Publications
Year of Publication: 2023
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, 29th 2023.
[ Details | DOI | PDF | PubMed | BibTeX ]
New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
Nantia Leonidou, Alina Renz, Reihaneh Mostolizadeh, and Andreas Dräger
PLOS Computational Biology 19(3): e1010903, March 23rd, 2023
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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 23rd, 2023
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SBOannotator: a Python Tool for the Automated Assignment of Systems Biology Ontology Terms
Nantia Leonidou, Elisabeth Fritze, Alina Renz, and Andreas Dräger
Preprints 2023, February, 17th 2023.
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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.
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Hierarchical modelling of microbial communities
Manuel Glöckler, Andreas Dräger, and Reihaneh Mostolizadeh
Bioinformatics, January 17th, 2023.
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Year of Publication: 2022
An integrated systems-biology platform for power-to-gas technology
Isabelle 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, Bastian Molitor.
BioRxiv, December 31st, 2022
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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, 17th 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 22nd, 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 15th, 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 29th, 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 25th, 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 12th, 2022.
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The Systems Biology Simulation Core Library
Hemil Panchiwala, Shalin Shah, Hannes Planatscher, Mykola Zakharchuk, Matthias König, and Andreas Dräger.
Bioinformatics, Volume 38, Issue 3, Pages 864-865, February 1st, 2022.
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Year of Publication: 2021
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.
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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 19th 2021.
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SBMLWebApp: Web-based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models
Takahiro G. Yamada, Kaito Ii, Matthias König, Martina Feierabend, Andreas Dräger, and Akira Funahashi.
Processes, 9(10), October 15th 2021
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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.
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Curating and Comparing 114 Strain-Specific Genome-Scale Metabolic Models of Staphylococcus aureus
Alina Renz and Andreas Dräger
npj Systems Biology and Applications 7, 30, June 29th 2021
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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, 24th 2021.
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Genome-Scale Metabolic Model of Infection with SARS-CoV-2 Mutants Confirms Guanylate Kinase as Robust Potential Antiviral Target
Alina Renz, Lina Widerspick, and Andreas Dräger
Genes, 2021, 12, 796. May 24th, 2021
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First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies
Alina Renz, Lina Widerspick, and Andreas Dräger
Metabolites, 11(4), 232, April 9th 2021
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Year of Publication: 2020
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 ]
Computational Model Informs Effective Control Interventions against Y. enterocolitica Co-Infection
Reihaneh Mostolizdadeh and Andreas Dräger.
Biology, 9(12), Special Issue Computational Biology, November 30th 2020.
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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 ]
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 13th 2020.
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Overview: Standards for Modeling in Systems Medicine
Andreas Dräger and Dagmar Waltemath
Systems Medicine. Integrative, Qualitative and Computational Approaches. Olaf Wolkenhauer (Editor), Volume 3, 2021, Pages 245–353, August 28th 2020.
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Clinical Applications of Metabolic Models in SBML Format
Alina Renz, Reihaneh Mostolizadeh, and Andreas Dräger
Reference Module in Biomedical Sciences, Elsevier, Januar 30th 2020
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The Systems Biology Graphical Notation: Current Status and Applications in Systems Medicine
Vasundra Touré, Andreas Dräger, Augustin Luna, Ugur Dogrusoz, and Adrien Rougny
Reference Module in Biomedical Sciences, Elsevier, Januar 25th 2020
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