Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0

Y Chen, J Gustafsson, A Tafur Rangel, M Anton… - Nature …, 2024 - nature.com
Genome-scale metabolic models (GEMs) are computational representations that enable
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 …

[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 …

[HTML][HTML] ECMpy 2.0: A Python package for automated construction and analysis of enzyme-constrained models

Z Mao, J Niu, J Zhao, Y Huang, K Wu, L Yun… - Synthetic and systems …, 2024 - Elsevier
Genome-scale metabolic models (GEMs) have been widely employed to predict
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 …

[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 …

Machine learning for the advancement of genome-scale metabolic modeling

P Kundu, S Beura, S Mondal, AK Das, A Ghosh - Biotechnology Advances, 2024 - Elsevier
Constraint-based modeling (CBM) has evolved as the core systems biology tool to map the
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

Y Wang, Z Mao, J Dong, P Zhang, Q Gao, D Liu… - Microbial Cell …, 2024 - Springer
Background Genome-scale metabolic models (GEMs) serve as effective tools for
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 …

[HTML][HTML] Omics data analysis reveals the system-level constraint on cellular amino acid composition

Y Huang, Z Mao, Y Zhang, J Zhao, X Luan, K Wu… - Synthetic and Systems …, 2024 - Elsevier
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 …