Computational Systems Biology

Dr. des. Alina Renz

MSc. in Bioinformatics

Alina Renz
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.

German Center for Infection Research (DZIF)
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.

Cluster of Excellence – Controlling Microbes to Fight Infections
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.

German Center for Infection Research (DZIF)
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

FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models

Karthik Raman, Miroslav Kratochvíl, Brett G. Olivier, Matthias König, Pratyay Sengupta, Dinesh Kumar Kuppa Baskaran, Tung V. N. Nguyen, Daniel Lobo, St Elmo Wilken, Krishna Kumar Tiwari, Aswathy K. Raghu, Indumathi Palanikumar, Lavanya Raajaraam, Maziya Ibrahim, Sanjaay Balakrishnan, Shreyanash Umale, Frank T. Bergmann, Tanisha Malpani, Venkata P. Satagopam, Reinhard Schneider, Moritz E. Beber, Sarah M. Keating, Mihail Anton, Alina Renz, Meiyappan Lakshmanan, Dong-Yup Lee, Lokanand Koduru, Reihaneh Mostolizadeh, Oscar Dias, Emanuel Cunha, Alexandre Oliveira, Yi Qing Lee, Karsten Zengler, Rodrigo Santibáñez-Palominos, Manish Kumar, Matteo Barberis, Bhanwar Lal Puniya, Tomáš Helikar, Hoang V. Dinh, Patrick F. Suthers, Costas D. Maranas, Isabella Casini, Seyed Babak Loghmani, Nadine Veith, Nantia Leonidou, Feiran Li, Yu Chen, Jens Nielsen, GaRyoung Lee, Sang Mi Lee, Gi Bae Kim, Pedro T. Monteiro, Miguel C. Teixeira, Hyun Uk Kim, Sang Yup Lee, Ulf W. Liebal, Lars M. Blank, Christian Lieven, Chaimaa Tarzi, Claudio Angione, Manga Enuh Blaise, Çelık Pinar Aytar, Mikhail Kulyashov, llya Akberdin, Dohyeon Kim, Sung Ho Yoon, Zhaohui Xu, Jyotshana Gautam, William T. Scott, Peter J. Schaap, Jasper J. Koehorst, Cristal Zuñiga, Gabriel Canto-Encalada, Sara Benito-Vaquerizo, Ivette Parera Olm, Maria Suarez-Diez, Qianquian Yuan, Hongwu Ma, Mohammad Mazharul Islam, Jason A. Papin, Francisco Zorrilla, Kiran Raosaheb Patil, Arianna Basile, Juan Nogales, Granado San León, Freddy Castillo-Alfonso, Roberto Olivares-Hernández, Gabriel Vigueras-Ramírez, Henning Hermjakob, Andreas Dräger, and Rahuman S. Malik-Sheriff
BioRxiv, September, 26th, 2024
[ Details | DOI | PDF | PubMed | BibTeX ]

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

Nantia Leonidou, Alina Renz, Benjamin Winnerling, Anastasiia Grekova, Fabian Grein, and Andreas Dräger
BioRxiv, December, 20th, 2023.
[ Details | DOI | Preprint | PDF | PubMed | BibTeX ]

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, 30th 2023.
[ Details | DOI | PDF | PubMed | BibTeX ]

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

Sanjeev Dahal, Alina Renz, Andreas Dräger, and Laurence Yang
Communications Biology, 6, 165, February 10th, 2023.
[ Details | DOI | Preprint | PDF | PubMed | BibTeX ]

Towards the human nasal microbiome: simulating D. pigrum and S. aureus

Reihaneh Mostolizadeh, Manuel Glöckler, and Andreas Dräger
Frontiers in Cellular and Infection Microbiology 2022, October 11th, 2022
[ Details | DOI | PDF | PubMed | BibTeX ]

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 12th, 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 15th 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 19th 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

Dawson D. Payne, Alina Renz, Laura J. Dunphy, Taylor Lewis, Andreas Dräger, and Jason A. Papin
npj Systems Biology and Applications 7, 37, October 8th 2021.
[ Details | DOI | Preprint | PubMed | PDF | BibTeX ]

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

Alina Renz, Lina Widerspick, and Andreas Dräger.
Bioinformatics, Volume 36, Issue Supplement_2, December 29th 2020, Pages i813-i821.
[ Details | DOI | Zenodo | PubMed | YouTube | PDF | BibTeX ]

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 26th 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 30th 2020
[ Details | DOI | PDF | PubMed | BibTeX ]