Prof. Dr. Jens Timmer (CIBSS-PI), Institute of Physics (Faculty of Physics and Mathematics), University of Freiburg
The topic of CIBSS is signalling across scales: from mechanistic understanding to control-of function. Mathematical models are perfectly suited for these three goals: Hypotheses about mechanisms of signalling dynamics can be implemented in mathematical models and tested against experimental data. Multi-scale models are the natural way to bridge scales and control-of-function maps to sensitivity analysis of the models. In this project we have three aims: First, we will develop new mathematical methods for modelling, especially for modelling large biological networks. Second, we will apply modelling to construct optimal optogenetic switches. Third, together with our experimental collaboration partners, we will apply mathematical modelling in the iterative cycle between experiment and modelling to specific signalling networks in order to understand their underlying mechanisms.
Publications resulting from the project
Pluripotency factors determine gene expression repertoire at zygotic genome activation.
Gao M, Veil M, Rosenblatt M, Riesle AJ, Gebhard A, Hass H, Buryanova L, Yampolsky LY, Grüning B, Ulianov SV, Timmer J, Onichtchouk D.
Nat Commun. 2022; doi: 10.1038/s41467-022-28434-1.
Liquid-liquid phase separation of light-inducible transcription factors increases transcription activation in mammalian cells and mice.
Schneider N, Wieland FG, Kong D, Fischer AAM, Hörner M, Timmer J, Ye H, Weber W.
Sci Adv. 2021; doi: 10.1126/sciadv.abd3568.