Research Focus on Systems Biology
Mathematical Modelling of Cellular Systems
Several years prior to the start of his role as founding director of the Max Planck Institute in Magdeburg, Professor Ernst Dieter Gilles became interested in the mathematical modelling of cellular systems. He therefore started a new line of research at his Institute of System Dynamics and Control Engineering at the Stuttgart University where he worked at the time. His vision was to transfer and use established methods from the fields of systems theory and control engineering for the computer-aided analysis of molecular biological processes.
His collaboration with Professor Joseph Lengeler from the University of Osnabrück in the mid 1990s proved to be a particularly fruitful and productive development. Both researchers showed a great deal of interest in the other's discipline – an essential prerequisite for interdisciplinary collaboration. Based on the example of the molecular regulation of sugar transport in the bacterium Escherichia coli, both work groups were able to demonstrate how an iterative cycle consisting of a combination of traditional molecular biological analyses with computer simulations can deliver tangible added value in the elucidation of cellular processes.
On the basis of these and other ground-breaking studies, Professor Gilles is considered one of the pioneers in the field of systems biology, a new methodological approach that became established in the increasingly data-driven field of biology at the turn of the new millennium.
Systems Biology Group at the MPI
Building upon the initial experiences of interdisciplinary collaboration, Professor Gilles established his Systems Biology group at the newly founded Max Planck Institute in Magdeburg in 1998. Right from the outset he insisted on a thoroughgoing integration of biologists and modellers in one group, who jointly worked on the analysis of various aspects of metabolic and regulatory processes at the cellular level.
The group published a series of papers and studies on systems biology which was highly recognized in the national and international community. The following are just a few examples:
- The first comprehensive computer-aided analysis of all metabolic pathways (so-called elementary modes) in the central metabolism of the bacterium Escherichia coli elucidated the relationship between structure and function in metabolic networks .
- The at that time largest dynamic model of a signal transduction pathway in a human cell enabled a simulation-driven analysis of important characteristics of the input-output behaviour of a central cellular signaling cascade . Later, other modelling techniques were developed which made possible the efficient simulation of highly complex signal transduction pathways  and .
- A mathematical model was developed that describes and explaines sugar absorption and catabolite repression regulation mechanisms in E. coli in a quantitative manner .
- The group developed several systems biology software tools which are also frequently used by other groups. Among others, these include CellNetAnalyzer  and ProMoT .
Research Partnerships for Systems Biology
From the outset, Professor Gilles' Systems Biology Group was very successful in obtaining third-party funding, and participated in several major research consortia. The establishment of the FORSYS Systems Biology Centre in Magdeburg (MaCS) in 2007 funded by the German Federal Ministry of Education and Research (BMBF), in which Professor Gilles played a significant role, was a milestone and a great success for the Systems Biology research at the MPI and University in Magdeburg.
The "Dynamic Systems" research centre, founded with funding from the state of Saxony-Anhalt, was also conceptually shaped by Professor Gilles, who also played a role in the creation of the successful "Biosystems Engineering" study course at the University of Magdeburg. All of these activities have contributed to Magdeburg's high profile in the field of system biology both in Germany and abroad.
Professor Gilles became an Emeritus of the Max Planck Institute in 2011. The Analysis and Redesign of Biological Networks group, which was formed in 2009, continues to carry out research into certain aspects of systems biology at the Max Planck Institute in Magdeburg. The group is headed by Dr.-Ing. Steffen Klamt, a former member of the Systems Biology Group.