Biochemical Network Analysis

Jürgen Zanghellini

Department of Analytical Chemistry

Deputy Head

Sensengasse 8
1090 Wien

T: +43-1-4277-52306

juergen.zanghellini(at)univie.ac.at

u:cris portal

Courses

Publications

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

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

Zehetner L, Széliová D, Kraus B, Hernandez Bort JA, Zanghellini J. Multi-omics driven genome-scale metabolic modeling improves viral vector yield in HEK293. Metabolic engineering. 2025 Sept;91:103-118. doi: 10.1016/j.ymben.2025.03.011

Graf AC, Libiseller-Egger J, Gotsmy M, Zanghellini J. Fedbatchdesigner: A User-Friendly Dashboard for Modeling and Optimizing Growth-Arrested Fed-Batch Processes. ACS Synthetic Biology. 2025 Aug 15;14(8):3252-3257. Epub 2025 Jul 21. doi: 10.1021/acssynbio.5c00357

Klamt S, Zanghellini J, Von Kamp A. Minimal cut sets in metabolic networks: From conceptual foundations to applications in metabolic engineering and biomedicine. Briefings in bioinformatics. 2025 Mar 1;26(2):bbaf188. doi: 10.1093/bib/bbaf188

Lázaro J, Joven T, Széliová D , Zanghellini J, Júlvez J. Multi-scale design and optimization of antibody production via flexible nets. Computational and Structural Biotechnology Journal. 2025 Jan;27:1498-1510. doi: 10.1016/j.csbj.2025.03.040

Széliová D , Müller S , Zanghellini J. Costs of ribosomal RNA stabilization affect ribosome composition at maximum growth rate. Communications Biology. 2024 Dec;7(1):196. doi: 10.1038/s42003-024-05815-4

Schlögel G, Lück R, Kittler S, Spadiut O, Kopp J, Zanghellini J et al. Optimizing bioprocessing efficiency with OptFed: Dynamic nonlinear modeling improves product-to-biomass yield. Computational and Structural Biotechnology Journal. 2024 Dec;23:3651-3661. doi: 10.1016/j.csbj.2024.09.024

Gotsmy M, Erian A, Marx H, Pflügl S, Zanghellini J. Predictive dynamic control accurately maps the design space for 2,3-butanediol production. Computational and Structural Biotechnology Journal. 2024 Dec;23:3850-3858. doi: 10.1016/j.csbj.2024.10.016

Projects

Fungi in museums and collections: a novel, highly sensitive, AI powered sensor system for the early stage detection of fungal contaminations

Zanghellini, Jürgen (Project Lead), Sterflinger , Katja (Co-Lead), Kellner , Elke (Co-Lead)

01/04/2026 31/03/2029

Active

Circular Bioengineering

Köllensperger, Gunda (Project Lead), Ludwig, Roland (Co-Lead), Bismarck, Alexander (Co-Lead), Zanghellini, Jürgen (Co-Lead), Woodward, Robert (Co-Lead)

01/12/2024 30/11/2029

Active

Prokaryote proteomics at high temperature for single cells

Zanghellini, Jürgen (Project Lead)

01/01/2024 31/12/2027

Active

Morpho-metabolischer Fingerabdruck von Ovarialkarzinom

Del Favero, Giorgia (Project Lead), Köllensperger, Gunda (Co-Lead), Gerner, Christopher (Co-Lead), Zanghellini, Jürgen (Co-Lead)

15/09/2022 14/09/2027

Active

Talks

Confessiones: what works and what doesn't

Jürgen Zanghellini

MATOMIC Meeting

Conference, Talk or oral contribution

19.5.2026

A Geometric View of Community Metabolism

Michael Predl , Stefan Müller , Diana Szeliova , Jürgen Zanghellini

10th Conference on Constraint-Based Reconstruction and Analysis
(COBRA2026)

