Pseudomonas

01/10/2008 – 30/09/2011

The project aims the reconstruction of metabolic and regulatory networks and further analysis of their topology and dynamics. The information source for this reconstruction is (1) the annotated genome and (2) transcriptome and proteome data. The metabolic network will be reconstructed from the annotated genome and as far as possible cross checked against the transcriptome and proteome data. This reconstruction includes the check for consistency of elementary and charge balances of the various transformation steps as a precondition for every method based on balancing chemical species. Topological analysis like, for example, detection of unused transformation steps, dead-ends, parallel routes, and elementary flux modes will be applied and a layout of the network performed. Together with the experimental groups time series of transcriptome profiling will be designed and performed. The measurements are then performed at transient conditions following the dynamic response to the stimulus of interest. The time dependent micro array data are afterwards used for reconstruction of regulatory networks. The project aims to apply network reverse engineering methods based on boolean algebra and deterministic differential equation approaches.