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| Smith LP, Bergmann FT, Garny A, et al. (2024) The simulation experiment description markup language (SED-ML): language specification for level 1 version 5. Journal of Integrative Bioinformatics |
| Bodeit O, Ben Samir I, Karr JR, et al. (2023) RBAtools: a programming interface for Resource Balance Analysis models. Bioinformatics Advances. 3: vbad056 |
| Karr J, Malik-Sheriff RS, Osborne J, et al. (2022) Model Integration in Computational Biology: The Role of Reproducibility, Credibility and Utility. Frontiers in Systems Biology. 2 |
| Shaikh B, Smith LP, Vasilescu D, et al. (2022) BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Research |
| Smith LP, Bergmann FT, Garny A, et al. (2021) The simulation experiment description markup language (SED-ML): language specification for level 1 version 4. Journal of Integrative Bioinformatics. 18: 20210021 |
| Maritan M, Autin L, Karr J, et al. (2021) Building Structural Models of a Whole Mycoplasma Cell. Journal of Molecular Biology. 434: 167351 |
| Tourigny DS, Goldberg AP, Karr JR. (2021) Simulating single-cell metabolism using a stochastic flux-balance analysis algorithm. Biophysical Journal |
| Dräger A, Helikar T, Barberis M, et al. (2021) SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. Bioinformatics (Oxford, England) |
| Shaikh B, Marupilla G, Wilson M, et al. (2021) RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats. Nucleic Acids Research |
| Roth YD, Lian Z, Pochiraju S, et al. (2020) Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior. Nucleic Acids Research |