The goals of the group which mainly consists of theoretical physicists are two-fold. On the one hand, we develop mathematical methods for analyzing and modelling biological systems, most often based on dynamic time-resolved data. This includes parameter estimation and uncertainty analysis for dynamical systems. On the other hand, we apply these methods in close collaboration with experimentalists in the field of signalling research and synthetic biology. Integrative mathematical models enable to look at biological systems in a way that traditional biological approaches and techniques does not allow. The final goal is not to have a mathematical model – a model is nice to have – but to use the model in order to unterstand biology.  By this approach, we aim to help to turn the life sciences from a qualitative descriptive into a quantitative predictive science.

Keywords:

Integrative mathematical modelling, Data analysis, Parameter estimation in dynamical systems, Signalling, Synthetic biology

10 selected publications

• Ochoa-Fernandez R, Abel NB, Wieland FG, Schlegel J, Koch LA, Miller B, Engesser R, Giuriani G, Brandl SM, Timmer J, Weber W, Ott T, Simon R, Zurbriggen MD (2020).
  PULSE: Optogenetic control of gene expression in plants insensitive to ambient light. Nat. Methods in press
• Synthetic biology-inspired design of signal-amplifying materials systems.
  Wagner HJ, Engesser R, Ermes K, Geraths C, Timmer J, Weber W (2019).
  Materials Today 22, 25-34
• Phytochrome-Based Extracellular Matrix with Reversibly Tunable Mechanical Properties.
  Hörner M, Raute K, Hummel B, Madl J, Creusen G, Thomas OS, Christen EH, Hotz N, Gübeli RJ, Engesser R, Rebmann B, Lauer J, Rolauffs B, Timmer J, Schamel WWA, Pruszak J, Römer W, Zurbriggen MD, Friedrich C, Walther A, Minguet S, Sawarkar R, Weber W (2019).
  Adv Mater. 31(12):e1806727.
• Resolving the combinatorial complexity of Smad protein complex formation and its link to gene expression.
  Lucarelli P, Schilling M, Kreutz C, Vlasov A, Boehm ME, Iwamoto N, Steiert B, Lattermann S, Wäsch M, Stepath M, Matter MS, Heikenwälder M, Hoffmann K, Deharde D, Damm G, Seehofer D, Muciek M, Gretz N, Lehmann WD, Timmer J, Klingmüller U (2018).
  Cell Syst. 6:75-89
• Driving the model to its limit: Profile likelihood based model reduction.
  Maiwald T, Hass H, Steiert B, Vanlier J, Engesser R, Raue A, Kipkeew F, Bock HH, Kaschek D, Kreutz C, Timmer J (2016).
  PLoS One 11, e0162366.
• Multi-chromatic control of mammalian gene expression and signaling.
  Müller K, Engesser R, Schulz S, Steinberg T, Tomakidi P, Weber CC, Ulm R, Timmer J, Zurbriggen MD, Weber W (2013).
  Nucleic Acids Res. 41, e124.
• A red/far-red light-responsive bi-stable toggle switch to control gene expression in mammalian cells.
  Müller K, Engesser R, Metzger S, Schulz S, Kämpf MM, Busacker M, Steinberg T, Tomakidi P, Ehrbar M, Nagy F, Timmer J, Zubriggen MD, Weber W (2013).
  Nucleic Acids Res. 41, e77.
• Photoconversion and nuclear trafficking cycles determine phytochrome A's response profile to far-red light.
  Rausenberger J, Tscheuschler A, Nordmeier W, Wüst F, Timmer J, Schäfer E, Fleck C, Hiltbrunner A (2011).
  Cell 146, 813-25.
• Zebrafish Pou5f1-dependent transcriptional networks in temporal control of early development.
  Onichtchouk D, Geier F, Polok B, Messerschmidt DM, Mössner R, Wendik B, Song S, Taylor V, Timmer J, Driever W (2010).
  Mol Syst Biol. 6, 354.
• Covering a broad dynamic range: information processing at the erythropoietin receptor.
  Becker V, Schilling M, Bachmann J, Baumann U, Raue A, Maiwald T, Timmer J, Klingmüller U (2010).
  Science 328, 1404-8.