Project for Bachelor or Master thesis

Information transmission in cellular signaling

The main task of cellular signaling networks is to transmit and process information about ligands or other cues (e.g. physical stimuli) to cellular targets. These targets can be transcription factors that eventually regulate the expression of genes as response to the cues, but it can also be metabolic enzymes changing their activity, e.g. due to phosphorylation changes. While the wiring of signaling networks is relatively well understood, it is not well investigated, which organization principles support the transmission and processing of information and ensure a clear discrimination of often weak or overlapping signals. Here, we want to apply the concept of Shannon information to systematically investigate which architecture and parameterization of signaling pathways allows for precise signal transfer and maximum channel capacity. We will start with well-known structures such as the MAP kinase cascade and then extend to typical signaling pathway features such as scaffolding, positive or negative feedback as well as pathways with high concentration of signaling molecules in off-states and their degradation after stimulation of the pathway (such as in Wnt signaling). The aim is to find limits, supporting structures and principles of information transfer in cellular signaling networks.

Requirements: Interest in mathematical modeling of cell processes, basic programming skills, interest in challenging biological questions. Since Shannon entropy had been discussed in the biophysics Master course, biophysics students would have the required background, but the offer is not limited to those.

Skills you will acquire: Learn how to formulate testable scientific questions. Improve your programming skills, especially in Julia. Contribution to a highly debated field in science.

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