The current survey aims to describe the main methodologies for extending the reconstruction and analysis of genome-scale metabolic models and phenotype simulation with Flux Balance Analysis mathematical frameworks, via the integration of Transcriptional Regulatory Networks and/or gene expression data. Although the surveyed methods are aimed at improving phenotype simulations obtained from these models, the perspective of reconstructing integrated genome-scale models of metabolism and gene expression for diverse prokaryotes is still an open challenge.
Keywords:flux balance analysis, gene expression and regulation, genome-scale metabolic models, genome-scale regulatory networks, metabolism, transcriptional regulatory networks
© 2020 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society