Welcome to Molecular Bioinformatics
Our group was established in March 2010. With the retirement of the head of the group, Prof. Dr. Ina Koch, in April 2025, the group was officially closed.
The group was working in the field of Bioinformatics and Computational Systems Biology. We were interested in algorithm and method development as well as applications to biological and medical questions. Thanks to the many interesting collaborations with experimenters and physicians, we primarily focused on two areas. The first one is related to computational protein structure analysis. Here, we developed a graph theory-based description for protein topologies based on PDB structures. We provided the results in the PTGL (Protein Graph Library) database.
The second focus was on modeling and analysis of biochemical systems. Here, we considered metabolic systems, signal transduction pathways, and gene regulatory networks. As for biochemical systems, the amount of data available is still insufficient in quantity and quality; we applied semi-quantitative analysis techniques provided by the Petri net theory. We adapted invariant analysis approaches to better describe biochemical systems, developing new concepts, for example, Mauritius Maps and Manatee invariants, which were also used for model reduction and to show the completeness and correctness of the Petri net model. We have implemented a widely used software called MonaLisa, which is still supported. Based on these concepts, we were able to perform useful single and multiple knockout in silico experiments. To model the dependencies of populations of bacteria from specific input molecules, for example, nutrition or antibiotics, in the human gut, we have been developing a first framework that combines Petri nets with agent-based models.
To acknowledge the meaningful role of Dr. Jörg Ackermann, who passed away suddenly, we uploaded a group photo from 2022.