Conference, Talk or oral contribution

17.3.2026

The Geometry of Microbial Cooperation: Linking Metabolism and Ecology

Jürgen Zanghellini , Michael Predl , Stefan Müller , Diana Szeliova

Talk or oral contribution

18.2.2026

The Geometry of Microbial Cooperation: Linking Metabolism and Ecology

Jürgen Zanghellini , Michael Predl , Stefan Müller , Diana Szeliova

Talk or oral contribution

18.2.2026

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

The Geometry of Cooperation: decoding microbial Interactions

Jürgen Zanghellini , Müller Stefan , Michael Predl , Diana Szeliova

Austrian Bioinformatics Workshop 2025

Seminar/Workshop, Talk or oral contribution

23.9.2025

From Microbes to Interactions with PyCoMo – Tackling the Challenges in Community Metabolic Modelling

Michael Predl , Jürgen Zanghellini

Metabolic Pathway Analysis 2025

Conference, Talk or oral contribution

28.7.2025

OptFed: Advancing Bioprocess Control with Data-Driven Optimization

Guido Schlögel , Rüdiger Lück , Stefan Kittler , Oliver Spadiut , Julian Kopp , Mathias Gotsmy , Jürgen Zanghellini

Metabolic Pathway Analysis 2025

Conference, Talk or oral contribution

28.7.2025

Why do cells invest in compartmentalization? The thermodynamic benefits of mitochondria

Diana Szeliova , Steffen Klamt , Pavlos Stephanos Bekiaris , Jürgen Zanghellini

Metabolic Pathway Analysis 2025

Conference, Talk or oral contribution

28.7.2025

Constraint-based modeling of microbial communities

Michael Predl , Diana Szeliova , Müller Stefan , Jürgen Zanghellini

summer school Economic Principles in Cell Biology 2025

Summer/Winter school, Talk or oral contribution

23.7.2025

Chemical crosslinking and quantitative mass spectrometry: Insights beyond distance information

Stefanie Brandstetter , Benjamin Neuditschko , Franz Herzog , Jürgen Zanghellini

Vienna Doctoral School in Chemistry – DoSChem: Panel B Retreat 2025

Conference, Talk or oral contribution

2.4.2025

Computational modeling of protein interactions using chemical crosslinking and mass spectrometry

Stefanie Brandstetter , Benjamin Neuditschko , Jürgen Zanghellini , Franz Herzog

Vienna Doctoral School in Chemistry – DoSChem: Panel B Retreat 2025

Conference, Talk or oral contribution

2.4.2025

OptFed: Advancing Bioprocess Control with Data-Driven Optimization

Guido Schlögel , Rüdiger Lück , Stefan Kittler , Oliver Spadiut , Julian Kopp , Mathias Gotsmy , Jürgen Zanghellini

Vienna Doctoral School in Chemistry – DoSChem: Panel B Retreat 2025

Conference, Talk or oral contribution

2.4.2025

Modeling of AAV Production Processes using HEK293-specific GSMMs

Leopold Zehetner , Jürgen Zanghellini

Webinar Series: Modeling and Simulation in Biotechnology and Biochemical Engineering

Seminar/Workshop, Talk or oral contribution

24.3.2025

Chemical crosslinking and quantitative mass spectrometry: Insights beyond distance information

Stefanie Brandstetter , Benjamin Neuditschko , Franz Herzog , Jürgen Zanghellini

1. Science Parade am Campus Krems – Entdecken, Vernetzen, Kooperieren

Conference, Talk or oral contribution

5.2.2025

The Metabolic Guide for Space Survival

Kristina Pulejkova , Jürgen Zanghellini

CCS Panacea? Unleashing the Debate – Symposium

Seminar/Workshop, Talk or oral contribution

12.12.2024

Boosting biotechnological production process with constraint-based process modeling

Jürgen Zanghellini , Mathias Gotsmy , Guido Schlögel , Leopold Zehetner

Workshop Metabolism and mathematical models: Two for a tango – 4th Edition

Seminar/Workshop, Talk or oral contribution

19.11.2024

VLP Production in Gene Therapy

Jürgen Zanghellini

BioProcess Forum

Seminar/Workshop, Talk or oral contribution

2.10.2024

Beyond exponential: exploring effective alternative feeding strategies in fed-batch fermentation

Andrea Graf , Jürgen Zanghellini

16^thÖGBMBT Annual Meeting 2024: „LIFE SCIENCES – TACKLING CHALLENGES OF THE 21ST CENTURY“

