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 …

Metabolic flux analysis and metabolic engineering of microorganisms

HU Kim, TY Kim, SY Lee - Molecular BioSystems, 2008 - pubs.rsc.org
Recent advances in metabolic flux analysis including genome-scale constraints-based flux
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 …

Using flux balance analysis to guide microbial metabolic engineering

KA Curran, NC Crook, HS Alper - Microbial Metabolic Engineering …, 2012 - Springer
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 …

Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways

N Tepper, T Shlomi - Bioinformatics, 2010 - academic.oup.com
Motivation: Computational modeling in metabolic engineering involves the prediction of
genetic manipulations that would lead to optimized microbial strains, maximizing the …

Design and application of genome-scale reconstructed metabolic models

I Rocha, J Förster, J Nielsen - Microbial Gene Essentiality: Protocols and …, 2008 - Springer
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 …

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 …

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 …

From annotated genomes to metabolic flux models and kinetic parameter fitting

D Segrè, J Zucker, J Katz, X Lin… - OMICS A Journal of …, 2003 - liebertpub.com
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 …

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 …