Publications | University of Tübingen

An integrated systems-biology approach reveals differences in formate metabolism in the genus Methanothermobacter

Isabella Casini, Tim McCubbin, Sofia Esquivel-Elizondo, Guillermo G. Luque, Daria Evseeva, Christian Fink, Sebastian Beblawy, Nicholas D. Youngblut, Ludmilla Aristilde, Daniel H. Huson, Andreas Dräger, Ruth E. Ley, Esteban Marcellin, Largus T. Angenent, and Bastian Molitor
iScience, September 22^nd, 2023
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Exploring the metabolic profiling of A. baumannii for antimicrobial development using genome-scale modeling

Nantia Leonidou, Yufan Xia, and Andreas Dräger
BioRxiv, September, 15^th 2023.
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Can Genome Sequencing Coupled to Flux Balance Analyses Offer Precision Guidance for Industrial Strain Development? The Lessons from Carbon Trafficking in Corynebacterium glutamicum ATCC 21573

Eldin Kurpejović, Daniel Wibberg, Gülsüm Merve Bastem, Arthur Burgardt, Tobias Busche, Fatma Ece Altınışık Kaya, Andreas Dräger, Volker F. Wendisch, and Berna Sarıyar Akbulut
OMICS: A Journal of Integrative Biology, 27:9, September 14^th, 2023.
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Advancements in Computational Modelling of Biological Systems: seventh annual SysMod meeting

Bhanwar Lal Puniya and Andreas Dräger
Bioinformatics, 14. September 2023.
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SBOannotator: a Python Tool for the Automated Assignment of Systems Biology Ontology Terms

Genome-scale metabolic models consistently predict in vitro characteristics of Corynebacterium striatum

Famke Bäuerle, Gwendolyn O. Gusak, L. Camus, S. Heilbronner, and Andreas Dräger
BioRxiv, April, 29^th 2023.
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New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells

Standard-GEM: Standardization of open-source genome-scale metabolic models

Mihail Anton, Eivind Almaas, Rui Benfeitas, Sara Benito-Vaquerizo, Lars M. Blank, Andreas Dräger, John M. Hancock, Cheewin Kittikunapong, Matthias König, Feiran Li, Ulf W. Liebal, Hongzhong Lu, Hongwu Ma, Radhakrishnan Mahadevan, Adil Mardinoglu, Jens Nielsen, Juan Nogales, Marco Pagni, Jason A. Papin, Kiran Raosaheb Patil, Nathan D. Price, Jonathan L. Robinson, Benjamín J. Sánchez, Maria Suarez Diez, Snorre Sulheim, L. Thomas Svensson, Bas Teusnik, Wanwipa Vongsangnak, Hao Wang, Ahmad A. Zeidan, and Eduard J. Kerkhoven.
BioRxiv, March 23^rd, 2023
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Genome-scale model of Pseudomonas aeruginosa metabolism unveils virulence and drug potentiation

Hierarchical modelling of microbial communities

Manuel Glöckler, Andreas Dräger, and Reihaneh Mostolizadeh
Bioinformatics, January 17^th, 2023.
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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, Filipe Cabreiro, Andreas Dräger, Michael Schindler, and Christoph Kaleta
Preprints 2022, October, 17^th 2022.
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Computational modelling in health and disease. Highlights of the 6th annual SysMod meeting

Anna Niarakis, Juilee Thakar, Matteo Barberis, María Rodríguez Martínez, Tomáš Helikar, Marc Birtwistle, Claudine Chaouiya, Laurence Calzone, and Andreas Dräger
Bioinformatics, September 22^nd, 2022.
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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, August 15^th, 2022
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FluxomicsExplorer: Differential visual analysis of flux sampling based on metabolomics

Constantin Holzapfel, Miriam Hoene, Xinjie Zhao, Chunxiu Hu, Cora Weigert, Andreas Nieß, Guowang Xu, Rainer Lehmann, Andreas Dräger, and Michael Krone
Computers & Graphics, August 29^th, 2022
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NCMW: A Python Package to Analyze Metabolic Interactions in the Nasal Microbiome

Manuel Glöckler, Andreas Dräger, and Reihaneh Mostolizadeh
Frontiers in Bioinformatics, February 25^th, 2022.
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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.
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The Systems Biology Simulation Core Library

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.
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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.
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SBMLWebApp: Web-based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models

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

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems

Andreas Dräger, Tomáš Helikar, Matteo Barberis, Marc Birtwistle, Laurence Calzone, Claudine Chaouiya, Jan Hasenauer, Jonathan R. Karr, Anna Niarakis, María Rodríguez Martínez, Julio Saez-Rodriguez, and Juilee Thakar.
Bioinformatics, btab229, 24^th 2021.
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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
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FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2

Computational Model Informs Effective Control Interventions against Y. enterocolitica Co-Infection

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.
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Genome-Scale Metabolic Modeling of Escherichia coli and Its Chassis Design for Synthetic Biology Applications

Bashir Sajo Mienda and Andreas Dräger.
Computational Methods in Synthetic Biology. Mario Andrea Marchisio (editor), part of the series Methods in Molecular Biology (MIMB, volume 2189), pp. 217-229, November 13^th 2020.
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Systems Medicine. Integrative, Qualitative and Computational Approaches