Publications of the group Biochemical Network Analysis
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, 23(1), Article 193. https://doi.org/10.1186/s12964-025-02144-9
Zehetner, L., Széliová, D., Kraus, B., Hernandez Bort, J. A., & Zanghellini, J. (2025). Multi-omics driven genome-scale metabolic modeling improves viral vector yield in HEK293. Metabolic engineering, 91, 103-118. https://doi.org/10.1016/j.ymben.2025.03.011
Graf, A. C., Libiseller-Egger, J., Gotsmy, M., & Zanghellini, J. (2025). Fedbatchdesigner: A User-Friendly Dashboard for Modeling and Optimizing Growth-Arrested Fed-Batch Processes. ACS Synthetic Biology, 14(8), 3252-3257. https://doi.org/10.1021/acssynbio.5c00357
Klamt, S., Zanghellini, J., & Von Kamp, A. (2025). Minimal cut sets in metabolic networks: From conceptual foundations to applications in metabolic engineering and biomedicine. Briefings in bioinformatics, 26(2), Article bbaf188. https://doi.org/10.1093/bib/bbaf188
Lázaro, J., Joven, T., Széliová, D., Zanghellini, J., & Júlvez, J. (2025). Multi-scale design and optimization of antibody production via flexible nets. Computational and Structural Biotechnology Journal, 27, 1498-1510. https://doi.org/10.1016/j.csbj.2025.03.040
2024
Széliová, D., Müller, S., & Zanghellini, J. (2024). Costs of ribosomal RNA stabilization affect ribosome composition at maximum growth rate. Communications Biology, 7(1), Article 196. https://doi.org/10.1038/s42003-024-05815-4
Schlögel, G., Lück, R., Kittler, S., Spadiut, O., Kopp, J., Zanghellini, J., & Gotsmy, M. (2024). Optimizing bioprocessing efficiency with OptFed: Dynamic nonlinear modeling improves product-to-biomass yield. Computational and Structural Biotechnology Journal, 23, 3651-3661. https://doi.org/10.1016/j.csbj.2024.09.024
Gotsmy, M., Erian, A., Marx, H., Pflügl, S., & Zanghellini, J. (2024). Predictive dynamic control accurately maps the design space for 2,3-butanediol production. Computational and Structural Biotechnology Journal, 23, 3850-3858. https://doi.org/10.1016/j.csbj.2024.10.016
Mildau, K., Büschl, C., Zanghellini, J., & Van Der Hooft, J. J. J. (2024). Combined LC-MS/MS feature grouping, statistical prioritization, and interactive networking in msFeaST. Bioinformatics, 40(10), Article btae584. https://doi.org/10.1093/bioinformatics/btae584
Gotsmy, M., Giannari, D., Mahadevan, R., & Zanghellini, J. (2024). Optimizing Fed-Batch Processes with Dynamic Control Flux Balance Analysis. IFAC-PapersOnLine, 58(23), 109-114. https://doi.org/10.1016/j.ifacol.2024.10.019
Activities of the group Biochemical Network Analysis
Showing entries 1 - 10 out of 135
Functional insights into Cereblon-mediated targeted protein degradation by chemical crosslinking and quantitative mass spectrometry
Stefanie Brandstetter
,
Jürgen Zanghellini
Joint DoSChem Retreat – 2026
Seminar/Workshop,
Poster presentation
25.2.2026 - 25.2.2026
Towards a novel tetraether lipid producer Haloferax volcanii
Ana Cristina Gouveia Carvalho
,
Jürgen Zanghellini
Joint DoSChem Retreat – 2026
Seminar/Workshop,
Poster presentation
25.2.2026 - 25.2.2026
Engineering Better AAV Factories: Predictive Flux Modeling Identifies HIF-1 as a Key Limiter of Productivity
Juan A. Hernandez Bort
,
Leopold Zehetner
,
Diana Szeliova
,
Jürgen Zanghellini
European Society of Gene & Cell Therapy: ESGCT Congress 32
Conference,
Poster presentation
7.10.2025 - 7.10.2025
Optimal allocation of enzyme resources in cells & Introduction to Growth Balance Analysis
Diana Szeliova
,
Hugo Dourado
CompSysBio 2025: Advanced Lecture Course on Computational Systems Biology
Lecture series, colloquium,
Talk or oral contribution
5.10.2025 - 5.10.2025
The Geometry of Cooperation: decoding microbial Interactions
Jürgen Zanghellini
,
Müller Stefan
,
Michael Predl
,
Diana Szeliova
24<sup>th </sup>Annual International Conference on Systems Biology (ICSB 2025)
Conference,
Poster presentation
5.10.2025 - 5.10.2025
Developing a XLMS Assay for the Characterization of Protein Conformations
Stefanie Brandstetter
,
Benjamin Neuditschko
,
Klaus Rumpel
,
Jürgen Zanghellini
,
Franz Herzog
EMBO Practical Course: Integrative modelling of biomolecular interactions
Seminar/Workshop,
Poster presentation
28.9.2025 - 28.9.2025
Developing a XLMS Assay for the Characterization of Protein Conformations
Stefanie Brandstetter
,
Benjamin Neuditschko
,
Klaus Rumpel
,
Jürgen Zanghellini
,
Franz Herzog
5th DoSChem International Student Symposium 2025
Conference,
Poster presentation
25.9.2025 - 25.9.2025
FedBatchDesigner: A user-friendly dashboard for modeling and optimizing growth-arrested fed-batch processes
Andrea Caroline Graf
,
Julian Libiseller-Egger
,
Guido Schlögel
,
Maria Jose Rimon Martinez
,
Mathias Gotsmy
,
Jürgen Zanghellini
5th DoSChem International Student Symposium 2025
Conference,
Poster presentation
25.9.2025 - 25.9.2025
From genome to metabolism: Pan genome-scale metabolic model reconstruction of the extremophile genus S<i>ulfolobus</i>
Maria Jose Rimon Martinez
,
Leopold Zehetner
,
Jürgen Zanghellini
5th DoSChem International Student Symposium 2025
Conference,
Poster presentation
25.9.2025 - 25.9.2025
Hybrid models in bioprocess optimization
Julian Libiseller-Egger
,
Andrea Graf
,
Jürgen Zanghellini
5th DoSChem International Student Symposium 2025
Conference,
Talk or oral contribution
25.9.2025 - 25.9.2025
Projects of the group Biochemical Network Analysis
Showing entries 1 - 4 out of 4
Morpho-metabolischer Fingerabdruck von Ovarialkarzinom
Del Favero, G. (Project Lead), Köllensperger, G. (Co-Lead), Gerner, C. (Co-Lead) & Zanghellini, J. (Co-Lead)
15/09/22 → 14/09/26
Project: Research funding
Prokaryote proteomics at high temperature for single cells
Zanghellini, J. (Project Lead)
1/01/24 → 31/12/27
Project: Research cooperation
Circular Bioengineering
Köllensperger, G. (Project Lead), Ludwig, R. (Co-Lead), Bismarck, A. (Co-Lead), Zanghellini, J. (Co-Lead) & Woodward, R. (Co-Lead)
1/12/24 → 30/11/29
Project: Research funding
Fungi in museums and collections: a novel, highly sensitive, AI powered sensor system for the early stage detection of fungal contaminations
Zanghellini, J. (Project Lead), Sterflinger , K. (Co-Lead) & Kellner , E. (Co-Lead)
1/04/26 → 31/03/29
Project: Research funding
Showing entries 1 - 4 out of 4