Conference, Talk or oral contribution

17.9.2024

Optimally designing multi-step fermentation processes

Jürgen Zanghellini

Talk or oral contribution

12.4.2024

Tailored mass spectral data exploration using the specXplore interactive dashboard

Kevin Mildau , Henry Ehlers , Christoph Bueschl , Justin J.J. van der Hooft , Jürgen Zanghellini

Benelux Metabolomics Days 2023

Conference, Talk or oral contribution

16.11.2023

Innovating Biopharmaceutical Production: Maximization of Yield and Quality with Multi-Phase Fed-Batch Processes

Jürgen Zanghellini

Austrian Bioinformatics Workshop 2023

Seminar/Workshop, Talk or oral contribution

25.9.2023

Designing an optimal fed-batch process using a comprehensive differential equation model

Guido Schlögel , Mathias Gotsmy , Jürgen Zanghellini

15^th ÖGMBT Annual Meeting

Conference, Talk or oral contribution

19.9.2023

Development of a genome-scale metabolic model tailored to a CHO fed-batch process platform

Martin Hold , Leopold Zehetner , Manuel Dallinger , David E. Ruckerbauer , Jürgen Zanghellini

15^th ÖGMBT Annual Meeting

Conference, Talk or oral contribution

19.9.2023

Unmasking nature's collaborators: Computing all feasible compositions of microbial communities

Marianne Mießkes , Jürgen Zanghellini

15^th ÖGMBT Annual Meeting

Conference, Talk or oral contribution

19.9.2023

Are Ribosomes Made for Maximal Growth? Insights from Resource Balance Analysis

Diana Szeliova , Müller Stefan , Jürgen Zanghellini

Metabolic Pathway Analysis 2023 (MPA 2023)

Conference, Talk or oral contribution

24.7.2023

Sulfate limitation increases specific plasmid DNA yield in E. coli fed-batch processes

Mathias Gotsmy , Florian Strobl , Florian Weiß , Petra Gruber , Barbara Kraus , Juergen Mairhofer , Jürgen Zanghellini

Metabolic Pathway Analysis 2023 (MPA 2023)

Conference, Talk or oral contribution

24.7.2023

Sulfate limitation increases specific plasmid DNA yield

Jürgen Zanghellini

Data Science Retreat

Panel discussion, round table, Talk or oral contribution

5.7.2023

Does ribosome composition maximize growth rate? The role of RNA instability

Diana Szeliova , Müller Stefan , Jürgen Zanghellini

Workshop Computational Systems Biology @univie

Seminar/Workshop, Talk or oral contribution

28.6.2023

Unmasking Nature's Collaborators: Computation of all feasible compositions of microbial communities

Marianne Mießkes , Jürgen Zanghellini

Workshop Computational Systems Biology @univie

Seminar/Workshop, Talk or oral contribution

28.6.2023

Visualizing cross-feeding interactions in community metabolic models

Michael Predl , Marianne Mießkes , Jürgen Zanghellini , Thomas Rattei

Workshop Computational Systems Biology @univie

Seminar/Workshop, Talk or oral contribution

28.6.2023

specXplore: An interactive dashboard for flexible exploration of mass spectral data

Kevin Mildau , H. Ehlers , Christoph Bueschl , Justin J.J. van der Hooft , Jürgen Zanghellini

Data 4 Omics Symposium

Conference, Talk or oral contribution

1.6.2023

specXplore: a tool for interactive and dynamic exploration of mass spectral embeddings and graphs

Kevin Mildau , Henry Ehlers , Christoph Bueschl , Justin J.J. van der Hooft , Jürgen Zanghellini

NMC Online Benelux Seminar Data Analyses Computational Metabolomics

Seminar/Workshop, Talk or oral contribution

30.3.2023

Carbon – Cycle Economy Demonstration (C-CED): operational concepts

Jürgen Zanghellini

Workshop Carbon – Cycle Economy Demonstration

Seminar/Workshop, Talk or oral contribution

14.3.2023

An interactive workflow for single-cell multiplexed image analysis

Gabriel Braun , Martin Schaier , Anna Schöberl , Sarah Theiner , Christoph Bueschl , Jürgen Zanghellini , Gunda Köllensperger

