Modeling, Simulation and Data Analysis University of Freiburg

Dr. Raphael Engesser

University of Freiburg
Institute of Physics, Jens Timmmer group
Hermann-Herder-Straße 3, Physik Hochhaus
Room 210
79104 Freiburg i.Br.
raphael.engesser ät
Tel +49 761 203 8531


Data-driven modeling and simulation of biological systems in multiple contexts.

Research Interests:
Mathematical modeling in the context of Synthetic Biology
-Optogenetics: Modeling of novel tools to control cellular functions by light
-Construction of synthetic circuits and networks in mammalian cells
-Synthetic pattern formation
Systems Biology
-IL1beta signaling in the liver
-TGFbeta signaling in the lung cancer context
-Formation of PhyB photobodies in plants
-Development of spatial structures and patterns
Mathematical modeling to guide the construction of smart biohybrid materials
-Information processing materials
-Development of sensors
-Control of physical properties of materials by light

Methodological interests:
-Parameter estimation in nonlinear systems, especially in ordinary differential equations
-Partial differential equations
-Turing instabilities
-Finite element method
-Particle-based stochastic simulations of reaction diffusion dynamics
-Statistics and data analysis
-Experimental design
-Uncertainty analysis
-Hypothetis testing

- A. Kulawik, R. Engesser, C. Ehtling, A. Raue, U. Albrecht, B. Hahn, W.D. Lehmann, M. Gästel, U. Klingmüller, D. Häussinger, J. Timmer, J.G. Bode: IL-1beta induced and p38MAPK-dependent activation of the mitogen-activated protein kinase (MAPK)-activated protein kinase (MK) 2 in hepatocytes: signal transduction with robust and concentration-independent signal amplification. J. Biological Chemistry 292, 2017, 6291-6302
- T. Maiwald, H. Hass, B. Steiert, J. Vanlier, R. Engesser, A. Raue, F. Kipkeew, H.H. Bock, D. Kaschek, C. Kreutz, J. Timmer: Driving the model to its limit: profile likelihood based model reduction. PLoS ONE 11, 2016, e0162366.
- A. Raue, B. Steiert, M. Schelker, C. Kreutz, T. Maiwald, H. Hass, J. Vanlier, C. Tönsing, L. Adlung, R. Engesser, W. Mader, T. Heinemann, J. Hasenauer, M. Schilling, T. Höfer, E. Klipp, F. Theis, U. Klingmüller, B. Schöberl, J. Timmer: Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems. Bioinformatics 31, 2015, 3558-3560
- K. Müller, R. Engesser, J. Timmer, M.D. Zurbriggen, W. Weber.
Orthogonal optogenetic triple-gene control in mammalian cells. ACS Synthetic Biology 3, 2014, 796-801
- K. Müller, R. Engesser, J. Timmer, F. Nagy, M.D. Zurbriggen, W. Weber: Synthesis of phycocyanobilin in mammalian cells. ChemComm 49, 2013, 8970-8972
- K. Müller, R. Engesser, S. Schulz, T. Steinberg, P. Tomakidi, C.C. Weber, R. Ulm, J. Timmer, M.D. Zurbriggen, W. Weber: Multi-chromatic control of mammalian gene expression and signaling. Nucleic Acids Research 41, 2013, e124
- K. Müller, R. Engesser, S. Metzger, S. Schulz, M.M. Kämpf, M. Busacker, T. Steinberg, P. Tomakidi, M. Ehrbar, F. Nagy, J. Timmer, M.D. Zurbriggen, W. Weber: A red/far-red light-responsive bi-stable toggle switch to control gene expression in mammalian cells. Nucleic Acids Research 41, 2013, e77
- M.M. Kämpf, R. Engesser, M. Busacker, M. Hörner, M. Karlsson, M.D. Zurbriggen, M. Fussenegger, J. Timmer, W. Weber. Rewiring and dosing of systems modules as a design approach for synthetic mammalian signaling networks. Molecular BioSystems 8, 2012, 1824-1832