Selected Publications

  1. Agmon, E. (2024). Prelude to a Compositional Systems Biology. arXiv. Available here

  2. Hickey, J.W., Agmon, E., Horowitz, N., Tan, T.-K., Lamore, M., Sunwoo, J.B., Covert, M.W., and Nolan, G.P. (2024). Integrating multiplexed imaging and multiscale modeling identifies tumor phenotype conversion as a critical component of therapeutic T cell efficacy. Cell Systems. Available here

  3. Vegesna, K.R., Mogre, S.S., Yu, J., Lyons, B., Raghunathan, A., Agmon, E., Akamatsu, M., and Johnson, G.T. (2024). Comparing spatial biophysical simulations across scales and methods. Biophysical Journal. Available here

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

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

  10. 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

  11. Agmon, E., and Covert, M.W. (2020). Building whole-cell computational models to predict cellular phenotypes and accelerate discovery. Computational Modeling: From Chemistry To Materials To Biology-Proceedings Of The 25th Solvay Conference On Chemistry. Available here

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

  13. 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

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

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

  16. 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