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Genome-scale reconstruction of the human astrocyte metabolic network
(Frontiers Research Foundation, 2017)
Pantograph: A template-based method for genome-scale metabolic model reconstruction
(Imperial College Press, 2015)
Genome-scale metabolic models are a powerful tool to study the inner workings of biological
systems and to guide applications. The advent of cheap sequencing has brought the opportunity to
create metabolic maps of ...
Genome-scale reconstruction of Salinispora tropica CNB-440 metabolism to study strain-specific adaptation
(Springer, 2015)
The first manually curated genome-scale metabolic model for Salinispora tropica strain CNB-440 was constructed. The reconstruction enables characterization of the metabolic capabilities for understanding and modeling the ...
The topology of genome-scale metabolic reconstructions unravels independent modules and high network flexibility
(2022)
The topology of metabolic networks is recognisably modular with modules weakly connected apart from sharing a pool of currency metabolites. Here, we defined modules as sets of reversible reactions isolated from the rest ...
Analysis of metabolic networks of Streptomyces leeuwenhoekii C34 by means of a genome scale model: Prediction of modifications that enhance the production of specialized metabolites
(Wiley, 2018)
The first genome scale model (GSM) for Streptomyces leeuwenhoekii C34 was developed to study the biosynthesis pathways of specialized metabolites and to find metabolic engineering targets for enhancing their production. ...
Metabolic modeling of Halomonas campaniensis improves polyhydroxybutyrate production under nitrogen limitation
(2024)
Poly-hydroxybutyrate (PHB) is an environmentally friendly alternative for conventional fossil fuel-based plastics that is produced by various microorganisms. Large-scale PHB production is challenging due to the comparatively ...
Traceability, reproducibility and wiki-exploration for "a-la-carte" reconstructions of genome-scale metabolic models
(Public Library Science, 2018-05)
Genome-scale metabolic models have become the tool of choice for the global analysis of microorganism metabolism, and their reconstruction has attained high standards of quality and reliability. Improvements in this area ...
Genome-scale metabolic modeling of the human milk oligosaccharide utilization by Bifidobacterium longum subsp. infantis
(2024)
Bifidobacterium longum subsp. infantis is a representative and dominant species in the infant gut and is considered a beneficial microbe. This organism displays multiple adaptations to thrive in the infant gut, regarded ...