Mathematical modelling for BIOSS

Prof. Dr. Jens Timmer (Institute of Physics, University of Freiburg)

In this BIOSS project we concentrate on the development and application of mathematical models to describe biological systems. This is done in the classical context of systems biology to obtain a deeper understanding of given biological systems, but mathematical models are also helpful in the context of synthetic biology in order to optimally design new synthetic tools and modules but also to characterize them in a quantitative manner. The modular design of synthetic systems is a perfect prerequisite to build and apply mathematical models.

In collaboration with the Weber group we will develop mathematical models to design novel synthetic optogenetic switches. With these switches it is possible to control and influence signalling pathways, e.g. the MAPK/ERK pathway. This gives great opportunities to gain new insights into the function of such signalling pathways. The high controllability of such modified pathways is leading to many novel experimental possibilities, which can be analysed by optimal experimental design methods to identify the experiments giving the maximal information about the examined pathway. In collaboration with the Radziwill group we will employ this methods to apply optogenetic control of RAF, AKT, and CNK1 to investigate cell fate decision concerning proliferation versus differentiation. We will use mathematical modelling to identify and validate the signalling network structure based on time-resolved quantitative biochemical and mass spectroscopy data. In collaboration with the Onichtchouk group, we investigate temporal control of cell fate decisions in the early development of zebrafish. Specifically, we will mathematically model the dynamical effects of SOXB1 mutants in order to understand the delayed but viable development based on transcription and phenotype data.