In silico evolution and reverse engineering of gene regulatory networks

Reverse engineering and modeling gene regulatory networks is a necessary 
first step in understanding cells at a system level. We have developed a 
new approach for reverse engineering gene networks, which consists of using 
a reconstruction process that is similar to the evolutionary process that 
created these networks. The aim is to integrate prior knowledge into the 
reverse engineering procedure, thus biasing the search towards biologically 
plausible solutions. To this end, we use in silico evolution with a biomimetic 
genome that abstracts and mimics the natural evolution of gene regulatory 
networks.

Our method won a gene network reverse engineering competition (DREAM 2007, 
New York). In this talk I summarize these results and present our recent 
work on reverse engineering the gap gene network of Drosophila melanogaster. 
Within this context, the role of gene network modeling will be discussed. 
Based on recent quantitative insights into gene regulation and a systematic 
exploration of the 'analog logic' implemented by gene networks, we compare 
existing and propose novel coarse-grained models with different trade-offs 
between accuracy and complexity.