The advent of genome‐scale models of metabolism has laid the foundation for the
development of computational procedures for suggesting genetic manipulations that lead to …

Background Computational modeling and analysis of metabolic networks has been
successful in metabolic engineering of microbial strains for valuable biochemical production …

Computational procedures for predicting metabolic interventions leading to the
overproduction of biochemicals in microbial strains are widely in use. However, these …

We introduce a computational framework termed OptReg that determines the optimal
reaction activations/inhibitions and eliminations for targeted biochemical production. A …

Motivation: Computational modeling in metabolic engineering involves the prediction of
genetic manipulations that would lead to optimized microbial strains, maximizing the …

Highlights•Computational tools identify new biological routes to chemicals.•Genome-scale
models suggest genetic engineering strategies to improve production.•Methods that …

Background Through genetic engineering it is possible to introduce targeted genetic
changes and hereby engineer the metabolism of microbial cells with the objective to obtain …

This paper introduces the hierarchical computational framework OptStrain aimed at guiding
pathway modifications, through reaction additions and deletions, of microbial networks for …

The identification of suitable intervention strategies increasing the productivity of
microorganisms is a central issue in metabolic engineering. Here, we introduce a …

In this study, we modify and extend the bilevel optimization framework OptKnock for
identifying gene knockout strategies in the Escherichia coli metabolic network, leading to the …