Schematic depiction of the computational approach. A genome-scale network and time-series transcriptomics data are used to extract time- and condition-specific minimal networks. Data for different environmental conditions are analyzed to weight genes based on differential expression and bimodal distribution analyses. The gene-reaction annotation of the network reconstruction is used to map the weights onto the metabolic model. A minimization approach is applied to extract minimal networks. EFM analysis is conducted on the minimal networks, and the resulting sets of EFMs and the derived fractional appearance profiles are employed to characterize the transitional behavior of the network and of individual reactions, respectively.