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, medical and material 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
See also the press release of the University of Freiburg

Methodological Interests:
-Statistical inference in nonlinear systems, especially in ordinary differential equations
-Experimental design and model reduction
-Partial differential equations
-Analysis of high-dimensional data
-Multivariate statistics
-Uncertainty analysis: from noise in data to uncertainties in parameter estimates to uncertainties in predictions
-Machine learning/deep learning for classification, prediction and pattern recognition
-Hypothetis testing
-Turing instabilities
-Finite element method
-Particle-based stochastic simulations of reaction diffusion dynamics

[16] H. J. Wagner, R. Engesser, K. Ermes, C. Geraths, J. Timmer, W. Weber:
Synthetic biology-inspired design of signal-amplifying materials systems. Materials Today 22, 2019, 25-34
[15] M. Hörner, K. Raute, B. Hummel, J. Madl, G. Creusen, O. S. Thomas, E. H. Christen, N. Hotz, R. J. Gübeli, R. Engesser, B. Rebmann, J. Lauer, B. Rolauffs, J. Timmer, W. W. A. Schamel, J. Pruszak, W. Römer, M. D. Zurbriggen, C. Friedrich, A. Walther, S. Minguet, R. Sawarkar, W. Weber:
Phytochrome-based extracellular matrix with reversibly tunable mechanical properties. Advanced Materials, 2019, 1806727
[14] H. J. Wagner, S. Kemmer, R. Engesser, J. Timmer, W. Weber:
Biofunctionalized Materials Featuring Feedforward and Feedback Circuits Exemplified by the Detection of Botulinum Toxin A. Advanced Science, 2018, 1801320. Journal Cover Picture.
[13] J. Baaske, P. Gonschorek, R. Engesser, A. Dominguez-Monedero, K. Raute, P. Fischbach, K. Müller, E. Cachat, W. Schamel, S. Minguet, J. Davies, J. Timmer, W. Weber, M.D. Zurbriggen:
Dual-controlled optogenetic system for the rapid down-regulation of protein levels in mammalian cells. Scientific Reports 8, 2018, 15024
[12] D. Engesser, R. Engesser, J. Stifter, L. Atzrodt, D. Böhringer, T. Reinhard:
Ist die Verordnung von vergrößernden Sehhilfen anhand der Krankenakte möglich oder bedarf es einer Beratung in einer Sehbehindertenambulanz?. Klinische Monatsblätter für Augenheilkunde 2018, in press
[11] C. Chatelle, R. Ochoa Fernandez, R. Engesser, N. Schneider, H. M. Beyer, A. Jones, J. Timmer, M. D. Zurbriggen, W. Weber:
A green light-responsive system for the control of transgene expression in mammalian and plant cells. ACS Synthetic Biology 8, 2018, 1349-1358
[10] H. J. Wagner, R. Engesser, K. Ermes, C. Geraths, J. Timmer, W. Weber:
Characterization of the synthetic biology-inspired implementation of a materials-based positive feedback loop. Data in Brief 19, 2018, 665-677
[9] H. M. Beyer, R. Engesser, M. Hörner, J. Koschmieder, P. Beyer, J. Timmer, M. D. Zurbriggen, W. Weber:
Synthetic Biology Makes Polymer Materials Count. Advanced Materials 30, 2018, 1800472. Journal Back Cover
[8] 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. Journal of Biological Chemistry 292, 2017, 6291-6302
[7] 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.
[6] 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
[5] 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
[4] K. Müller, R. Engesser, J. Timmer, F. Nagy, M.D. Zurbriggen, W. Weber:
Synthesis of phycocyanobilin in mammalian cells. Chemical Communications 49, 2013, 8970-8972
[3] 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
[2] 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
[1] 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