Paull, M.L., Akhter, S., Bray, S.R., Weaver, D.S., Keseler, I.M., Karp, P.D., Morrison, J.H., and Covert, M.W. (2020). Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation. Science. Available here

  8. Talman, L., Agmon, E., Peirce, S.M., and Covert, M.W. (2019). Multiscale models of infection. Current Opinion in Biomedical Engineering. Available here

  9. Agmon, E., Solon, J., Bassereau, P., and Stockwell, B.R. (2018). Modeling the effects of lipid peroxidation during ferroptosis on membrane properties. Scientific Reports. Available here

  10. Agmon, E. and Stockwell, B.R. (2017). Lipid homeostasis and regulated cell death. Current Opinion in Chemical Biology. Available here

  11. Agmon, E., Gates, A.J., and Beer, R.D. (2016). The structure of ontogenies in a model protocell. Artificial Life. Available here

  12. Agmon, E., Gates, A.J., Churavy, V. and Beer, R.D. (2016). Exploring the space of viable configurations in a model of metabolism-boundary co-construction. Artificial Life. Available here