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 | RegulomeXplorer | ecmtool | FedBatchDesigner | PeakBot
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 2026, 'Elementary vectors reveal minimal interactions in microbial communities', Journal of the Royal Society Interface, vol. 23, no. 239, 20250869. https://doi.org/10.1098/rsif.2025.0869
Di Giusto, P, Choi, DH, Antonakoudis, A, Duraikannan, VG, Craveur, P, Cowie, NL, Ganapathy, T, Ramesh, K, Benavidez-López, S, Orellana, CA, Jiménez, NE, Dworkin, LA, Morrissey, J, Marin de Mas, I, Strain, B, Valdez-Cruz, NA, Trujillo-Roldán, MA, Marzluf, J, Martínez, VS, Zehetner, L, Altamirano, C, Vega-Letter, AM, Priem, B, Cao, HC, Hold, M, Ma, J, Hong, YF, Gopalakrishnan, S, Enuh, BM, Tarzi, C, Pang, KT, Angione, C, Zanghellini, J, Kontoravdi, C, Hefzi, H, Betenbaugh, MJ, Nielsen, LK, Lakshmanan, M, Lee, DY, Richelle, A & Lewis, NE 2026, 'A community reconstruction of Chinese hamster metabolism and structural systems biology elucidate metabolic rewiring in lactate-free CHO cells', Cell Systems, vol. 17, no. 6, 101574. https://doi.org/10.1016/j.cels.2026.101574
Economic Cell Collective, Szeliova, D & Müller, S 2026, Economic Principles in Cell Biology. https://doi.org/10.5281/zenodo.18088026
Kushwaha, M, Liebermeister, W, Noor, E, Sechkar, K & Szeliova, D 2026, Benefit and cost of a protein. in Economic Principles in Cell Biology (Textbook ). https://doi.org/10.5281/zenodo.18087995
2025
Karasová, M, Jobst, M, Framke, D, Bergen, J, Meier-Menches, S, Keppler, B, Koellensperger, G, Zanghellini, J, Gerner, C & Del Favero, G 2025, 'Mechanical cues rewire lipid metabolism and support chemoresistance in epithelial ovarian cancer cell lines OVCAR3 and SKOV3', Cell communication and signaling, vol. 23, no. 1, 193. https://doi.org/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)