Current status and applications of genome-scale metabolic models

Genome-scale metabolic models (GEMs) computationally describe gene-protein-reaction associations for entire metabolic genes in an organism, and can be simulated to predict metabolic fluxes for various systems-level metabolic studies. Since the first GEM for Haemophilus influenzae was reported in 199...

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Published inGenome Biology Vol. 20; no. 1; pp. 121 - 18
Main Authors Gu, Changdai, Kim, Gi Bae, Kim, Won Jun, Kim, Hyun Uk, Lee, Sang Yup
Format Journal Article
LanguageEnglish
Published England BioMed Central 13.06.2019
BMC
Subjects
Bacteria
Cancer
Digital Object Identifier
E coli
Gene expression
Genomes
Genotype & phenotype
Linear programming
Metabolism
Metabolites
Optimization techniques
Organisms
Phylogenetics
Prostate
Review
Scale models
Taxonomy
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Summary:Genome-scale metabolic models (GEMs) computationally describe gene-protein-reaction associations for entire metabolic genes in an organism, and can be simulated to predict metabolic fluxes for various systems-level metabolic studies. Since the first GEM for Haemophilus influenzae was reported in 1999, advances have been made to develop and simulate GEMs for an increasing number of organisms across bacteria, archaea, and eukarya. Here, we review current reconstructed GEMs and discuss their applications, including strain development for chemicals and materials production, drug targeting in pathogens, prediction of enzyme functions, pan-reactome analysis, modeling interactions among multiple cells or organisms, and understanding human diseases.
ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-019-1730-3