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Univ.-Prof. Dipl.-Ing. Dr. Jürgen Zanghellini
Jürgen Zanghellini
T: +43-1-4277-52306
https://chemnet.univie.ac.at/
Summer term 2023
270013 SE Writing of the Bachelor´s Thesis
270103 PR Bachelor Laboratory Course B - Analytical Chemistry and Food Chemistry
270190 VU Introduction to metabolic modelling
270191 VU Introduction to R
270194 VU *omics Integration
Winter term 2022
270013 SE Writing of the Bachelor´s Thesis
270030 VU Cellular energetics
270103 PR Bachelor Laboratory Course B - Analytical Chemistry and Food Chemistry
270151 VU Computational Systems Biology: from enzymes to networks
Summer term 2022
270125 SE Current topics in multi-omics network analysis
270127 VU Introduction to metabolic modelling
270135 VU *omics Integration
270147 VU Introduction to R
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), [btad095]. https://doi.org/10.1093/bioinformatics/btad095
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. https://doi.org/10.1002/biot.202200636
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, [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, [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), [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), [e1009843]. https://doi.org/10.1371/journal.pcbi.1009843
Buchner, B. A., & Zanghellini, J. (2021). EFMlrs: a Python package for elementary flux mode enumeration via lexicographic reverse search. BMC Bioinformatics, 22(1), [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
Brunmair, J., Gotsmy, M., Niederstaetter, L., Neuditschko, B., Bileck, A., Slany, A., Feuerstein, M. L., Langbauer, C., Janker, L., Zanghellini, J., Meier-Menches, S. M., & Gerner, C. (2021). Finger sweat analysis enables short interval metabolic biomonitoring in humans. Nature Communications, 12(1), [5993]. https://doi.org/10.1038/s41467-021-26245-4
Stor, J., Ruckerbauer, D. E., Szeliova, D., Zanghellini, J., & Borth, N. (2021). Towards rational glyco-engineering in CHO: from data to predictive models. Current Opinion in Biotechnology, 71, 9-17. https://doi.org/10.1016/j.copbio.2021.05.003
Herrmann, H. A., Rusz, M., Baier, D., Jakupec, M. A., Keppler, B. K., Berger, W., Koellensperger, G., & Zanghellini, J. (2021). Thermodynamic Genome-Scale Metabolic Modeling of Metallodrug Resistance in Colorectal Cancer. Cancers, 13(16), [4130]. https://doi.org/10.3390/cancers13164130
Szeliova, D., Stor, J., Thiel, I., Weinguny, M., Hanscho, M., Lhota, G., Borth, N., Zanghellini, J., Ruckerbauer, D. E., & Rocha, I. (2021). Inclusion of maintenance energy improves the intracellular flux predictions of CHO. PLoS Computational Biology, 17(6), [e1009022]. https://doi.org/10.1371/journal.pcbi.1009022
Széliová, D., Iurashev, D., Ruckerbauer, D. E., Koellensperger, G., Borth, N., Melcher, M., & Zanghellini, J. (2021). Error propagation in constraint-based modeling of Chinese hamster ovary cells. Biotechnology Journal, 16(4), [2000320]. https://doi.org/10.1002/biot.202000320
Libiseller-Egger, J., Coltman, B., Gerstl, M. P., & Zanghellini, J. (2020). Environmental flexibility does not explain metabolic robustness. Npj systems biology and applications, 6(1), [39]. https://doi.org/10.1038/s41540-020-00155-5
Széliová, D., Ruckerbauer, D. E., Galleguillos, S. N., Petersen, L. B., Natter, K., Hanscho, M., Troyer, C., Causon, T., Schoeny, H., Christensen, H. B., Lee, D. Y., Lewis, N. E., Koellensperger, G., Hann, S., Nielsen, L. K., Borth, N., & Zanghellini, J. (2020). What CHO is made of: Variations in the biomass composition of Chinese hamster ovary cell lines. Metabolic engineering, 61, 288-300. https://doi.org/10.1016/j.ymben.2020.06.002
Zwirzitz, B., Wetzels, S. U., Dixon, E. D., Stessl, B., Zaiser, A., Rabanser, I., Thalguter, S., Pinior, B., Roch, F-F., Strachan, C., Zanghellini, J., Dzieciol, M., Wagner, M., & Selberherr, E. (2020). The sources and transmission routes of microbial populations throughout a meat processing facility. Npj biofilms and microbiomes, 6(1), [26]. https://doi.org/10.1038/s41522-020-0136-z
Hamdi, A., Szeliova, D., Ruckerbauer, D. E., Rocha, I., Borth, N., & Zanghellini, J. (2020). Key Challenges in Designing CHO Chassis Platforms. Group Processes and Intergroup Relations, 8(6), [643]. https://doi.org/10.3390/pr8060643
Burgard, J., Grünwald-Gruber, C., Altmann, F., Zanghellini, J., Valli, M., Mattanovich, D., & Gasser, B. (2020). The secretome of Pichia pastoris in fed-batch cultivations is largely independent of the carbon source but changes quantitatively over cultivation time. Microbial Biotechnology, 13(2), 479-494. https://doi.org/10.1111/1751-7915.13499
Strachan, C. R. (Author), Mueller, A. J. (Author), Ghanbari, M. (Author), Neubauer, V. (Author), Zwirzitz, B. (Author), Thalguter, S. (Author), Dziecol, M. (Author), Wetzels, S. U. (Author), Zanghellini, J. (Author), Wagner, M. (Author), & Schmitz-Esser, S. (Author). (2019). A prospective role for the rumen in generating antibiotic resistance. Web publication, Unknown publisher. https://doi.org/10.1101/729681

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

Jürgen Zanghellini (Invited speaker)

