Publications of the group Biochemical Network Analysis
Showing entries 21 - 30 out of 61
2023
Gotsmy, M., Strobl, F., Weiß, F., Gruber, P., Kraus, B., Mairhofer, J., & Zanghellini, J. (2023). Sulfate limitation increases specific plasmid DNA yield and productivity in E. coli fed-batch processes. Microbial Cell Factories, 22(1), Article 242. https://doi.org/10.1186/s12934-023-02248-2
Zehetner, L., Széliová, D., Kraus, B., Graninger, M., Zanghellini, J., & Hernandez Bort, J. A. (2023). Optimizing VLP production in gene therapy: Opportunities and challenges for in silico modeling. Biotechnology Journal, 18(7), Article 2200636. https://doi.org/10.1002/biot.202200636
Buchner, B., Clement, T. J., de Groot, D. H., & Zanghellini, J. (2023). ecmtool: fast and memory-efficient enumeration of elementary conversion modes. Bioinformatics (Oxford, England), 39(3), Article btad095. https://doi.org/10.1093/bioinformatics/btad095
2022
El Abiead, Y., Bueschl, C., Panzenboeck, L., Wang, M., Doppler, M., Seidl, B., Zanghellini, J., Dorrestein, P. C., & Koellensperger, G. (2022). Heterogeneous multimeric metabolite ion species observed in LC-MS based metabolomics data sets. Analytica Chimica Acta, 1229, Article 340352. https://doi.org/10.1016/j.aca.2022.340352
Mildau, K., van der Hooft, J. J. J., Flasch, M., Warth, B., El Abiead, Y., Koellensperger, G., Zanghellini, J., & Bueschl, C. (2022). Homologue Series Detection and Management in LC-MS data with homologueDiscoverer. Bioinformatics, 38(22), 5139-5140. Article btac647. https://doi.org/10.1093/bioinformatics/btac647
Gotsmy, M., Brunmair, J., Bueschl, C., Gerner, C., & Zanghellini, J. (2022). Probabilistic quotient's work and pharmacokinetics' contribution: countering size effect in metabolic time series measurements. BMC Bioinformatics, 23(1), Article 379. https://doi.org/10.1186/s12859-022-04918-1
Bueschl, C., Doppler, M., Varga, E., Seidl, B., Flasch, M., Warth, B., & Zanghellini, J. (2022). PeakBot: machine-learning-based chromatographic peak picking. Bioinformatics, 38(13), 3422-3428. https://doi.org/10.1093/bioinformatics/btac344
Müller, S., Szeliova, D., & Zanghellini, J. (2022). Elementary vectors and autocatalytic sets for resource allocation in next-generation models of cellular growth. PLoS Computational Biology, 18(2), Article e1009843. https://doi.org/10.1371/journal.pcbi.1009843
2021
Buchner, B. A., & Zanghellini, J. (2021). EFMlrs: a Python package for elementary flux mode enumeration via lexicographic reverse search. BMC Bioinformatics, 22(1), Article 547. https://doi.org/10.1186/s12859-021-04417-9
Müller, S., Szeliova, D., & Zanghellini, J. (2021). Elementary vectors and autocatalytic sets for computational models of cellular growth. bioRxiv. https://doi.org/10.1101/2021.10.31.466640
Showing entries 21 - 30 out of 61
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 → 14/09/27
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