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| Data-driven modeling and simulation of biological, medical and material systems in multiple contexts. |
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| 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 |
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| Methodological Interests: |
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| - | 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 |
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| Publications: |
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| [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 |
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| [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 |
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| [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. |
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| [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 |
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| [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 |
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| [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 |
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| [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 |
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| [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 |
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| [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 |
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| [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. |
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| [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 |
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| [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 |
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| [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 |
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| [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 |
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| [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 |
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| [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 |
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