Optimization and control of metabolic networks

Metabolism, which comprises the complete set of biochemical reactions in a living cell, is one of the most complex cellular processes. Metabolic networks connect biochemical reactions via substrate and product substances called metabolites. Analysis of metabolic networks via network theory, stoichiometry, optimization and control tools is one of central topics in systems biology and allows for in depth comprehending the complex molecular mechanisms of an organism. In this paper, we first introduce metabolic flux balance analysis and its application in prediction of gene essentiality, synthetic lethality, and disease biomarkers. Then we review metabolic control models including strain optimization models, drug target discovery models and other metabolic intervention models. Finally, we look at new progresses in this area and present our work in these aspects including a metabolite-centric mass flow model. This overview gives a general framework for metabolic network analysis and its application in diverse areas.