Computational Systems Biology

Computational Systems Biology of Infections

and Antimicrobial-Resistant Pathogens

This image shows the systems biology research group in November 2022.

Welcome to the Draeger Research Group!

The Dräger research group (est. July 2018) applies computer-aided systems biology, focusing on infections and antimicrobial-resistant pathogens. The research covers all steps from the biological phenomenon to its simulation in the computer, including the reconstruction of biological systems, their mathematical modeling, the standardization of these models, the development of specialized software solutions, and the application of machine learning and data visualization. Deriving model-driven new hypotheses from combating increasing antibiotic resistance systematically constitutes a primary aim.

Relocated to Halle (Saale)

This working group continues its activities at the Martin Luther University Halle-Wittenberg in Halle (Saale). Further information can be found here.

Systems Biology: A short overview

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Latest Publications

  1. From FAIR to CURE: Guidelines for Computational Models of Biological Systems
    H. M. Sauro, E. Agmon, M. L. Blinov, J. H. Gennari, J. Hellerstein, A. Heydarabadipour, P. Hunter, B. E. Jardine, E. May, D. P. Nickerson, L. P. Smith, G. D. Bader, F. T. Bergmann, P. M. Boyle, A. Dräger, J. R. Faeder, S. Feng, J. Freire, F. Fröhlich, J. A. Glazier, T. E. Gorochowski, T. Helikar, S. Hoops, P. Imoukhuede, S. M. Keating, M. König, R. Laubenbacher, L. M. Loew, C. F. Lopez, W. W. Lytton, A. McCulloch, P. Mendes, C. J. Myers, J. G. Myers, L. Mulugeta, A. Niarakis, D. D. van Niekerk, B. G. Olivier, A. A. Patrie, E. M. Quardokus, N. Radde, J. M. Rohwer, S. Sahle, J. C. Schaff, T. J. Sego, J. Shin, J. L. Snoep, R. Vadigepalli, H. S. Wiley, D. Waltemath, and I. Moraru
    Arxiv, February, 21st, 2025
    [ Details | DOI | PDF | PubMed | BibTeX ]
  2. MCC: Automated Mass and Charge Curation at Genome-Scale Applied to C. tuberculostearicum
    R. Mostolizadeh, F. Mier, and A. Dräger
    BioRxiv, November 22nd, 2024
    [ Details | DOI | PDF | PubMed | BibTeX ]
  3. COMBINE 2024 - Conference of the Computational Modeling in Biology Network : September 1-5, 2024, University of Stuttgart
    Contributions by B. Ziadah, D. V. Molnár, M. Gaas, A. Neumann, N. Roßbach, D. Eltzner, G. O. Döbel, C. Brune, N. Leonidou, and A. Dräger
    [ Details | DOI | PDF | PubMed | BibTeX ]
  4. FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models
    K. Raman, M. Kratochvíl, B. G. Olivier, M. König, P. Sengupta, D. K. K. Baskaran, T. V. N. Nguyen, D. Lobo, S. E. Wilken, K. K. Tiwari, A. K. Raghu, I. Palanikumar, L. Raajaraam, M. Ibrahim, S. Balakrishnan, S. Umale, F. T. Bergmann, T. Malpani, V. P. Satagopam, R. Schneider, M. E. Beber, S. M. Keating, M. Anton, A. Renz, M. Lakshmanan, D.-Y. Lee, L. Koduru, R. Mostolizadeh, O. Dias, E. Cunha, A. Oliveira, Y. Q. Lee, K. Zengler, R. Santibáñez-Palominos, M. Kumar, M. Barberis, B. L. Puniya, T. Helikar, H. V. Dinh, P. F. Suthers, C. D. Maranas, I. Casini, S. B. Loghmani, N. Veith, N. Leonidou, F. Li, Y. Chen, J. Nielsen, G. Lee, S. M. Lee, G. B. Kim, P. T. Monteiro, M. C. Teixeira, H. U. Kim, S. Y. Lee, U. W. Liebal, L. M. Blank, C. Lieven, C. Tarzi, C. Angione, M. E. Blaise, Ç. P. Aytar, M. Kulyashov, l. Akberdin, D. Kim, S. H. Yoon, Z. Xu, J. Gautam, W. T. Scott, P. J. Schaap, J. J. Koehorst, C. Zuñiga, G. Canto-Encalada, S. Benito-Vaquerizo, I. P. Olm, M. Suarez-Diez, Q. Yuan, H. Ma, M. M. Islam, J. A. Papin, F. Zorrilla, K. R. Patil, A. Basile, J. Nogales, G. San León, F. Castillo-Alfonso, R. Olivares-Hernández, G. Vigueras-Ramírez, H. Hermjakob, A. Dräger, and R. S. Malik-Sheriff
