Publications

Pankaew, S., Noel, V., Paulevé, L., Thieffry, D., Barillot, E., & Calzone, L. (2026). AstroLogics: A simulation-based framework for the analysis of Boolean model ensembles. Bioinformatics (Oxford, England), btag555. Advance online publication. https://doi.org/10.1093/bioinformatics/btag555

Kuhn, C. K., Schmidt, D., Rade, M., Selke, J., Tretbar, U. S., Merz, M., Grau, J., & Reiche, K. (2026). CERTOMICS: trusted single-cell multiomics pipeline for high-resolution profiling of adoptive cellular immunotherapies. Bioinformatics (Oxford, England), 42(3), btag096. https://doi.org/10.1093/bioinformatics/btag096

Rade, M., Fandrei, D., Kreuz, M., Seiffert, S., Grahnert, A., Friedrich, M., Wiemers, T., Born, P., Fischer, L., Weidner, H., Hofbauer, L. C., Baber, R., Wang, S. Y., Bach, E., Hoffmann, S., Scolnick, J., Friedrich, M., Keramati, F., Brazda, P., Sebestyen, Z., … Merz, M. (2025). A longitudinal single-cell atlas to predict outcome and toxicity after BCMA-directed CAR T cell therapy in multiple myeloma. Cancer cell, S1535-6108(25)00490-8. Advance online publication. https://doi.org/10.1016/j.ccell.2025.10.014

Ruscone, M., Tsirvouli, E., Checcoli, A., Turei, D., Barillot, E., Saez-Rodriguez, J., Martignetti, L., Flobak, Å., & Calzone, L. (2025). NeKo: A tool for automatic network construction from prior knowledge. PLoS computational biology, 21(9), e1013300. https://doi.org/10.1371/journal.pcbi.1013300

Weirauch, U., Kreuz, M., Birkenbihl, C., Alb, M., Quaranta, M., Calzone, L., Orozco-Ruiz, S., Binder, S., Fischer, L., Clavreul, S., Maguri, M., Ferle, M., Rade, M., Azarias, G., Hydren, J. R., Jamarik, J., Schwarz, D., Sebestyen, Z., Kuball, J., Popp, G., … CERTAINTY Consortium (2025). Design specifications for biomedical virtual twins in engineered adoptive cellular immunotherapies. NPJ digital medicine, 8(1), 493. https://doi.org/10.1038/s41746-025-01809-6