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 …
Using genome-scale models to predict biological capabilities
Constraint-based reconstruction and analysis (COBRA) methods at the genome scale have
been under development since the first whole-genome sequences appeared in the mid …
been under development since the first whole-genome sequences appeared in the mid …
Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints
Genome‐scale metabolic models (GEM s) are widely used to calculate metabolic
phenotypes. They rely on defining a set of constraints, the most common of which is that the …
phenotypes. They rely on defining a set of constraints, the most common of which is that the …
Turnover number predictions for kinetically uncharacterized enzymes using machine and deep learning
The turnover number k cat, a measure of enzyme efficiency, is central to understanding
cellular physiology and resource allocation. As experimental k cat estimates are unavailable …
cellular physiology and resource allocation. As experimental k cat estimates are unavailable …
Metabolite concentrations, fluxes and free energies imply efficient enzyme usage
In metabolism, available free energy is limited and must be divided across pathway steps to
maintain a negative Δ G throughout. For each reaction, Δ G is log proportional both to a …
maintain a negative Δ G throughout. For each reaction, Δ G is log proportional both to a …
Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0
Genome-scale metabolic models (GEMs) are computational representations that enable
mathematical exploration of metabolic behaviors within cellular and environmental …
mathematical exploration of metabolic behaviors within cellular and environmental …
Mitochondrial ATP generation is more proteome efficient than glycolysis
Metabolic efficiency profoundly influences organismal fitness. Nonphotosynthetic organisms,
from yeast to mammals, derive usable energy primarily through glycolysis and respiration …
from yeast to mammals, derive usable energy primarily through glycolysis and respiration …
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 …
Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli
BD Bennett, EH Kimball, M Gao, R Osterhout… - Nature chemical …, 2009 - nature.com
Absolute metabolite concentrations are critical to a quantitative understanding of cellular
metabolism, as concentrations impact both the free energies and rates of metabolic …
metabolism, as concentrations impact both the free energies and rates of metabolic …
Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction
Growth is a fundamental process of life. Growth requirements are well‐characterized
experimentally for many microbes; however, we lack a unified model for cellular growth …
experimentally for many microbes; however, we lack a unified model for cellular growth …