ZMB Member Farnoush Farahpour

ZMB Member
Farnoush Farahpour

Next ZMB-Member
portrait photo of ZMB member Farnoush Farahpour
© F. Farahpour

Dr. Farnoush Farahpour

Faculty of Biology
University of Duisburg-Essen
Universitätsstr. 2
45141 Essen

Research Overview

Overcoming Complexity of Biological Systems: from Data Analysis to Mathematical Modeling
Biological systems are complex. This complexity arises from the collective behavior of many interacting units and can occur at all levels of the biological world, from molecular and cellular levels to the individual and population levels. These systems may show simultaneously several aspects of complexity, for example by being dynamic, non-linear, self-organized, and multi-layered. To understand complex biological systems, it is not sufficient to identify and characterize the individual units in the system but a comprehensive understanding of the interactions between the units and seeing them as a community is necessary. This approach has proven its capabilities in providing mechanistic insights in the study of complex phenomena in all fields of biology from theoretical models of evolution to the transnational studies of complex diseases such as cancer or diabetes.

In our research, we focus on the development of computational methods, including data analysis tools and statistical and mathematical models, for understanding the dynamics and behavior of complex biological systems. We have active research projects on developing reliable tools to infer interactions of biological units, for example in microbial communities or T cell receptor repertoires. We also use different mathematical modeling approaches, including stochastic individual-based models, to study mechanisms of diversity generation and maintenance in biological communities, and multi-level models, for systems biology problems, like radio therapy-induced immune responses.

Selected Publications

    Journal articles

  • Srinivas, Nalini; Peiffer, Lukas; Horny, Kai; Lei, Kuan Cheok; Buus, Terkild B.; Kubat, Linda; Luo, Meng; Yin, Menghong; Spassova, Ivelina; Sucker, Antje; Farahpour, Farnoush; Kehrmann, Jan; Ugurel, Selma; Livingstone, Elisabeth; Gambichler, Thilo; Ødum, Niels; Becker, Jürgen C.
    Single-cell RNA and T-cell receptor sequencing unveil mycosis fungoides heterogeneity and a possible gene signature
    In: Frontiers in Oncology Vol. 14 (2024) 1408614
  • Kitanovski, Simo; Cao, Yingying; Ttoouli, Dimitris; Farahpour, Farnoush; Wang, Jun; Hoffmann, Daniel
    scBubbletree: computational approach for visualization of single cell RNA-seq data
    In: BMC Bioinformatics Vol. 25 (2024) Nr. 1, 302
  • Reinold, Johanna; Farahpour, Farnoush; Schoerding, Ann-Kathrin; Fehring, Christian; Dolff, Sebastian; Konik, Margarethe; Korth, Johannes; van Baal, Lukas; Buer, Jan; Witzke, Oliver; Westendorf, Astrid M.; Kehrmann, Jan
    The Fungal Gut Microbiome Exhibits Reduced Diversity and Increased Relative Abundance of Ascomycota in Severe COVID-19 Illness and Distinct Interconnected Communities in SARS-CoV-2 Positive Patients
    In: Frontiers in Cellular and Infection Microbiology Vol. 12 (2022) 848650
  • Reinold, Johanna; Farahpour, Farnoush; Fehring, Christian; Dolff, Sebastian; Konik, Margarethe; Korth, Johannes; van Baal, Lukas; Hoffmann, Daniel; Buer, Jan; Witzke, Oliver; Westendorf, Astrid; Kehrmann, Jan
    A Pro-Inflammatory Gut Microbiome Characterizes SARS-CoV-2 Infected Patients and a Reduction in the Connectivity of an Anti-Inflammatory Bacterial Network Associates With Severe COVID-19
    In: Frontiers in Cellular and Infection Microbiology Vol. 11 (2021) 747816
  • Pfeiffer, Lukas; Farahpour, Farnoush; Sriram, Ashwin; Spassova, Ivelina; Hoffmann, Daniel; Kubat, Linda; Stoitzner, Patrizia; Gambichler, Thilo; Sucker, Antje; Ugurel, Selma; Schadendorf, Dirk; Becker, Jürgen C.
    BRAF and MEK inhibition in melanoma patients enables reprogramming of tumor infiltrating lymphocytes
    In: Cancer Immunology, Immunotherapy Vol. 70 (2021) Nr. 6, pp. 1635 - 1647
  • Spassova, Ivelina; Ugurel, Selma; Terheyden, Patrick; Sucker, Antje; Hassel, Jessica C.; Ritter, Cathrin; Kubat, Linda; Habermann, Daniel; Farahpour, Farnoush; Saeedghalati, Mohammadkarim; Peiffer, Lukas; Kumar, Rajiv; Schrama, David; Hoffmann, Daniel; Schadendorf, Dirk; Becker, Jürgen C.
    Predominance of Central Memory T Cells with High T-Cell Receptor Repertoire Diversity is Associated with Response to PD-1/PD-L1 Inhibition in Merkel Cell Carcinoma
    In: Clinical Cancer Research Vol. 26 (2020) Nr. 9, pp. 2257 - 2267
  • Kehrmann, Jan; Menzel, Jannis; Saeedghalati, Mohammadkarim; Obeid, Rima; Schulze, Christina; Holzendorf, Volker; Farahpour, Farnoush; Reinsch, Nico; Klein-Hitpaß, Ludger; Streeck, Hendrik; Hoffmann, Daniel; Buer, Jan; Esser, Stefan
    Gut Microbiota in Human Immunodeficiency Virus-Infected Individuals Linked to Coronary Heart Disease
    In: The Journal of Infectious Diseases (JID) Vol. 219 (2019) Nr. 3, pp. 497 - 508
  • Farahpour, Farnoush; Saeedghalati, Mohammadkarim; Brauer, Verena S.; Hoffmann, Daniel
    Trade-off shapes diversity in eco-evolutionary dynamics
    In: eLife Vol. 7 (2018) pp. e36273
  • Saeedghalati, Mohammadkarim; Farahpour, Farnoush; Budeus, Bettina; Lange, Anja; Westendorf, Astrid; Seifert, Marc; Küppers, Ralf; Hoffmann, Daniel
    Quantitative Comparison of Abundance Structures of Generalized Communities : from B-Cell Receptor Repertoires to Microbiomes
    In: PLoS Computational Biology Vol. 13 (2017) Nr. 1, e1005362