Dr. des. Alina Renz

MSc. in Bioinformatics

Office

Department for Computer Science
Institute for Biomedical Informatics (IBMI)
Sand 14 ･ Ground floor ･ Office C106
+49 7071 29-70488
‬renzspam prevention@informatik.uni-tuebingen.de

Research interests

Molecular Biology / Molecular Medicine:
Molecular, biochemical and metabolic mechanisms in prokaryotes and eukaryotes in health and disease
Systems Biology:
Constraint-based modeling of metabolic networks
Visualization:
Visualization of metabolic processes in genome-scale metabolit networks

Research projects

Federal Ministry of Education and Research (BMBF)

Identification of robust antiviral drug targets against SARS-CoV-2

This start-up project supports the identification of robust targets for the treatment of COVID-19 to be experimentally verified in subsequent projects.

Funded by the Federal Ministry of Education and Research (BMBF) and the Baden-Württemberg Ministry of Science as part of the Excellence Strategy of the German Federal and State Governments.

Cluster of Excellence – Controlling Microbes to Fight Infections

Computer Modeling and Experimental Validation of Microbial Interactions

Collaborative Project

The project № EXC-2124/05.037_0 is funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation, doi:10.13039/501100001659) under Germanyʼs Excellence Strategy – EXC 2124 – 390838134 and supported by the Cluster of Excellence CMFI (Controling Microbes to Fight Infections) from May 2021 to April 2024 as a collaboration with the group of Dr. Simon Heilbronner.

Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens

Project TTU 08.703 is funded by the German Center for Infection Research (DZIF, doi:10.13039/100009139) within the Deutsche Zentren der Gesundheitsforschung (BMBF-DZG, German Centers for Health Research of the Federal Ministery of Education and Research), grant № 8020708703. The research group is part of the network for research on Healthcare-Associated and Antibiotic Resistant Bacterial Infections (HAARBI). Funding period: July 2018 to June 2022.

Computer Modeling and Experimental Validation of Microbial Interactions

Explorative Project

The project № EXC-2124/05.051_0 was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation, doi:10.13039/501100001659) under Germanyʼs Excellence Strategy – EXC 2124 – 390838134 and supported by the Cluster of Excellence CMFI (Controling Microbes to Fight Infections) from January 2020 to April 2021.

Conceptual Design of a German infection-related OMICS Data Exchange (GirOD) Platform

Funded by the German Center for Infection Research (DZIF, doi:10.13039/100009139)

Publications

Genome-scale metabolic model of Staphylococcus epidermidis ATCC 12228 matches in vitro conditions

Metabolic Modeling Elucidates Phenformin and Atpenin A5 as Broad-Spectrum Antiviral Drugs

Alina Renz, Mirjam Hohner, Maximilian Breitenbach, Jonathan Josephs-Spaulding, Johanna Dürrwald, Lena Best, Raphaël Jami, Georgios Marinos, Nantia Leonidou, Filipe Cabreiro, Andreas Dräger, Michael Schindler, and Christoph Kaleta
Preprints 2023, November, 30^th 2023.
[ Details | DOI | PDF | PubMed | BibTeX ]

SBOannotator: a Python Tool for the Automated Assignment of Systems Biology Ontology Terms

New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells

Genome-scale model of Pseudomonas aeruginosa metabolism unveils virulence and drug potentiation

A Computational Model of Bacterial Population Dynamics in Gastrointestinal Yersinia enterocolitica Infections in Mice

Janina K. Geißert, Erwin Bohn, Reihaneh Mostolizadeh, Andreas Dräger, Ingo B. Autenrieth, Sina Beier, Oliver Deusch, Alina Renz, Martin Eichner, and Monika S. Schütz.
Biology, 11(2), 297; February 12^th, 2022.
[ Details | DOI | Preprint | PDF | PubMed | BibTeX ]

High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032

Martina Feierabend, Alina Renz, Elisabeth Zelle, Katharina Nöh, Wolfgang Wiechert, and Andreas Dräger
Frontiers in Microbiology, November 15^th 2021.
[ Details | DOI | PDF | PubMed | BibTeX ]

