Publications & Tools
We develop computational methods and software to understand, predict and engineer biological systems. Here, we share the tools, publications, projects and ideas that emerge from this work.
Tools | Publications | Projects | Talks | Science communication
Tools
The software tools and code developed by our team are available on GitHub.
ContiDesigner | ecmtool | FedBatchDesigner | PeakBot | Finger sweat analysis
Jürgen Zanghellini during video recordings for the Massive Open Online Course accompanying the open-access textbook Economic Principles in Cell Physiology. Coming soon.
Events
Publications
2026
Müller S, Predl M, Széliová D, Zanghellini J. Elementary vectors reveal minimal interactions in microbial communities. Journal of the Royal Society Interface. 2026 Jun 24;23(239):20250869. doi: 10.1098/rsif.2025.0869
Di Giusto P, Choi DH, Antonakoudis A, Duraikannan VG, Craveur P, Cowie NL et al. A community reconstruction of Chinese hamster metabolism and structural systems biology elucidate metabolic rewiring in lactate-free CHO cells. Cell Systems. 2026 Jun 17;17(6):101574. doi: 10.1016/j.cels.2026.101574
Economic Cell Collective, Szeliova D, Müller S. Economic Principles in Cell Biology. 2026. doi: 10.5281/zenodo.18088026
Kushwaha M, Liebermeister W, Noor E, Sechkar K, Szeliova D. Benefit and cost of a protein. In Economic Principles in Cell Biology (Textbook ). 2026 doi: 10.5281/zenodo.18087995
2025
Karasová M, Jobst M, Framke D, Bergen J, Meier-Menches S, Keppler B et al. Mechanical cues rewire lipid metabolism and support chemoresistance in epithelial ovarian cancer cell lines OVCAR3 and SKOV3. Cell communication and signaling. 2025 Dec;23(1):193. doi: 10.1186/s12964-025-02144-9
Projects
Circular Bioengineering
Fungi in museums and collections: a novel, highly sensitive, AI powered sensor system for the early stage detection of fungal contaminations
Prokaryote proteomics at high temperature for single cells
Morpho-metabolischer Fingerabdruck von Ovarialkarzinom
Talks
Confessiones: what works and what doesn't
A Geometric View of Community Metabolism
(COBRA2026)
Genome-scale metabolic modeling of the fungal genus Komagataella
(COBRA2026)
Pan genome-scale metabolic modeling of Sulfolobus genus reveals medium - dependent metabolic diversity
(COBRA2026)