What is flux balance analysis?
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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 …
associations for entire metabolic genes in an organism, and can be simulated to predict …
Reconstructing organisms in silico: genome-scale models and their emerging applications
Escherichia coli is considered to be the best-known microorganism given the large number
of published studies detailing its genes, its genome and the biochemical functions of its …
of published studies detailing its genes, its genome and the biochemical functions of its …
iML1515, a knowledgebase that computes Escherichia coli traits
Figure 1 iML1515 genome-scale reconstruction.(a) The iML1515 model contains 1,515
open reading frames that encode enzymes that catalyze 2,719 reactions involving 1,192 …
open reading frames that encode enzymes that catalyze 2,719 reactions involving 1,192 …
High-throughput generation, optimization and analysis of genome-scale metabolic models
Genome-scale metabolic models have proven to be valuable for predicting organism
phenotypes from genotypes. Yet efforts to develop new models are failing to keep pace with …
phenotypes from genotypes. Yet efforts to develop new models are failing to keep pace with …
Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
Reconstructed microbial metabolic networks facilitate a mechanistic description of the
genotype–phenotype relationship through the deployment of constraint-based …
genotype–phenotype relationship through the deployment of constraint-based …
The biomass objective function
Flux balance analysis (FBA) is a mathematical approach for analyzing the flow of
metabolites through a metabolic network. To computationally predict cell growth using FBA …
metabolites through a metabolic network. To computationally predict cell growth using FBA …
A systematic assessment of current genome-scale metabolic reconstruction tools
Background Several genome-scale metabolic reconstruction software platforms have been
developed and are being continuously updated. These tools have been widely applied to …
developed and are being continuously updated. These tools have been widely applied to …
The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis
By the time the complete genome sequence of the soil bacterium Pseudomonas putida
KT2440 was published in 2002 (Nelson et al.,) this bacterium was considered a potential …
KT2440 was published in 2002 (Nelson et al.,) this bacterium was considered a potential …
What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira
Leptospirosis, caused by spirochetes of the genus Leptospira, is a globally widespread,
neglected and emerging zoonotic disease. While whole genome analysis of individual …
neglected and emerging zoonotic disease. While whole genome analysis of individual …