SR-FBA (Steady-State Regulatory Flux Balance Analysis) 
SR-FBA is a method for predicting the steady-state metabolic and regulatory behaviors in large-scale integrated metabolic-regulatory models. [implementation]
A Genome-Scale Computational Study of the Interplay between Transcriptional Regulation and Metabolism.
T. Shlomi, Y. Eisenberg, R. Sharan, E. Ruppin.