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 …
Genome-scale metabolic network models for industrial microorganisms metabolic engineering: current advances and future prospects
Z Gong, J Chen, X Jiao, H Gong, D Pan, L Liu… - Biotechnology …, 2024 - Elsevier
The construction of high-performance microbial cell factories (MCFs) is the centerpiece of
biomanufacturing. However, the complex metabolic regulatory network of microorganisms …
biomanufacturing. However, the complex metabolic regulatory network of microorganisms …
[HTML][HTML] Evaluation of enzyme-constrained genome-scale model through metabolic engineering of anaerobic co-production of 2, 3-butanediol and glycerol by …
G Sjöberg, A Reķēna, M Fornstad, PJ Lahtvee… - Metabolic …, 2024 - Elsevier
Enzyme-constrained genome-scale models (ecGEMs) have potential to predict phenotypes
in a variety of conditions, such as growth rates or carbon sources. This study investigated if …
in a variety of conditions, such as growth rates or carbon sources. This study investigated if …
[HTML][HTML] ECMpy 2.0: A Python package for automated construction and analysis of enzyme-constrained models
Genome-scale metabolic models (GEMs) have been widely employed to predict
microorganism behaviors. However, GEMs only consider stoichiometric constraints, leading …
microorganism behaviors. However, GEMs only consider stoichiometric constraints, leading …
Dynamically Regulating Glucose Uptake to Reduce Overflow Metabolism with a Quorum-Sensing Circuit for the Efficient Synthesis of d-Pantothenic Acid in Bacillus …
P Yuan, M Xu, C Mao, H Zheng, D Sun - ACS Synthetic Biology, 2023 - ACS Publications
In response to a high concentration of glucose, Bacillus subtilis, a microbial chassis for
producing many industrial metabolites, rapidly takes up glucose using the …
producing many industrial metabolites, rapidly takes up glucose using the …
[HTML][HTML] Enzyme-constrained metabolic model and in silico metabolic engineering of Clostridium ljungdahlii for the development of sustainable production processes
A Caivano, W van Winden, G Dragone… - Computational and …, 2023 - Elsevier
Constraint-based genome-scale models (GEMs) of microorganisms provide a powerful tool
for predicting and analyzing microbial phenotypes as well as for understanding how these …
for predicting and analyzing microbial phenotypes as well as for understanding how these …
Machine learning for the advancement of genome-scale metabolic modeling
Constraint-based modeling (CBM) has evolved as the core systems biology tool to map the
interrelations between genotype, phenotype, and external environment. The recent …
interrelations between genotype, phenotype, and external environment. The recent …
Construction of an enzyme-constrained metabolic network model for Myceliophthora thermophila using machine learning-based kcat data
Background Genome-scale metabolic models (GEMs) serve as effective tools for
understanding cellular phenotypes and predicting engineering targets in the development of …
understanding cellular phenotypes and predicting engineering targets in the development of …
[HTML][HTML] Upgrading a cyanobacterial genome-scale model by inclusion of enzymatic constraints
F Andrews, NS Scrutton, JM Schwartz - Algal Research, 2024 - Elsevier
Over the past decade, several genome-scale metabolic models have been constructed for
the model cyanobacteria Synechocystis sp. PCC 6803. These allow us to investigate how …
the model cyanobacteria Synechocystis sp. PCC 6803. These allow us to investigate how …
[HTML][HTML] Omics data analysis reveals the system-level constraint on cellular amino acid composition
Proteins play a pivotal role in coordinating the functions of organisms, essentially governing
their traits, as the dynamic arrangement of diverse amino acids leads to a multitude of folded …
their traits, as the dynamic arrangement of diverse amino acids leads to a multitude of folded …