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 …
Genome-scale modeling of yeast metabolism: retrospectives and perspectives
Yeasts have been widely used for production of bread, beer and wine, as well as for
production of bioethanol, but they have also been designed as cell factories to produce …
production of bioethanol, but they have also been designed as cell factories to produce …
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism
Genome-scale metabolic models (GEMs) represent extensive knowledgebases that provide
a platform for model simulations and integrative analysis of omics data. This study …
a platform for model simulations and integrative analysis of omics data. This study …
OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities
AR Zomorrodi, CD Maranas - PLoS computational biology, 2012 - journals.plos.org
Microorganisms rarely live isolated in their natural environments but rather function in
consolidated and socializing communities. Despite the growing availability of high …
consolidated and socializing communities. Despite the growing availability of high …
Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA
Malonyl-coenzyme A is an important precursor metabolite for the biosynthesis of
polyketides, flavonoids and biofuels. However, malonyl-CoA naturally synthesized in …
polyketides, flavonoids and biofuels. However, malonyl-CoA naturally synthesized in …
Path2Models: large-scale generation of computational models from biochemical pathway maps
Background Systems biology projects and omics technologies have led to a growing
number of biochemical pathway models and reconstructions. However, the majority of these …
number of biochemical pathway models and reconstructions. However, the majority of these …
Improving metabolic flux predictions using absolute gene expression data
Background Constraint-based analysis of genome-scale metabolic models typically relies
upon maximisation of a cellular objective function such as the rate or efficiency of biomass …
upon maximisation of a cellular objective function such as the rate or efficiency of biomass …
Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli
The metabolism of microorganisms is regulated through two main mechanisms: changes of
enzyme capacities as a consequence of gene expression modulation (“hierarchical control”) …
enzyme capacities as a consequence of gene expression modulation (“hierarchical control”) …
[HTML][HTML] A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes
K Smallbone, HL Messiha, KM Carroll, CL Winder… - FEBS letters, 2013 - Elsevier
We present an experimental and computational pipeline for the generation of kinetic models
of metabolism, and demonstrate its application to glycolysis in Saccharomyces cerevisiae …
of metabolism, and demonstrate its application to glycolysis in Saccharomyces cerevisiae …
Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network
Background Efforts to improve the computational reconstruction of the Saccharomyces
cerevisiae biochemical reaction network and to refine the stoichiometrically constrained …
cerevisiae biochemical reaction network and to refine the stoichiometrically constrained …