Computational Systems Biology of Infections
and Antimicrobial-Resistant Pathogens
Welcome to the Draeger Research Group!
The Dräger working group was founded in July 2018 and since then has been dedicated to computer-aided systems biology with a focus on infections and antimicrobial-resistant pathogens. The research foci of the group cover all steps from the biological phenomenon to its simulation in the computer. The work includes the reconstruction of biological systems, their mathematical modeling, the standardization of these models, as well as the development of specialized software solutions and the application of methods of machine learning. A primary goal is to derive model-driven new hypotheses to combat increasing antibiotic resistance systematically.
Systems Biology: A short overview
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Special Issue “Metabolic Modeling of the Human Nasal Microbiome”
We are pleased to announce a Special Issue of the journal Metabolites dedicated to metabolic modeling of the human nasal microbiome.
As the bridge between the environment and the internal body, the nose plays a vital role in the defense against various infectious diseases: Various commensal and pathogenic bacterial species plus viruses recurringly colonize highly diverse habitats within the nostrils. While antiviral treatments may not even always be available, the spread of antibiotic resistance leads to a situation in which many harmful pathogens no longer reliably respond to antibacterial medication. At the same time, a complex interplay of commensal bacterial, human body cells, and further nasal inhabitants may reduce the risk for severe infections and possibly enable alternative treatment strategies. This Special Issue collects studies that investigate systems biology modeling approaches of the human nasal microbiome.
For more information, visit mdpi.com/si/88426.
Possible topics include, in particular:
- Biology of the nose and its colonization
- Reconstructions of computer models of the nasal inhabitants and relevant host cells
- Interactions and intervention options
- Software for simulation and visualization
Latest Publications
- COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms
M. Ostaszewski, A. Niarakis, A. Mazein, I. Kuperstein, R. Phair, A. Orta-Resendiz, V. Singh, S. S. Aghamiri, M. L. Acencio, E. Glaab, A. Ruepp, G. Fobo, C. Montrone, Barbara Brauner, Goar Frishman, L. C. Monraz Gómez, J. Somers, M. Hoch, S. Kumar Gupta, J. Scheel, H. Borlinghaus, T. Czauderna, F. Schreiber, A. Montagud, M. Ponce de Leon, A. Funahashi, Y. Hiki, N. Hiroi, T. G. Yamada, A. Dräger, A. Renz, M. Naveez, Z. Bocskei, F. Messina, D. Börnigen, L. Fergusson, M. Conti, M. Rameil, V. Nakonecnij, J. Vanhoefer, L. Schmiester, M. Wang, E. E. Ackerman, J. E. Shoemaker, J. Zucker, K. L. Oxford, J. Teuton, E. Kocakaya, G. Y. Summak, K. Hanspers, M. Kutmon, S. Coort, L. Eijssen, F. Ehrhart, R. D. A. B., D. Slenter, M. Martens, R. Haw, B. Jassal, L. Matthews, M. Orlic-Milacic, A. Senff-Ribeiro, K. Rothfels, V. Shamovsky, R. Stephan, C. Sevilla, T. M. Varusai, J.-M. Ravel, R. Fraser, V. Ortseifen, S. Marchesi, P. Gawron, E. Smula, L. Heirendt, V. Satagopam, G. Wu, A. Riutta, M. Golebiewski, S. Owen, C. Goble, X. Hu, R. Overall, D. Maier, A. Bauch, J. A. Bachman, B. M. Gyori, C. Vega, V. Grouès, M. Vazquez, P. Porras, L. Licata, M. Iannuccelli, F. Sacco, D. Turei, A. Luna, O. Babur, S. Soliman, A. Valdeolivas, M. Esteban-Medina, M. Peña-Chilet, T. Helikar, B. Lal Puniya, A. Nesterova, A. Yuryev, A. de Waard, D. Modos, A. Treveil, M. L. Olbei, B. De Meulder, A. Naldi, A. Dugourd, V. Noël, L. Calzone, C. Sander, E. Demir, T. Korcsmaros, T. C. Freeman, F. Auge, J. S. Beckmann, J. Hasenauer, O. Wolkenhauer, E. Willighagen, A. R. Pico, C. Evelo, M. Gillespie, L. D. Stein, H. Hermjakob, P. DʼEustachio, J. Saez-Rodriguez, J. Dopazo, A. Valencia, H. Kitano, E. Barillot, C. A., R. Balling, R. Schneider, and the COVID-19 Disease Map Community
Molecular Systems Biology 17: e10387, October 19th 2021.
