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Simon Merkt


Simon Merkt large


Endenicher Allee 64, 53115 Bonn, Germany

📞  +49 (0) 228 73 62246

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Short CV

Simon Merkt obtained his B.Sc degree in mathematics at the University of Regensburg including an exchange at the University of Aberdeen. He did his M.Sc at the University of Bonn in mathematics with focus on partial differential equations. In April 2019 he joined the group of Jan Hasenauer at the University of Bonn as Ph.D. student .


  • CanPathPro – Integration of heterogeneous experimental data into a large-scale cancer model and analysis of proteomics data
  • Modelling cell development on single cell RNA sequencing data with PDEs
  • SEIR models of Covid19 spread in Ethiopia


[4] P. Stapor, L. Schmiester, C. Wierling, S. Merkt, D. Pathirana, B. M. H. Lange, D. Weindl, and J. Hasenauer. Mini-batch optimization enables training of ODE models on large-scale datasets. Nature Communications, 13(1):34, 2022. DOI: 10.1038/s41467-021-27374-6

[3] E. K. Gudina, S. Ali, E. Girma, A. Gize, B. Tegene, G. B. Hundie, W. T. Sime, R. Ambachew, A. Gebreyohanns, M. Bekele, A. Bakuli, K. Elsbernd, S. Merkt, L. Contento, M. Hoelscher, J. Hasenauer, A. Wieser, and A. Kroidl. Seroepidemiology and model-based prediction of SARS-CoV-2 in Ethiopia: longitudinal cohort study among front-line hospital workers and communities. The Lancet Global Health, 9(11):e1517-e1527, November 2021. DOI: <\p>

[2] E. Raimúndez, E. Dudkin, J. Vanhoefer, E. Alamoudi, S. Merkt, L. Fuhrmann, F. Bai, and J. Hasenauer. COVID-19 outbreak in Wuhan demonstrates the limitations of publicly available case numbers for epidemiological modeling. Epidemics, 34:100439, March 2021. DOI:
[1] L. Schmiester*, Y. Schälte*, F. T. Bergmann, T. Camba, E. Dudkin, J. Egert, F. Fröhlich, L. Fuhrmann, A. L. Hauber, S. Kemmer, P. Lakrisenko, C. Loos, S. Merkt, W. Müller, D. Pathirana, E. Raimúndez, L. Refisch, M. Rosenblatt, P. L. Stapor, P. Städter, D. Wang, F.-G. Wieland, J. R. Banga, J. Timmer, A. F. Villaverde, S. Sahle, C. Kreutz, J. Hasenauer**, and D. Weindl**. PEtab---Interoperable specification of parameter estimation problems in systems biology. PLOS Computational Biology, 17(1):1-10, January 2021. DOI: 10.1371/journal.pcbi.1008646