14 Mar 2023

Activity: Talks and presentations › Talk or oral contribution › Science to Science

An interactive workflow for single-cell multiplexed image analysis

Gabriel Braun (Speaker), Martin Schaier (Contributor), Anna Schöberl (Contributor), Sarah Theiner (Contributor), Christoph Bueschl (Contributor), Jürgen Zanghellini (Contributor) & Gunda Köllensperger (Contributor)

29 Jan 2023

Activity: Talks and presentations › Talk or oral contribution › Science to Science

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

Diana Szeliova (Speaker), Müller Stefan (Contributor) & Jürgen Zanghellini (Contributor)

28 Sep 2022

Activity: Talks and presentations › Talk or oral contribution › Science to Science

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

Gabriel Braun (Keynote speaker), Martin Schaier (Contributor), Anna Schöberl (Contributor), Sarah Theiner (Contributor), Christoph Bueschl (Contributor), Jürgen Zanghellini (Contributor) & Gunda Köllensperger (Contributor)

19 Sep 2022

Activity: Talks and presentations › Talk or oral contribution › Science to Science

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

Leopold Zehetner (Speaker), Diana Szeliova (Contributor), B. Kraus (Contributor), Jürgen Zanghellini (Contributor) & Juan A. Hernandez Bort (Contributor)

13 Jun 2022

Activity: Talks and presentations › Talk or oral contribution › Science to Science

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

Jürgen Zanghellini (Invited speaker)

23 May 2022

Activity: Talks and presentations › Talk or oral contribution › Science to Science

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

Jürgen Zanghellini (Invited speaker)

9 Dec 2021

Activity: Talks and presentations › Talk or oral contribution › Science to Science

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

Jürgen Zanghellini (Invited speaker)

3 Dec 2021

Activity: Talks and presentations › Talk or oral contribution › Science to Science

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

Mathias Gotsmy (Speaker), Julia Brunmair (Contributor), Andrea Bileck (Contributor), Astrid Slany (Contributor), Samuel Matthias Meier-Menches (Contributor), Christopher Gerner (Contributor) & Jürgen Zanghellini (Contributor)

23 Sep 2021

Activity: Talks and presentations › Talk or oral contribution › Science to Science

PeakBot: Machine learning based chromatographic peak picking

Christoph Bueschl (Speaker), M. Doppler (Contributor), Elisabeth Varga (Contributor) & Jürgen Zanghellini (Contributor)

7 Sep 2021

Activity: Talks and presentations › Talk or oral contribution › Science to Science

Beyond metabolism

Jürgen Zanghellini (Invited speaker)

26 Aug 2021

Activity: Talks and presentations › Talk or oral contribution › Science to Science

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

Mathias Gotsmy (Speaker), Samuel Matthias Meier-Menches (Contributor), Christopher Gerner (Contributor), Jürgen Zanghellini (Contributor), Julia Brunmair (Contributor), Andrea Bileck (Contributor) & Astrid Slany (Contributor)

25 Jul 2021

Activity: Talks and presentations › Talk or oral contribution › Science to Science

Finger Sweat Analysis Enables Metabolic Biomonitoring in Humans

Julia Brunmair (Speaker), Mathias Gotsmy (Contributor), Andrea Bileck (Contributor), Jürgen Zanghellini (Contributor), Samuel Matthias Meier-Menches (Contributor) & Christopher Gerner (Contributor)

22 Jun 2021

Activity: Talks and presentations › Talk or oral contribution › Science to Science

Numerical simulation of microbial processes

Jürgen Zanghellini (Invited speaker)

14 Apr 2021

Activity: Talks and presentations › Talk or oral contribution › Science to Science

Improving Quantitative Genome-Scale Metabolic Modeling of CHO

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

1 Mar 2021

Activity: Talks and presentations › Talk or oral contribution › Science to Science

Reliable Quantitative Finger Sweat Metabolome Analysis

Mathias Gotsmy (Speaker), Julia Brunmair (Contributor), Andrea Bileck (Contributor), Astrid Slany (Contributor), Samuel Matthias Meier-Menches (Contributor), Christopher Gerner (Contributor) & Jürgen Zanghellini (Contributor)

23 Feb 2021

Activity: Talks and presentations › Talk or oral contribution › Science to Science

Vom Nutzen und Nachteil von Netzwerken für das Leben

Jürgen Zanghellini (Invited speaker)

9 Oct 2020

Activity: Talks and presentations › Talk or oral contribution › Science to Science

Die Vermessung von CHO: Requirements for accurate FBA predictions

Jürgen Zanghellini (Invited speaker)

15 Jul 2020

Activity: Talks and presentations › Talk or oral contribution › Science to Science

Cellular robustness is not a byproduct of environmental flexibility

Jürgen Zanghellini (Speaker), Julian Julian Libiseller-Egger (Contributor), Benjamin L. Coltman (Contributor) & Matthias P. Gerstl (Contributor)

13 Jul 2020

Activity: Talks and presentations › Talk or oral contribution › Science to Science

Maintenance energy is essential for accurate predictions of intracellular fluxes in CHO

Diana Széliová (Speaker), David E. Ruckerbauer (Contributor), Jerneja Štor (Contributor), Isabella Thiel (Contributor), Isabel Rocha (Contributor), Nicole Borth (Contributor) & Jürgen Zanghellini (Contributor)

13 Jul 2020

Activity: Talks and presentations › Talk or oral contribution › Science to Science

Predictive modelling of CHO requires high precision data

Jürgen Zanghellini (Invited speaker)

3 Jul 2020

Activity: Talks and presentations › Talk or oral contribution › Science to Science

Department of Analytical Chemistry

Sensengasse 8
1090 Wien

T: +43-1-4277-52306

juergen.zanghellini@univie.ac.at