European Winter Conference on Plasma Spectrochemistry (EWCPS2023)

Conference, Talk or oral contribution

29.1.2023

Analyzing Optimal and Non-Optimal Resource Allocations in Whole-Cell Models

Diana Szeliova , Müller Stefan , Jürgen Zanghellini

8th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2022)

Conference, Talk or oral contribution

28.9.2022

A human-in-the-loop workflow for single-cell multiplexed image analysis

Gabriel Braun , Martin Schaier , Anna Schöberl , Sarah Theiner , Christoph Bueschl , Jürgen Zanghellini , Gunda Köllensperger

2^nd International DoSChem Student Symposium

Conference, Talk or oral contribution

19.9.2022

Implementation of a Genome-Scale Metabolic Model for Process Optimization of AAV-Production in HEK293 Cells

Leopold Zehetner , Diana Szeliova , B. Kraus , Jürgen Zanghellini , Juan A. Hernandez Bort

Vienna Doctoral School in Chemistry – DoSChem: Panel B Retreat 2022

Conference, Talk or oral contribution

13.6.2022

If all you have is a hammer, everything looks like a nail: On the ubiquitous of elementary flux modes

Jürgen Zanghellini

MATOMIC - Mathematical Modelling for Microbial Community Induced Metabolic Diseases

Panel discussion, round table, Talk or oral contribution

23.5.2022

Thermodynamic Genome-Scale Metabolic Modeling of Metallodrug Resistance in Colorectal Cancer

Jürgen Zanghellini

BOLD-100 Mini Symposium Winter 2022

Seminar/Workshop, Talk or oral contribution

9.12.2021

If all you have is a hammer, everything looks like a nail: On the ubiquitous of elementary flux modes

Jürgen Zanghellini

Talk or oral contribution

3.12.2021

Identification of linked metabolites allows a reliable and quantitative analysis of the finger sweat

Mathias Gotsmy , Julia Brunmair , Andrea Bileck , Astrid Slany , Samuel Matthias Meier-Menches , Christopher Gerner , Jürgen Zanghellini

1st DoSChem International Student Symposium

Conference, Talk or oral contribution

23.9.2021

PeakBot: Machine learning based chromatographic peak picking

Christoph Bueschl , M. Doppler , Elisabeth Varga , Jürgen Zanghellini

Virtual young researcher APMRS annual conference

Conference, Talk or oral contribution

7.9.2021

Beyond metabolism

Jürgen Zanghellini

Science & Innovation Forums (online)

Seminar/Workshop, Talk or oral contribution

26.8.2021

Identification of Metabolic Pairs Allow a Reliable and Quantitative Analysis of the Finger Sweat Metabolome

Mathias Gotsmy , Samuel Matthias Meier-Menches , Christopher Gerner , Jürgen Zanghellini , Julia Brunmair , Andrea Bileck , Astrid Slany

2021 Metabolic Pathway Analysis

Conference, Talk or oral contribution

25.7.2021

Finger Sweat Analysis Enables Metabolic Biomonitoring in Humans

Julia Brunmair , Mathias Gotsmy , Andrea Bileck , Jürgen Zanghellini , Samuel Matthias Meier-Menches , Christopher Gerner

Metabolomics 2021 Online: 17th Annual Conference of the Metabolomics Society

Conference, Talk or oral contribution

22.6.2021

Numerical simulation of microbial processes

Jürgen Zanghellini

Underground Sun.Conversion: Interner Stakeholder-Workshop (online)

Seminar/Workshop, Talk or oral contribution

14.4.2021

Improving Quantitative Genome-Scale Metabolic Modeling of CHO

Diana Széliová , David E. Ruckerbauer , Jerneja Štor , Dmytro Iurashev , Harald Schöny , Michael Hanscho , Stephan Hann , Gunda Köllensperger , Isabel Rocha , Nicole Borth , Jürgen Zanghellini

7th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2021)

Conference, Talk or oral contribution

1.3.2021