[ Details | DOI | Preprint | PubMed | PDF | BibTeX ] - SBMLWebApp: Web-based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models
T. G. Yamada, K. Ii, M. König, M. Feierabend, A. Dräger, and A. Funahashi
Processes, 9(10), October 15th 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
D. D. Payne, A. Renz, L. J. Dunphy, T. Lewis, A. Dräger, and J. A. Papin
npj Systems Biology and Applications 7, 37, October 8th 2021.
[ Details | DOI | Preprint | PubMed | PDF | BibTeX ] - The Systems Biology Simulation Core Library
H. Panchiwala, S. Shah, H. Planatscher, M. Zakharchuk, M. König, and A. Dräger
Bioinformatics, September 23rd 2021.
[ Details | Preprint | DOI | PubMed | PDF | BibTeX ] - Genome-scale modeling of Pseudomonas aeruginosa PA14 unveils its broad metabolic capabilities and role of metabolism in drug potentiation
S. Dahal, A. Renz, A. Dräger, and L. Yang
BioRxiv, September 22nd 2021.
[ Details | DOI | PDF | BibTeX ] - Curating and Comparing 114 Strain-Specific Genome-Scale Metabolic Models of Staphylococcus aureus
A. Renz and A. Dräger
npj Systems Biology and Applications 7, 30, June 29th 2021
[ Details | DOI | Preprint | PubMed | PDF | BibTeX ] - SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems
A. Dräger, T. Helikar, M. Barberis, M. Birtwistle, L. Calzone, C. Chaouiya, J. Hasenauer, J. R. Karr, A. Niarakis, M. Rodríguez Martínez, J. Saez-Rodriguez, and J. Thakar
Bioinformatics, btab229, June 24th 2021.
[ Details | DOI | Preprint | PubMed | PDF | BibTeX ] - Genome-Scale Metabolic Model of Infection with SARS-CoV-2 Mutants Confirms Guanylate Kinase as Robust Potential Antiviral Target
A. Renz, L. Widerspick, and A. Dräger
Genes, 2021, 12, 796. May 24th, 2021
[ Details | DOI | Preprint | PubMed | PDF | BibTeX ] - First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies
A. Renz, L. Widerspick, and A. Dräger
Metabolites, 11(4), 232, April 9th 2021
[ Details | DOI | PubMed | PDF | BibTeX ] - FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2
A. Renz, L. Widerspick, and A. Dräger
Bioinformatics, Volume 36, Issue Supplelment_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
R. Mostolizadeh and A. Dräger
Biology, 9(12), Special Issue Computational Biology, November 30th 2020.
[ Details | DOI | Preprints | PubMed | PDF | BibTeX ] - Longitudinal multi-omics analyses identify responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories
J. P. Bernardes, N. Mishra, F. Tran, T. Bahmer, L. Best, J. I. Blase, D. Bordoni, J. Franzenburg, U. Geisen, J. Josephs-Spaulding, P. Köhler, A. Künstner, E. Rosati, A. C. Aschenbrenner, P. Bacher, N. Baran, T. Boysen, B. Brandt, N. Bruse, J. Dörr, A. Dräger, G. Elke, D. Ellinghaus, J. Fischer, M. Forster, A. Franke, S. Franzenburg, N. Frey, A. Friedrichs, J. Fuß, A. Glück, J. Hamm, F. Hinrichsen, M. P. Höppner, S. Imm, R. Jünker, S. Kaiser, Y. H. Kan, R. Knoll, C. Lange, G. Laue, C. Lier, M. Lindner, G. Marinos, R. Markewitz, J. Nattermann, R. Noth, P. Pickkers, K. F. Rabe, A. Renz, C. Röcken, J. Rupp, A. Schaffarzyk, A. Scheffold, J. Schulte-Schrepping, D. Schunck, D. Skowasch, T. Ulas, K.-P. Wandinger, M. Wittig, J. Zimmermann, H. Busch, B. F. Hoyer, C. Kaleta, J. Heyckendorf, M. Kox, J. Rybniker, S. Schreiber, J. Schultze, and P. Rosenstiel
Immunity, November 26th 2020.
[ Details | DOI | MedRxiv | PubMed | PDF | BibTeX ] - Genome-Scale Metabolic Modeling of Escherichia coli and Its Chassis Design for Synthetic Biology Applications
B. S. Mienda and A. Dräger
Computational Methods in Synthetic Biology. M. A. Marchisio (editor), part of the series Methods in Molecular Biology (MIMB, volume 2189), pages 217-229, November 13th 2020
[ Details | DOI | PubMed | PDF | BibTeX ]