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

  1. BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree
    C. J. Norsigian, N. Pusarla, J. L. McConn, J. T. Yurkovich, A. Dräger, B. O. Palsson, and Z. King
    Nucleic Acids Research, gkz1054, November 7th 2019
    [ Details | DOI | PDF | PubMed | BibTeX ]
  2. Community standards to facilitate development and address challenges in metabolic modeling
    M. A. Carey, A. Dräger, J. A. Papin, J. T. Yurkovich
    bioRxiv, July 15 2019.
    [ DOI | PDF ]
  3. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2
    M. Hucka, F. T. Bergmann, C. Chaouiya, A. Dräger, S. Hoops, S. M. Keating, M. König, N. Le Novère, C. J. Myers, B. G. Olivier, S. Sahle, J. C. Schaff, R. Sheriff, L. P. Smith, D. Waltemath, D. J. Wilkinson, and F. Zhang.
    Journal of Integrative Bioinformatics, June 20th 2019.
    [ Details | DOI | Link | PubMed | BibTeX ]
  4. Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0
    A. Rougny, V. Touré, S. Moodie, I. Balaur, T. Czauderna, H. Borlinghaus, U. Dogrusoz, A. Mazein, A. Dräger, M. L. Blinov, A. Villéger, R. Haw, E. Demir, H. Mi, A. Sorokin, F. Schreiber, and A. Luna.
    Journal of Integrative Bioinformatics, June 13th 2019.
    [ Details | DOI | Link | PubMed | BibTeX ]
  5. Insights into Dynamic Network States Using Metabolomics Data
    Reihaneh Mostolizadeh​​​​​Andreas Dräger and Neema Jamshidi.
    In: Angelo D’Alessandro (eds) High-Throughput Metabolomics.
    Methods in Molecular Biology, volume 1978, Chapter, pages 243-258. Humana, New York, NY, May 2019.
    [ DetailsDOI | link | PubMed | BibTeX ]
  6. The 2017 Network Tools and Applications in Biology (NETTAB) Workshop: aims, topics, and outcomes
    P. Romano, A. Céol, A. Dräger, A. Fiannaca, R. Giugno, M. La Rosa, L. Milanesi, U. Pfeffer, R. Rizzo, S.-Y. Shin, J. Xia, and A. Urso
    BMC Bioinformatics, April 18th 2019.
    DOI | PDF | PubMedBibTeX ]
  7. Harmonizing semantic annotations for computational models in biology
    M. L. Neal, M. König, D. Nickerson, G. Mısırlı, R. Kalbasi, A. Dräger, K. Atalag, V. Chelliah, M. Cooling, D. L. Cook, S. Crook, M. de Alba, S. H. Friedman, A. Garny, J. H. Gennari, P. Gleeson, M. Golebiewski, M. Hucka, N. Juty, C. Myers, B. G. Olivier, H. M. Sauro, M. Scharm, J. L Snoep, V. Touré, A. Wipat, O. Wolkenhauer, and D. Waltemath. 
    Briefings in Bioinformatics, November 21st 2018.
    DOI | PDF | PubMed | BibTeX ]
  8. Visualizing metabolic network dynamics through time-series metabolomics 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.
    bioRxiv, September 26th 2018.
    [ DetailsDOI | PDF ]
  9. Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655
    Y. Gao, J. T. Yurkovich, S. Woo Seo, I. Kabimoldayev, A. Dräger, K. Chen, A. V. Sastry, X. Fang, N. Mih, L. Yang, J. Eichner, B.-K. Cho, D. Kim, and B. O. Palsson.
    Nucleic Acids Research, August 23rd 2018.
    [ DOI | PDF | PubMed | BibTeX ]
  10. Hopf bifurcation in a model for adult T‐cell leukemia
    R. Mostolizadeh, and Z. Afsharnezhad.
    Mathematical Methods in the Applied Sciences, July 26th 2018.
    [ DOI | PDF ]
  11. Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite
    C. Lieven, M. E. Beber, B. G. Olivier, F. T. Bergmann, P. Babaei, J. A. Bartell, L. M. Blank, S. Chauhan, K. Correia, C. Diener, A. Dräger, B. E. Ebert, J. N. Edirisinghe, R. M. T. Fleming, B. Garcia-Jimenez, W. van Helvoirt, C. Henry, H. Hermjakob, M. J. Herrgård, H. U. Kim, Z. A. King, J. J. Koehorst, S. Klamt, E. Klipp, M. Lakshmanan, N. Le Novère, D.-Y. Lee, S. Y. Lee, S. Lee, N. E. Lewis, H. Ma, D. Machado, R. Mahadevan, P. Maia, A. Mardinoglu, G. L. Medlock, J. Monk, J. Nielsen, L. K. Nielsen, J, Nogales, I. Nookaew, O. Resendis, B. O. Palsson, J. A. Papin, K. R. Patil, N. D. Price, A. Richelle, I. Rocha, P. Schaap, R. S. M. Sheriff, S. Shoaie, N. Sonnenschein, B. Teusink, P. Vilaca, J. O. Vik, J. A. Wodke, J. C. Xavier, Q. Yuan, M. Zakhartsev, and C. Zhang.
    BioRxiv, June 21st 2018.
    [ DetailsDOI | PDF ]