Genome-scale modeling for metabolic engineering
E Simeonidis, ND Price - Journal of Industrial Microbiology and …, 2015 - academic.oup.com
We focus on the application of constraint-based methodologies and, more specifically, flux
balance analysis in the field of metabolic engineering, and enumerate recent developments …
balance analysis in the field of metabolic engineering, and enumerate recent developments …
Metabolic flux analysis and metabolic engineering of microorganisms
Recent advances in metabolic flux analysis including genome-scale constraints-based flux
analysis and its applications in metabolic engineering are reviewed. Various computational …
analysis and its applications in metabolic engineering are reviewed. Various computational …
Constraint‐based strain design using continuous modifications (CosMos) of flux bounds finds new strategies for metabolic engineering
C Cotten, JL Reed - Biotechnology journal, 2013 - Wiley Online Library
In recent years, a growing number of metabolic engineering strain design techniques have
employed constraint‐based modeling to determine metabolic and regulatory network …
employed constraint‐based modeling to determine metabolic and regulatory network …
Using flux balance analysis to guide microbial metabolic engineering
Metabolic engineers modify biological systems through the use of modern molecular biology
tools in order to obtain desired phenotypes. However, due to the extreme complexity and …
tools in order to obtain desired phenotypes. However, due to the extreme complexity and …
Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways
Motivation: Computational modeling in metabolic engineering involves the prediction of
genetic manipulations that would lead to optimized microbial strains, maximizing the …
genetic manipulations that would lead to optimized microbial strains, maximizing the …
Design and application of genome-scale reconstructed metabolic models
In this chapter, the process for the reconstruction of genome-scale metabolic networks is
described, and some of the main applications of such models are illustrated. The …
described, and some of the main applications of such models are illustrated. The …
OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains
J Kim, JL Reed - BMC systems biology, 2010 - Springer
Background Computational modeling and analysis of metabolic networks has been
successful in metabolic engineering of microbial strains for valuable biochemical production …
successful in metabolic engineering of microbial strains for valuable biochemical production …
Mathematical optimization applications in metabolic networks
AR Zomorrodi, PF Suthers, S Ranganathan… - Metabolic …, 2012 - Elsevier
Genome-scale metabolic models are increasingly becoming available for a variety of
microorganisms. This has spurred the development of a wide array of computational tools …
microorganisms. This has spurred the development of a wide array of computational tools …
From annotated genomes to metabolic flux models and kinetic parameter fitting
Significant advances in system-level modeling of cellular behavior can be achieved based
on constraints derived from genomic information and on optimality hypotheses. For steady …
on constraints derived from genomic information and on optimality hypotheses. For steady …
Use of randomized sampling for analysis of metabolic networks
J Schellenberger, BØ Palsson - Journal of biological chemistry, 2009 - ASBMB
Genome-scale metabolic network reconstructions in microorganisms have been formulated
and studied for about 8 years. The constraint-based approach has shown great promise in …
and studied for about 8 years. The constraint-based approach has shown great promise in …