Identifying genes of gene regulatory networks using formal concept analysis.

In order to understand the behavior of a gene regulatory network, it is essential to know the genes that belong to it. Identifying the correct members (e.g.

Modeling feedback loops in the H-NS-mediated regulation of the Escherichia coli bgl operon.

The histone-like nucleoid-associated protein H-NS is a global transcriptional repressor that controls approximately 5% of all genes in Escherichia coli and other enterobacteria. H-NS binds to DNA with low specificity. Nonetheless, repression of some loci is exceptionally specific.

Systematic component selection for gene-network refinement.

Motivation: A quantitative description of interactions between cell components is a major challenge in Computational Biology. As a method of choice, differential equations are used for this purpose, because they provide a detailed insight into the dynamic behavior of the system. In most cases, the number of time points of experimental time series is usually too small to estimate the parameters of a model of a whole gene regulatory network based on differential equations, such that one needs to focus on subnetworks consisting of only a few components.