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta-Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frishman, Luis Cristóbal Monraz Gómez, Julia Somers, Matti Hoch, Shailendra Kumar Gupta, Julia Scheel, Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber, Arnau Montagud, Miguel Ponce de Leon, Akira Funahashi, Yusuke Hiki, Noriko Hiroi, Takahiro G. Yamada, Andreas Dräger, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Börnigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang, Emily E. Ackerman, Jason E. Shoemaker, Jeremy Zucker, Kristie L. Oxford, Jeremy Teuton, Ebru Kocakaya, Gökçe Yağmur Summak, Kristina Hanspers, Martina Kutmon, Susan Coort, Lars Eijssen, Friederike Ehrhart, Rex D. A. B., Denise Slenter, Marvin Martens, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic-Milacic, Andrea Senff-Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Cristoffer Sevilla, Thawfeek Mohamed Varusai, Jean-Marie Ravel, Rupsha Fraser, Vera Ortseifen, Silvia Marchesi, Piotr Gawron, Ewa Smula, Laurent Heirendt, Venkata Satagopam, Guanming Wu, Anders Riutta, Martin Golebiewski, Stuart Owen, Carole Goble, Xiaoming Hu, Rupert Overall, Dieter Maier, Angela Bauch, John A. Bachman, Benjamin M Gyori, Carlos Vega, Valentin Grouès, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco, Denes Turei, Augustin Luna, Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas, Marina Esteban-Medina, Maria Peña-Chilet, Tomáš Helikar, Bhanwar Lal Puniya, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Dezso Modos, Agatha Treveil, Marton Laszlo Olbei, Bertrand De Meulder, Aurélien Naldi, Aurélien Dugourd, Vincent Noël, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C. Freeman, Franck Augé, Jacques S. Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon Willighagen, Alexander R. Pico, Chris Evelo, Marc Gillespie, Lincoln D. Stein, Henning Hermjakob, Peter DʼEustachio, Julio Saez-Rodriguez, Joaquin Dopazo, Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider, and the COVID-19 Disease Map Community
Molecular Systems Biology 17: e10387, October 19^th 2021.
[ Details | DOI | Preprint | PubMed | PDF | BibTeX ]

An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism

Curating and Comparing 114 Strain-Specific Genome-Scale Metabolic Models of Staphylococcus aureus

Genome-Scale Metabolic Model of Infection with SARS-CoV-2 Mutants Confirms Guanylate Kinase as Robust Potential Antiviral Target

First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies

Alina Renz, Lina Widerspick, and Andreas Dräger
Metabolites, 11(4), 232, April 9^th 2021
[ Details | DOI | PubMed | PDF | BibTeX ]

FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2

Longitudinal multi-omics analyses identify responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories

Joana P. Bernardes, Neha Mishra, Florian Tran, Thomas Bahmer, Lena Best, Johanna I. Blase, Dora Bordoni, Jeanette Franzenburg, Ulf Geisen, Jonathan Josephs-Spaulding, Philipp Köhler, Axel Künstner, Elisa Rosati, Anna C. Aschenbrenner, Petra Bacher, Nathan Baran, Teide Boysen, Burkhard Brandt, Niklas Bruse, Jonathan Dörr, Andreas Dräger, Gunnar Elke, David Ellinghaus, Julia Fischer, Michael Forster, Andre Franke, Sören Franzenburg, Norbert Frey, Anette Friedrichs, Janina Fuß, Andreas Glück, Jacob Hamm, Finn Hinrichsen, Marc P. Höppner, Simon Imm, Ralf Juenker, Sina Kaiser, Ying H. Kan, Rainer Knoll, Christoph Lange, Georg Laue, Clemes Lier, Matthias Lindner, Georgios Marinos, Robert Markewitz, Jacob Nattermann, Rainer Noth, Peter Pickkers, Klaus F. Rabe, Alina Renz, Christoph Röcken, Jan Rupp, Annika Schaffarzyk, Alexander Scheffold, Jonas Schulte-Schrepping, Domagoj Schunck, Dirk Skowasch, Thomas Ulas, Klaus-Peter Wandinger, Michael Wittig, Johannes Zimmermann, Hauke Busch, Bimba F. Hoyer, Christoph Kaleta, Jan Heyckendorf, Matthijs Kox, Jan Rybniker, Stefan Schreiber, Joachim Schultze, and Philip Rosenstiel.
Immunity, November 26^th 2020.
[ Details | DOI | MedRxiv | PDF | PubMed | BibTeX ]

Clinical Applications of Metabolic Models in SBML Format

Alina Renz, Reihaneh Mostolizadeh, and Andreas Dräger
Reference Module in Biomedical Sciences, Elsevier, Januar 30^th 2020
[ Details | DOI | PDF | PubMed | BibTeX ]