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.
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Latest Publications
- FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2
A. Renz, L. Widerspick, and A. Dräger
Accepted in Bioinformatics, preprint from February 15th 2020.
[ Details | DOI | PDF | BibTeX ] - A Computational Model to Inform Effective Control Interventions against Yersinia enterocolitica Coinfection
R. Mostolizadeh and A. Dräger
Preprints, October 19th 2020.
[ Details | DOI | PDF | BibTeX ] - Longitudinal multi-omics analysis identifies 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
MedRxiv, September 18th 2020.
[ Details | DOI | PubMed | PDF | BibTeX ] - Overview: Standards for Modeling in Systems Medicine
A. Dräger and D. Waltemath
Systems Medicine. Integrative, Qualitative and Computational Approaches. Olaf Wolkenhauer (Editor), Volume 3, 2021, Pages 245–353
[ Details | DOI | PubMed | PDF | BibTeX ] - Community standards to facilitate development and address challenges in metabolic modeling
M. A. Carey, A. Dräger, M. E. Beber, J. A. Papin, and J. T. Yurkovich
Molecular Systems Biology, August 26th 2020.
[ Details | DOI | PubMed | BioRxiv | PDF | BibTeX ] - SBML Level 3: an extensible format for the exchange and reuse of biological models
S. M. Keating, D. Waltemath, M. König, F. Zhang, A. Dräger, C. Chaouiya, F. T. Bergmann, A. Finney, C. Gillespie, T. Helikar, S. Hoops, R. Malik-Sheriff, S. Moodie, I. Moraru, C. J. Myers, A. Naldi, B. Olivier, S. Sahle, J. Schaff, L. P. Smith, M. Swat, D. Thieffry, L. Watanabe, D. Wilkinson, M. L. Blinov, K. Begley, J. Faeder, H. Gómez, T. M. Hamm, Y. Inagaki, W. Liebermeister, A. Lister, D. Lucio, E. Mjolsness, C. Proctor, K. Raman, N. Rodriguez, C. Shaffer, B. Shapiro, J. Stelling, N. Swainston, N. Tanimura, J. Wagner, M. Meier-Schellersheim, H. Sauro, B. Ø. Palsson, H. Bolouri, H. Kitano, A. Funahashi, H. Hermjakob, J. C. Doyle, M. Hucka, and the SBML Level 3 Community members: R. R. Adams, N. A. Allen, B. R. Angermann, M. Antoniotti, G. D. Bader, J. Červený, M. Courtot, C. D. Cox, P. Dalle Pezze, E. Demir, W. S. Denney, H. Dharuri, J. Dorier, D. Drasdo, A. Ebrahim, J. Eichner, J. Elf, L. Endler, C. T. Evelo, C. Flamm, R. M. T. Fleming, M. Fröhlich, M. Glont, E. Gonçalves, M. Golebiewski, H. Grabski, A. Gutteridge, D. Hachmeister, L. A. Harris, B. D. Heavner, R. Henkel, W. S. Hlavacek, B. Hu, D. R. Hyduke, H. Jong, N. Juty, P. D. Karp, J. R. Karr, D. B. Kell, R. Keller, I. Kiselev, S. Klamt, E. Klipp, C. Knüpfer, F. Kolpakov, F. Krause, M. Kutmon, C. Laibe, C. Lawless, L. Li, L. M. Loew, R. Machne, Y. Matsuoka, P. Mendes, H. Mi, F. Mittag, P. T. Monteiro, K. N. Natarajan, P. M. F. Nielsen, T. Nguyen, A. Palmisano, J.‐B. Pettit, T. Pfau, R. D. Phair, T. Radivoyevitch, J. M. Rohwer, O. A. Ruebenacker, J. Saez‐Rodriguez, M. Scharm, H. Schmidt, F. Schreiber, M. Schubert, R. Schulte, S. C. Sealfon, K. Smallbone, S. Soliman, M. I. Stefan, D. P. Sullivan, K. Takahashi, B. Teusink, D. Tolnay, I. Vazirabad, A. Kamp, U. Wittig, C. Wrzodek, F. Wrzodek, I. Xenarios, A. Zhukova, and J. Zucker.
Molecular Systems Biology, August 26th 2020
[ Details | DOI | PubMed | PDF | BibTeX ] - Model-based prediction of bacterial population dynamics in gastrointestinal infection
J. Geißert, E. Bohn, R. Mostolizadeh, A. Dräger, I. Autenrieth, S. Beier, O. Deusch, M. Eichner, and M. Schütz
BioRxiv, August 11th 2020.
