I would greatly appreciate suggestions on how to infer and reconstruct a genome-scale regulatory network on a microorganism of interest which its regulatory machinery is not well known. Further, the idea is to construct a genome-scale regulatory model which I can use to integrate with a genome-scale metabolic model to get a genome-scale cellular model. Finally, I would use the latter to simulates phenotypes and mainly to optimize the production of a compound of interest on our microorganism.

I have available steady state RNA-seq gene expression data of the wild-type strain in two different condition.

Which method of the reverse engineering approaches would help me to infer and reconstruct a gene regulatory network successfully?