Systems Biology

The research of our group is focussed in the area of molecular systems biology. We are developing and applying different modelling and data integration techniques to generate suitable computational models of biological systems and processes. The analysis of these models helps to gain insight into dynamic and stationary properties of the investigated networks which in turn gives the basis for suggesting further promising experiments.

We are also performing experimental validation of the models using cell cultivation facilities.

Currently we are pursuing the following research activities:

Mammalian signaling networks

One main focus lays in the development and analysis of mathematical models of pro- and anti-apoptotic signalling in mammalian cells. We are interested in understanding and influencing the signalling protein networks that govern the decision between life and programmed cell death. Furthermore we focus on deciphering the characteristics of disease related PDGF signaling networks. Different modelling techniques and experimental validation using mammalian cell cultivation are applied. Specific current projects – all of them in close collaboration with biological experts - are:

•  Modelling and analysis of the NFкB-dependent UVB induced apoptosis.

•  Systems Biology approach to Reconstruction and Modeling of NFkB signaling in hepatocellular carcinoma: From -omics to dynamics.

•  Identification of perturbation-sensitive targets and disease markers in PDGF signaling related diseases

•  Evaluation of influences of 1α,25(OH)2D3 on atherosclerosis

Integrated metabolic and genetic modelling of adipogenesis

We are developing computational tools for integrating high-throughput data sets with constraint based models of metabolic networks. In a proof of principle study we (in close collaboration with biological experts) currently integrate transcriptomics and metabolomics data with a genome wide model of human metabolism and furthermore with a model of combinatorial gene regulation by multiple microRNAs to describe and further analyze adipocyte differentiation. Subprojects are:

•  Integrated metabolic modelling of the adipogenesis

•  Combinatorial gene regulation by multiple microRNAs during adipocyte differentiation: a systems biology approach.

Tool development

Most of the computational tools we are developing are applicable to a wide range of biological systems and processes. Ongoing work comprises:

•  Qualitative modeling of signaling networks, using Boolean and Probabilistic Boolean modelling

•  Integrated metabolic modelling & model reduction

•  Global sensitivity analysis

•  Data integration and network curation