Selected Publications

Integrative, multiscale modeling

  1. 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, btac049. Available here

Whole-cell models

  1. Skalnik, C.J., Agmon, E., Spangler, R.K., Talman, L., Morrison, J.H., Peirce, S.M., and Covert, M.W. (in review). Whole-Colony Modeling of Escherichia coli. Preprint
  2. Agmon, E., and Spangler, R.K. (2020). A multi-scale approach to modeling E. coli chemotaxis. Entropy, 22: 1101. Available here
  3. 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, 369, eaav3751. Available here

Lipid homeostasis and coarse-grained membrane models

  1. Agmon, E., Solon, J., Bassereau, P., and Stockwell, B.R. (2018). Modeling the effects of lipid peroxidation during ferroptosis on membrane properties. Scientific Reports, 8(1): 5155. Available here
  2. Agmon, E. and Stockwell, B.R. (2017). Lipid homeostasis and regulated cell death. Current Opinion in Chemical Biology. 39: 83-89. Available here


  1. Agmon, E., Gates, A.J., and Beer, R.D. (2016). The structure of ontogenies in a model protocell. Artificial Life 22 (4): 499-517. Available here
  2. 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, 22 (2): 153-171. Available here