Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods.

TitleConstraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods.
Publication TypeJournal Article
Year of Publication2012
AuthorsLewis NE, Nagarajan H, Palsson BO
JournalNat Rev Microbiol
Volume10
Issue4
Pagination291-305
Date Published2012 Apr
ISSN1740-1534
KeywordsBuchnera, Computer Simulation, Energy Metabolism, Escherichia coli, Genome, Bacterial, Genome, Fungal, Genotype, Metabolic Engineering, Metabolic Networks and Pathways, Models, Biological, Phenotype
Abstract

Reconstructed microbial metabolic networks facilitate a mechanistic description of the genotype-phenotype relationship through the deployment of constraint-based reconstruction and analysis (COBRA) methods. As reconstructed networks leverage genomic data for insight and phenotype prediction, the development of COBRA methods has accelerated following the advent of whole-genome sequencing. Here, we describe a phylogeny of COBRA methods that has rapidly evolved from the few early methods, such as flux balance analysis and elementary flux mode analysis, into a repertoire of more than 100 methods. These methods have enabled genome-scale analysis of microbial metabolism for numerous basic and applied uses, including antibiotic discovery, metabolic engineering and modelling of microbial community behaviour.

DOI10.1038/nrmicro2737
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/22367118?dopt=Abstract
PMCPMC3536058
Alternate JournalNat. Rev. Microbiol.
PubMed ID22367118