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Genome-scale transcriptional activation by non-homologous end joining-mediated integration in Yarrowia lipolytica
BackgroundGenome-scale screening can be applied to efficiently mine for unknown genes with phenotypes of interest or special functions. It is also...
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Reconstruction of genome-scale metabolic models of non-conventional yeasts: current state, challenges, and perspectives
Non-conventional yeasts are promising cell factories to produce lipids and oleochemicals, metabolites of industrial interest ( e.g ., organics acids,...
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Reconstruction of a genome-scale metabolic model and in-silico flux analysis of Aspergillus tubingensis: a non-mycotoxinogenic citric acid-producing fungus
BackgroundAspergillus tubingensis is a citric acid-producing fungus that can utilize sugars in hydrolysate of lignocellulosic biomass such as...
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Elucidating dynamic anaerobe metabolism with HRMAS 13C NMR and genome-scale modeling
Anaerobic microbial metabolism drives critical functions within global ecosystems, host–microbiota interactions, and industrial applications, yet...
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Genome-scale modeling of Chinese hamster ovary cells by hybrid semi-parametric flux balance analysis
Flux balance analysis (FBA) is currently the standard method to compute metabolic fluxes in genome-scale networks. Several FBA extensions employing...
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Reconstruction of Genome-Scale Metabolic Model for Hansenula polymorpha Using RAVEN
Genome-scale metabolic models (GEMs) provide a useful framework for modeling the metabolism of microorganisms. While the applications of GEMs are...
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A genome-scale metabolic model of the effect of dissolved oxygen on 1,3-propanediol fermentation by Klebsiella pneumoniae
Although 1,3-propanediol (1,3-PD) is usually considered an anaerobic fermentation product from glycerol by Klebsiella pneumoniae , microaerobic...
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Novel context-specific genome-scale modelling explores the potential of triacylglycerol production by Chlamydomonas reinhardtii
Gene expression data of cell cultures is commonly measured in biological and medical studies to understand cellular decision-making in various...
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Genome-scale metabolic model analysis of Pichia pastoris for enhancing the production of S-adenosyl-l-methionine
Komagataella phaffii , formerly Pichia pastoris ( P. pastoris ), is a promising methylotrophic yeast used in industry to produce recombinant protein and...
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Towards next-generation cell factories by rational genome-scale engineering
Metabolic engineering holds the promise to transform the chemical industry and to support the transition into a circular bioeconomy, by engineering...
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Improvement of Lutein Production in Auxenochlorella protothecoides Using Its Genome-Scale Metabolic Model and a System-Oriented Approach
Lutein is a valuable metabolite widely used in the food, pharmaceutical, cosmetic, and aquaculture industries. Marigold flowers are the most common...
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From formic acid to single-cell protein: genome-scale revealing the metabolic network of Paracoccus communis MA5
With the increase in population growth and environmental pollution, the daily protein supply is facing great challenges. Single-cell protein (SCP)...
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Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum
BackgroundMicrobial production of propionate from diluted streams of ethanol (e.g., deriving from syngas fermentation) is a sustainable alternative...
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A new strategy for dynamic metabolic flux estimation by integrating transient metabolome data into genome-scale metabolic models
Metabolic flux analysis (MFA) is a powerful tool for studying microbial cell physiology. Isotope-based MFA is the accepted standard for studying...
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Metabolic engineering of Bacillus subtilis based on genome-scale metabolic model to promote fengycin production
Fengycin is an important lipopeptide antibiotic that can be produced by Bacillus subtilis . However, the production capacity of the unmodified wild...
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Genome-scale Modeling of Metabolism and Macromolecular Expression and Their Applications
Genome-scale models (GEMs) are predictive tools to study genotype-phenotype relationships in biological systems. Initially, genome-scale models were...
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Genome-scale model reconstruction of the methylotrophic yeast Ogataea polymorpha
BackgroundOgataea polymorpha is a thermotolerant, methylotrophic yeast with significant industrial applications. While previously mainly used for...
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Genome-scale insights into the metabolic versatility of Limosilactobacillus reuteri
BackgroundLimosilactobacillus reuteri (earlier known as Lactobacillus reuteri ) is a well-studied lactic acid bacterium, with some specific strains...
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Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions
BackgroundGenome-scale metabolic model (GSMM) is a powerful tool for the study of cellular metabolic characteristics. With the development of...
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Construction and Validation of a Genome-Scale Metabolic Network of Thermotoga sp. Strain RQ7
Thermotoga are anaerobic hyperthermophiles that have a deep lineage to the last universal ancestor and produce biological hydrogen gas accompanying...
