Research statement

Based on an education in mathematics and computer science the core of my research in systems biology is the development of algorithms, first in structural molecular biology, then in metabolic modeling. In the software I developed the emphasis is not only the effciency of the final implementation but also an efficient development process and software flexible enough to explore the properties of a system in a scientific way. In colloboration with medical doctors, biologist, and biophsicists I was also involved in the interpretation of the computation results. Thus, I developed algorithms which followed the lines of thinking of the biologist and medical scientist. In molecular geometry I implemented a 3D search algorithm with the emphasis on speed to utilize database searches of molecular interfaces in the DFG-Forschgruppe Molekulare Bibliotheken. In modeling of metabolic networks I introduced a new approach and developed the software FASIMU for the exploration of metabolic networks with flux-balance optimizitions. It was also used for the testing in reconstruction projects of genome-wide metabolic networks for human cells HepatoNet1 and Recon2.

Currently, I'm involved in several projects based on omics data for which I develop specifically adapted tools which utilize available domain knowledge to generate testable hypotheses. One of these tools is ModeScore whose purpose is the understanding of metabolic functions through expression profiles. A crucial aspect of my work is the integration of different types of large-scale data — for the metabolic modeling metabolite concentrations, flux data, proteome data of the enzymes and transporters, and the expression of genes coding and controlling them.

Visualization is an integral part of my computational work in systems biology. It is based on the notion that derivatization of measured data should not be taken too far, instead, raw data should be visualized in the context of computed results. In molecular geometry I created images with pymol and rasmol, this figure was chosen for the title page of the conference proceedings. For metabolic networks I developed a plugin faBiNA to draw network diagrams with visual elements showing computed results. For the visulization of expression data I intrduced a special diagram type.

In my future career I plan a stronger focus on Bioinformatics and to contribute bridging the gap between the large amount of biological data gathered and Systems Biology.