[ Details | DOI | PDF | BibTeX ] - Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2
F. Zhang, L. P. Smith, M. L. Blinov, J. Faeder, W. S. Hlavacek, J.-J. Tapia, S. M. Keating, N. Rodriguez, A. Dräger, L. A. Harris, A. Finney, B. Hu, M. Hucka, and M. Meier-Schellersheim
Journal of Integrative Bioinformatics, July 6th 2020.
[ Details | DOI | PubMed | PDF | BibTeX ] - Systems biology graphical notation markup language (SBGNML) version 0.3
F. T. Bergmann, T. Czauderna, U. Dogrusoz, A. Rougny, A. Dräger, V. Touré, A. Mazein, M. L. Blinov, and A. Luna
Journal of Integrative Bioinformatics, June 22nd 2020.
[ Details | DOI | PubMed | PDF | BibTeX ] - COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms
M. Ostaszewski, A. Mazein, M. E. Gillespie, I. Kuperstein, A. Niarakis, H. Hermjakob, A. R. Pico, E. L. Willighagen, C. T. Evelo, J. Hasenauer, F. Schreiber, A. Dräger, E. Demir, O. Wolkenhauer, L. I. Furlong, E. Barillot, J. Dopazo, A. Orta-Resendiz, F. Messina, A. Valencia, A. Funahashi, H. Kitano, C. Auffray, R. Balling, and R. Schneider
Scientific Data 7, 136. May 5th 2020.
[ Details | DOI | PubMed | PDF | BibTeX ] - Visualizing metabolic network dynamics through time-series metabolomic data
L. F. Buchweitz, J. T. Yurkovich, C. Blessing, V. Kohler, F. Schwarzkopf, Z. A. King, L. Yang, F. Jóhannsson, Ó. Sigurjónsson, Ó. Rolfsson, J. Heinrich, and A. Dräger.
BMC Bioinformatics 21, 130. April 3rd 2020.
[ Details | DOI | PubMed | BioRxiv | PDF | BibTeX ] - MEMOTE for standardized genome-scale metabolic model testing
C. Lieven, M. E. Beber, B. G. Olivier, F. T. Bergmann, M. Ataman, P. Babaei, J. A. Bartell, L. M. Blank, S. Chauhan, K. Correia, C. Diener, A. Dräger, B. E. Ebert, J. N. Edirisinghe, J. P. Faria, A. M. Feist, G. Fengos, R. M. T. Fleming, B. García-Jiménez, V. Hatzimanikatis, W. van Helvoirt, C. S. Henry, H. Hermjakob, M. J. Herrgård, A. Kaafarani, H. U. Kim, Z. A. King, S. Klamt, E. Klipp, J. J. Koehorst, M. König, M. Lakshmanan, D.-Y. Lee, S. Y. Lee, S. Lee, N. E. Lewis, F. Liu, H. Ma, D. Machado, R. Mahadevan, P. Maia, A. Mardinoglu, G. L. Medlock, J. M. Monk, J. Nielsen, L. K. Nielsen, J. Nogales, I. Nookaew, B. O. Palsson, J. A. Papin, K. R. Patil, N. D. Price, O. Resendis-Antonio, A. Richelle, I. Rocha, B. J. Sánchez, P. J. Schaap, R. S. M. Sheriff, S. Shoaie, N. Sonnenschein, B. Teusink, P. Vilaça, J. O. Vik, J. A. H. Wodke, J. C. Xavier, Q. Yuan, M. Zakhartsev, and C. Zhang.
Nature Biotechnology, March 2nd 2020.
[ Details | DOI | BioRxiv | PDF | PubMed | BibTeX ] - Clinical Applications of Metabolic Models in SBML Format
A. Renz, R. Mostolizadeh, and A. Dräger
Reference Module in Biomedical Sciences, Elsevier, January 30th 2020
[ Details | DOI | PDF | PubMed | BibTeX ] - The Systems Biology Graphical Notation: Current Status and Applications in Systems Medicine
V. Touré, A. Dräger, A. Luna, U. Dogrusoz, and A. Rougny
Reference Module in Biomedical Sciences, Elsevier, January 25th 2020
[ Details | DOI | PDF | PubMed | BibTeX ]