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

Y Chen, J Gustafsson, A Tafur Rangel, M Anton… - Nature protocols, 2024 - nature.com
Genome-scale metabolic models (GEMs) are computational representations that enable
mathematical exploration of metabolic behaviors within cellular and environmental …

[HTML][HTML] Relieving metabolic burden to improve robustness and bioproduction by industrial microorganisms

J Mao, H Zhang, Y Chen, L Wei, J Liu, J Nielsen… - Biotechnology …, 2024 - Elsevier
Metabolic burden is defined by the influence of genetic manipulation and environmental
perturbations on the distribution of cellular resources. The rewiring of microbial metabolism …

Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction

F Li, L Yuan, H Lu, G Li, Y Chen, MKM Engqvist… - Nature Catalysis, 2022 - nature.com
Enzyme turnover numbers (k cat) are key to understanding cellular metabolism, proteome
allocation and physiological diversity, but experimentally measured k cat data are sparse …

Genome-scale models in human metabologenomics

A Mardinoglu, BØ Palsson - Nature Reviews Genetics, 2025 - nature.com
Metabologenomics integrates metabolomics with other omics data types to comprehensively
study the genetic and environmental factors that influence metabolism. These multi-omics …

Adaptations in metabolism and protein translation give rise to the Crabtree effect in yeast

C Malina, R Yu, J Björkeroth, EJ Kerkhoven… - Proceedings of the …, 2021 - pnas.org
Aerobic fermentation, also referred to as the Crabtree effect in yeast, is a well-studied
phenomenon that allows many eukaryal cells to attain higher growth rates at high glucose …

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 …

Genome-scale modeling of yeast metabolism: retrospectives and perspectives

Y Chen, F Li, J Nielsen - FEMS Yeast Research, 2022 - academic.oup.com
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 …

Quantitative principles of microbial metabolism shared across scales

D Sher, D Segrè, MJ Follows - Nature Microbiology, 2024 - nature.com
Metabolism is the complex network of chemical reactions occurring within every cell and
organism, maintaining life, mediating ecosystem processes and affecting Earth's climate …

Cell factory design with advanced metabolic modelling empowered by artificial intelligence

H Lu, L **ao, W Liao, X Yan, J Nielsen - Metabolic Engineering, 2024 - Elsevier
Advances in synthetic biology and artificial intelligence (AI) have provided new opportunities
for modern biotechnology. High-performance cell factories, the backbone of industrial …

[HTML][HTML] Metabolic engineering of human gut microbiome: recent developments and future perspectives

P Li, S Roos, H Luo, B Ji, J Nielsen - Metabolic Engineering, 2023 - Elsevier
Many studies have demonstrated that the gut microbiota is associated with human health
and disease. Manipulation of the gut microbiota, eg supplementation of probiotics, has been …