Optimization Methods in Metabolic Networks

by Costas D. Maranas, Ali R. Zomorrodi

This book provides, for the first time, a tutorial on the computational tools that use mathematical optimization concepts and representations for the curation, analysis and redesign of metabolic networks. It presents optimization formulation fundamentals and relevant algorithmic solution techniques followed by a wide array of related applications in metabolic networks.It is designed to serve as a textbook for an advanced elective course on metabolic or biological networks and modeling.

It provides optimization formulation fundamentals and relevant algorithmic solution techniques for different classes of optimization problem including LP, NLP, MILP and MINLP. Particular emphasis is placed on explaining the most efficient ways of formulating a biological problem using mathematical optimization. At the metabolic network level, this book introduces fundamentals of metabolic network modelling and discusses, in details, optimization-based methods to address a wide range of relevant problems in metabolic network curation, analysis and redesign. It covers, among others, algorithms for flux coupling analysis, automated model refinement, thermodynamic analysis of metabolic networks, metabolic pathway design and metabolic flux analysis (MFA). In addition, it delves into computational strain algorithms based on bilevel optimization techniques to identify the most promising engineering interventions (i.e., gene knock-in/out/up/downs) for biological production systems.

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