Integrative, multiscale modeling
- 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
- 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
- Agmon, E., and Spangler, R.K. (2020). A multi-scale approach to modeling E. coli chemotaxis. Entropy, 22: 1101. Available here
- 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
- 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
- Agmon, E. and Stockwell, B.R. (2017). Lipid homeostasis and regulated cell death. Current Opinion in Chemical Biology. 39: 83-89. Available here
Protocells
- 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
- 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