2025
Sauro, H. M., Agmon, E., Blinov, M. L., Gennari, J. H., … Niarakis, A., … Wiley, H. S., Waltemath, D., Moraru, I. (2025). From FAIR to CURE: Guidelines for Computational Models of Biological Systems. arXiv preprint. DOI: 10.48550/arXiv.2502.15597
Fonseca, LL., Böttcher, L., Mehrad, B., Laubenbacher, R. (2025). Optimal control of agent-based models via surrogate modeling. PLoS Comput Biol. 21(1):e1012138. DOI: 10.1371/journal.pcbi.1012138
2024
Niarakis, A., Laubenbacher, R., An, G., Ilan, Y., Fisher, J., Flobak, Å., … & Glazier, J. A. (2024). Immune digital twins for complex human pathologies: applications, limitations, and challenges. NPJ systems biology and applications, 10(1), 141. DOI: 10.1038/s41540-024-00450-5
Immune Digital Twins Working Group. (2024). Building an international and interdisciplinary community to develop immune digital twins for complex human pathologies. Building Immune Digital Twins (BIDT), Institut Pascal, University of Paris Saclay. Zenodo. DOI: 10.5281/zenodo.10783684
Laubenbacher, R., Mehrad, B., Shmulevich, I., Trayanova, N. (2024). Digital twins in medicine. Nat Comput Sci. 4(3):184-191. DOI: 10.1038/s43588-024-00607-6
Böttcher, L., Fonseca, LL., Laubenbacher, R. (2024). Control of Medical Digital Twins with Artificial Neural Networks. Phil. Trans. R. Soc. A, 383: 20240228.
Laubenbacher, R., Adler, F., An, G., Castiglione, F., Eubank, S., Fonseca, LL., Glazier, J., Helikar, T., Jett-Tilton, M., Kirschner, D., Macklin, P., Mehrad, B., Moore, B., Pasour, V., Shmulevich, I., Smith, A., Voigt, I., Yankeelov, TE., Ziemssen, T. (2024). Toward mechanistic medical digital twins: some use cases in immunology. Front. Digit. Health 6:1349595. DOI: 10.3389/fdgth.2024.1349595
Laubenbacher, R., Adler, F., An, G., Castiglione, F., Eubank, S., Fonseca, LL., Glazier, J., Helikar, T., Jett-Tilton, M., Kirschner, D., Macklin, P., Mehrad, B., Moore, B., Pasour, V., Shmulevich, I., Smith, A., Voigt, I., Yankeelov, TE., Ziemssen, T. (2024). Forum on immune digital twins: a meeting report. npj Systems Biology and Applications. 2056-7189. DOI: 10.1038/s41540-024-00345-5
Zerrouk, N., Augé, F., & Niarakis, A. (2024). Building a modular and multi-cellular virtual twin of the synovial joint in Rheumatoid Arthritis. npj Digital Medicine, 7, 379. DOI: 10.1038/s41746-024-01396-y
Aghakhani, S., Niarakis, A., & Soliman, S. (2024). MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps. Journal of Integrative Bioinformatics, 2024, 20230048. DOI: 10.1515/jib-2023-0048
Zerrouk, N., Alcraft, R., Hall, B. A., Augé, F., & Niarakis, A. (2024). Large-scale computational modelling of the M1 and M2 synovial macrophages in rheumatoid arthritis. npj Systems Biology and Applications, 10, 10. DOI: 10.1038/s41540-024-00337-5
2023
Niarakis, A., Ostaszewski, M., Mazein, A., Kuperstein, I., Kutmon, M., et al. (2023). Drug-Target identification in COVID-19 disease mechanisms using computational systems biology approaches. Frontiers in Immunology, 14. DOI: 10.3389/fimmu.2023.1282859
Rodríguez Martínez, M., Barberis, M., & Niarakis, A. (2023). Computational modelling of immunological mechanisms: From statistical approaches to interpretable machine learning. ImmunoInformatics, 12, 100029. DOI: 10.1016/j.immuno.2023.100029
Singh, V., Naldi, A., Soliman, S., & Niarakis, A. (2023). A large-scale Boolean model of the Rheumatoid Arthritis Fibroblast-Like Synoviocytes predicts drug synergies in the arthritic joint. npj Systems Biology and Applications, 9, 33. DOI: 10.1038/s41540-023-00294-5
Aghakhani, S., Silva-Saffar, S. E., Soliman, S., & Niarakis, A. (2023). Hybrid computational modeling highlights reverse Warburg effect in breast cancer-associated fibroblasts. Computational and Structural Biotechnology Journal. DOI: 10.1016/j.csbj.2023.08.015
2022
Laubenbacher, R., Niarakis, A., Helikar, T., An, G., Shapiro, B., Malik-Sheriff, R. S., Sego, T. J., Knapp, A., Macklin, P., & Glazier, J. A. (2022). Building digital twins of the human immune system: Toward a roadmap. Npj Digital Medicine, 5(1), 64. DOI: 10.1038/s41746-022-00610-z
Aghakhani, S., Soliman, S., & Niarakis, A. (2022). Metabolic Reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: a Hybrid Modeling Approach. PLOS Computational Biology, 18(12), e1010408. DOI: 10.1371/journal.pcbi.1010408
Niarakis, A., Thakar, J., Barberis, M., Rodriguez Martinez, M., Helikar, T., Birtwistle, M., Chaouiya, C., Calzone, L., & Drager, A. (2022). Computational modelling in health and disease. Highlights of the 6th annual SysMod meeting. Bioinformatics, 38(21), 4990–4993. DOI: 10.1093/bioinformatics/btac609
Zerrouk, N., Aghakhani, S., Singh, V., Augé, F., & Niarakis, A. (2022). A Mechanistic Cellular Atlas of the Rheumatic Joint. Frontiers in Systems Biology, 2. DOI: 10.3389/fsysb.2022.925791
Niarakis, A., Waltemath, D., Glazier, J., Schreiber, F., Keating, S. M., Nickerson, D., Chaouiya, C., Siegel, A., Noël, V., Hermjakob, H., Helikar, T., Soliman, S., & Calzone, L. (2022). Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. Briefings in Bioinformatics, bbac212. DOI: 10.1093/bib/bbac212