Computational Systems Biology (Former Research Group)

Vision and Research Strategy

The National Center for Biotechnology Information (NCBI) recently announced "1,000 prokaryotic genomes are now completed and available in the Genome database". The increasing trend will provide us with thousands of sequenced organisms in the next years. However, this is only the first step in understanding how cells survive, reproduce and adapt their behavior while being exposed to changing environmental conditions. Complex molecular regulation mechanisms are responsible for this task, such as transcriptional gene regulatory interactions. Thus, the large-scale reconstruction and analysis of the emerging molecular biological networks is one of the most important tasks in modern systems biology and is of immense importance for biotechnology and human medicine, but is also cost-intensive, time-consuming, and impossible to perform for each species separately.

The Computational Systems Biology group develops techniques for the analysis of all relevant components of these networks, including tools for their reconstruction. This comprises methods based on the DNA sequence, such as remote homology detection and transcription factor binding motif discovery, as well as network-based approaches, such as inter-species transfers of knowledge about gene regulatory networks. We develop methods for the online identification of case-specific key pathways, word-sense disambiguation in biomedical texts, and clustering problems. Soon, we will contribute to large-scale metabolomics experiments and to the comprehensive systems biology analysis of tuberculosis.

Composition of Group

The Computational Systems Biology Group was founded in March 2010 in the Cluster of Excellence. The group develops informatics tools for the reconstruction and analysis of biological networks, as well as biological sequence analysis methods. Currently, the group consists of Dr. Jan Baumbach (head), five PhD students (two of whom started in October 2010), one postdoc, and five student programmers.

Research Topics and Achievements

Projects and Collaborations

Prof. Dr. Jan Baumbach

Prof. Dr. Jan Baumbach

Jan Baumbach is a professor at the department of Mathematics and Computer Science at the University of Southern Denmark.

Fon: +49-8161-71-2136