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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Latest Publications
- 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 ] - Curating and Comparing 114 Strain-Specific Genome-Scale Metabolic Models of Staphylococcus aureus
A. Renz and A. Dräger
Preprints, April 8th 2021
[ Details | DOI | 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
BioRxiv, March 11th 2021.
[ Details | DOI | 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 ] - The Systems Biology Simulation Core Library
H. Panchiwala, S. Shah, H. Planatscher, M. Zakharchuk, M. König, and A. Dräger
Preprints, December 11th 2020.
[ Details | DOI | 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 ] - 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
Zenodo, preprint, October 31st 2020.
[ Details | DOI | PDF | BibTeX ] - 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
BioRxiv, October 28th 2020.
[ Details | DOI | 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, August 28th 2020
[ 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 ]