Network-based functional modeling of genomics, transcriptomics and metabolism in bacteria.

Molecular entities present in a cell (mRNA, proteins, metabolites,…) do not act in isolation, but rather in cooperation with each other to define an organisms form and function. Their concerted action can be viewed as networks of interacting entities that are active under certain conditions within the cell or upon certain environmental signals. A main challenge in systems biology is to model these networks, or in other words studying which entities interact to form cellular systems or accomplish similar functions. On the contrary, viewing a single entity or an experimental dataset in the light of an interaction network can reveal previous unknown insights in biological processes. In this review we give an overview of how integrated networks can be reconstructed from multiple omics data and how they can subsequently be used for network-based modeling of cellular function in bacteria.