    BioRxiv, September, 26th, 2024
    [ Details | DOI | PDF | PubMed | BibTeX ]
  5. Exploring the metabolic profile of A. baumannii for antimicrobial development using genome-scale modeling
    N. Leonidou, Y. Xia, L. Friedrich, M. S. Schütz, and A. Dräger
    PLOS Pathongens, September, 23rd, 2024.
    [ Details | Preprint | DOI | PDF | PubMed | BibTeX ]
  6. Perspectives on computational modeling of biological systems and the significance of the SysMod community
    B. L. Puniya, M. Verma, C. Damiani, S. Bakr, and A. Dräger
    Bioinformatics Advances, 26. Juni 2024
    [ Details | DOI | PDF | PubMed | BibTeX ]
  7. Genome-Scale Modeling of Rothia mucilaginosa Reveals Insights into Metabolic Capabilities and Therapeutic Strategies for Cystic Fibrosis
    N. Leonidou, L. Ostyn, T. Coenye, A. Crabbé, and A. Dräger
    Microbiology Spectrum, April 23rd, 2024
    [ Details | DOI | Preprint | PDF | PubMed | BibTeX ]
  8. Genome-scale metabolic model of Staphylococcus epidermidis ATCC 12228 matches in vitro conditions
    N. Leonidou, A. Renz, B. Winnerling, A. Grekova, F. Grein, A. Dräger
    BioRxiv, December 20th, 2023
    [ Details | DOI | PDF | PubMed | BibTeX ]
  9. Metabolic Modeling Elucidates Phenformin and Atpenin A5 as Broad-Spectrum Antiviral Drugs
    A. Renz, M. Hohner, M. Breitenbach, J. Josephs-Spaulding, J. Dürrwald, L. Best, R. Jami, G. Marinos, N. Leonidou, F. Cabreiro, A. Dräger, M. Schindler und C. Kaleta
    Preprints 2023, November 30th, 2023.
    [ Details | DOI | PDF | PubMed | BibTeX ]
  10. Genome-scale metabolic models consistently predict in vitro characteristics of Corynebacterium striatum
    F. Bäuerle, G. O. Döbel, L. Camus, S. Heilbronner, and A. Dräger
    Frontiers in Bioinformatics, Section Network Bioinformatics, October, 23rd 2023.
    [ Details | DOI | Preprint | PDF | PubMed | BibTeX ]
  11. An integrated systems-biology approach reveals differences in formate metabolism in the genus Methanothermobacter
    I. Casini, T. McCubbin, S. Esquivel-Elizondo, G. G. Luque, D. Evseeva, C. Fink, S. Beblawy, N. D. Youngblut, L. Aristilde, D. H. Huson, A. Dräger, R. E. Ley, E. Marcellin, L. T. Angenent, B. Molitor.
    iScience, September 22nd, 2023
    [ Details | DOI | Preprint | PDF | PubMed | BibTeX ]
  12. 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
    E. Kurpejović, D. Wibberg, G. M. Bastem, A. Burgardt, T. Busche, F. E. A. Kaya, A. Dräger, V. F. Wendisch und B. S. Akbulut
    OMICS: A Journal of Integrative Biology, September 14th, 2023.
    [ Details | DOI | PDF | PubMed | BibTeX ]
  13. Advancements in Computational Modelling of Biological Systems: seventh annual SysMod meeting
    B. L. Puniya and A. Dräger
    Bioinformatics, September 14st 2023.
    [ Details | DOI | PDF | PubMed | BibTeX ]
  14. SBOannotator: a Python Tool for the Automated Assignment of Systems Biology Ontology Terms
    N. Leonidou, E. Fritze, A. Renz, and A. Dräger
    Bioinformatics, July 14th 2023.
    [ Details | DOI | Preprint | PDF | PubMed | BibTeX ]
  15. Standard-GEM: Standardization of open-source genome-scale metabolic models
    M. Anton,  E. Almaas, R. Benfeitas, S. Benito-Vaquerizo, L. M. Blank, A. Dräger, J. M. Hancock, C. Kittikunapong, M. König, F. Li, U. W. Liebal, H. Lu, H. Ma, R. Mahadevan, A. Mardinoglu, J. Nielsen, J. Nogales, M. Pagni, J. A. Papin, K. R. Patil, N. D. Price, J. L. Robinson, B. J. Sánchez, M. Suarez Diez, S. Sulheim, L. T. Svensson, B. Teusnik, W. Vongsangnak, H. Wang, A. A. Zeidan, and E. J. Kerkhoven
    BioRxiv, March 23rd, 2023.
    [ Details | DOI | PDF | PubMed | BibTeX ]

Complete List of Publications