Computational Systems Biology

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Dr. Jan Baumbach

Nowadays, we have the whole-genome sequence for more than 1,000 organisms available, trend increasing. However, the DNA sequence is only the first step in understanding how cells survive, reproduce and adapt their behavior while being exposed to changing environmental conditions. The Computational Systems Biology research group studies the responsible complex molecular regulation mechanisms. We develop bioinformatics tools for the large-scale reconstruction and analysis of the emerging molecular biological networks, one of the most important tasks in modern biology and of immense importance for biotechnology and human medicine but cost-intensive, time- consuming, and impossible to perform for any species in the wet lab separately.

Our projects

In our research projects, we develop techniques for the computational analysis of all relevant components of these networks including tools for their reconstruction. This comprises methods solely based on the DNA sequence, such as remote homology detection and the online discovery of transcription factor binding motifs, as well as network-based approaches, such as inter- species transfers of knowledge about gene regulatory networks and their analysis in the context of gene expression data. In the last case, for instance, we develop methods for the identification of case-specific key pathways (KeyPathwayMiner). Recently, we developed and established Transitivity Clustering, a novel data partitioning approach that finds frequent application in various biological data analysis tasks worldwide.