Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods.
|Title||Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods.|
|Publication Type||Journal Article|
|Year of Publication||2012|
|Authors||Lewis NE, Nagarajan H, Palsson BO|
|Journal||Nat Rev Microbiol|
|Date Published||2012 Apr|
|Keywords||Buchnera, Computer Simulation, Energy Metabolism, Escherichia coli, Genome, Bacterial, Genome, Fungal, Genotype, Metabolic Engineering, Metabolic Networks and Pathways, Models, Biological, Phenotype|
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.
|Alternate Journal||Nat. Rev. Microbiol.|