Selected Publications

  1. Smith, Lucian P; Malik-Sheriff, Rahuman S; Nguyen, Tung V N; Hermjakob, Henning; Karr, Jonathan; Shaikh, Bilal; Drescher, Logan; Moraru, Ion I; Schaff, James C; Agmon, Eran; Patrie, Alexander A; Blinov, Michael L; Hellerstein, Joseph L; May, Elebeoba E; Nickerson, David P; Gennari, John H; Sauro, Herbert M. (2025). Verification and reproducible curation of the BioModels repository. PLOS Computational Biology. Available here

  2. Qiu, Xihua; Liu, Yamin; Vera-Licona, Paola; Agmon, Eran; Kshitiz; Suhail, Yasir. (2025). Hif-1 responsive IFFLs to explain specific transcriptional responses to cycling hypoxia in cancers. NPJ systems biology and applications. Available here

  3. Sauro, Herbert M; Agmon, Eran; Blinov, Michael L; Gennari, John H; Hellerstein, Joe; Heydarabadipour, Adel; Hunter, Peter; Jardine, Bartholomew E; May, Elebeoba; Nickerson, David P; Smith, Lucian P; Bader, Gary D; Bergmann, Frank; Boyle, Patrick M; Dräger, Andreas; Faeder, James R; Feng, Song; Freire, Juliana; Fröhlich, Fabian; Glazier, James A; Gorochowski, Thomas E; Helikar, Tomas; Hoops, Stefan; Imoukhuede, Princess; Keating, Sarah M; Konig, Matthias; Laubenbacher, Reinhard; Loew, Leslie M; Lopez, Carlos F; Lytton, William W; McCulloch, Andrew; Mendes, Pedro; Myers, Chris J; Myers, Jerry G; Mulugeta, Lealem; Niarakis, Anna; van Niekerk, David D; Olivier, Brett G; Patrie, Alexander A; Quardokus, Ellen M; Radde, Nicole; Rohwer, Johann M; Sahle, Sven; Schaff, James C; Sego, T J; Shin, Janis; Snoep, Jacky L; Vadigepalli, Rajanikanth; Wiley, H Steve; Waltemath, Dagmar; Moraru, Ion. (2025). From FAIR to CURE: Guidelines for Computational Models of Biological Systems. arXiv. Available here

  4. Lyons, Blair; Mogre, Saurabh S; Vegesna, Karthik; Yu, Jessica S; Hansen, Mark; Raghunathan, Aadarsh; Johnson, Graham T; Agmon, Eran; Akamatsu, Matthew. (2025). Comparing simulations of actin filament compression reveals tradeoff between computational cost and capturing supertwist. microPublication Biology. Available here

  5. Agmon, Eran, and Spangler, Ryan. (2025). Process Bigraphs and the Architecture of Compositional Systems Biology. arXiv. Available here

  6. Agmon, E. (2024). Foundations of a Compositional Systems Biology. arXiv. Available here

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

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

  15. 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

  16. 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

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

  18. 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

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

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

  21. 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