Computational Systems Biology of Infections

and Antimicrobial-Resistant Pathogens

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.


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

  1. 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, F. Cabreiro, A. Dräger, M. Schindler und C. Kaleta
    Preprints 2022, 2022100223, October 17th, 2022.
    [ Details | DOI | PDF | PubMed | BibTeX ]
  2. Computational modelling in health and disease. Highlights of the 6th annual SysMod meeting
    A. Niarakis, J. Thakar, M. Barberis, M. Rodríguez Martínez, T. Helikar, M. Birtwistle, C. Chaouiya, L. Calzone, and A. Dräger
    Bioinformatics, September 22nd, 2022.
    Details | DOI | PDF | PubMed | BibTeX ]
  3. Towards the human nasal microbiome: simulating D. pigrum and S. aureus
    R. MostolizadehM. Glöckler, and A. Dräger
    Frontiers in Cellular and Infection Microbiology 2022, August 15th, 2022
    [ Details | DOI | PDF | PubMed | BibTeX ]
  4. FluxomicsExplorer: Differential visual analysis of flux sampling based on metabolomics
    C. Holzapfel, M. Hoene, X. Zhao, C. Hu, C. Weigert, A. Nieß, G. Xu, R. Lehmann, A. Dräger, and M. Krone
    Computers & Graphics, August 29th, 2022.
    [ DetailsDOI | PDF | PubMed | BibTeX ]
  5. New Workflow Predicts Drug Targets Against SARS-CoV-2 via Metabolic Changes in Infected Cells
    N. Leonidou, A. Renz, R. Mostolizadeh, and A. Dräger
    Preprints 2022, March 22nd, 2022.
    [ Details | DOI | PDF | PubMed | BibTeX ]
  6. NCMW: A Python Package to Analyze Metabolic Interactions in the Nasal Microbiome
    M. Glöckler, A. Dräger, and R. Mostolizadeh
    Frontiers in Bioinformatics, February 25th, 2022.
    [ Details | DOI | PDF | PubMed | BibTeX ]
  7. A Computational Model of Bacterial Population Dynamics in Gastrointestinal Yersinia enterocolitica Infections in Mice
    J. K. Geißert, E. Bohn, R. Mostolizadeh, A. Dräger, I. B. Autenrith, S. Beier, O. Deutsch, A. Renz, M. Eichner, and M. S. Schütz
    Biology 11(2), 297, Februar 12th, 2022.
    [ Details | DOI | Preprint | PDF | PubMed | BibTeX ]
  8. The Systems Biology Simulation Core Library
    H. Panchiwala, S. Shah, H. Planatscher, M. Zakharchuk, M. König, and A. Dräger
    Bioinformatics, Volume 38, Issue 3, Pages 864-865, February 1st, 2022.
    [ Details | Preprint | DOI | PubMedPDF | BibTeX ]
  9. High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032
    M. Feierabend, A. Renz, E. Zelle, K. Nöh, W. Wichert, and A. Dräger
    Frontiers in Microbiology, November 15th, 2021.
    [ Details | DOI | PDF | PubMed | BibTeX ]
  10. 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 ]
  11. 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 ]
  12. 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 ]
  13. Genome-scale modeling of Pseudomonas aeruginosa PA14 unveils its broad metabolic capabilities and role of metabolism in drug potentiation
    S. Dahal, A. RenzA. Dräger, and L. Yang
    BioRxiv, September 22nd, 2021.
    [ Details | DOI | PDF | BibTeX ]