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Biomolecules
Volume 12
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Review

Construction of Multiscale Genome-Scale Metabolic Models: Frameworks and Challenges

by
Xinyu Bi
1,2,
Yanfeng Liu
1,2,
Jianghua Li
1,2,
Guocheng Du
1,2,
Xueqin Lv
1,2 and
Long Liu
1,2,*
1
Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
2
Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi 214122, China
*
Author to whom correspondence should be addressed.
Biomolecules 2022, 12(5), 721; https://doi.org/10.3390/biom12050721
Submission received: 23 April 2022 / Revised: 15 May 2022 / Accepted: 16 May 2022 / Published: 19 May 2022
(This article belongs to the Special Issue Computational Biology for Metabolic Modelling and Pathway Design)
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Abstract

Genome-scale metabolic models (GEMs) are effective tools for metabolic engineering and have been widely used to guide cell metabolic regulation. However, the single gene–protein-reaction data type in GEMs limits the understanding of biological complexity. As a result, multiscale models that add constraints or integrate omics data based on GEMs have been developed to more accurately predict phenotype from genotype. This review summarized the recent advances in the development of multiscale GEMs, including multiconstraint, multiomic, and whole-cell models, and outlined machine learning applications in GEM construction. This review focused on the frameworks, toolkits, and algorithms for constructing multiscale GEMs. The challenges and perspectives of multiscale GEM development are also discussed.
Keywords: multiscale genome-scale metabolic models; multiconstraint models; multiomics models; machine learning; whole-cell models multiscale genome-scale metabolic models; multiconstraint models; multiomics models; machine learning; whole-cell models

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MDPI and ACS Style

Bi, X.; Liu, Y.; Li, J.; Du, G.; Lv, X.; Liu, L. Construction of Multiscale Genome-Scale Metabolic Models: Frameworks and Challenges. Biomolecules 2022, 12, 721. https://doi.org/10.3390/biom12050721

AMA Style

Bi X, Liu Y, Li J, Du G, Lv X, Liu L. Construction of Multiscale Genome-Scale Metabolic Models: Frameworks and Challenges. Biomolecules. 2022; 12(5):721. https://doi.org/10.3390/biom12050721

Chicago/Turabian Style

Bi, Xinyu, Yanfeng Liu, Jianghua Li, Guocheng Du, Xueqin Lv, and Long Liu. 2022. "Construction of Multiscale Genome-Scale Metabolic Models: Frameworks and Challenges" Biomolecules 12, no. 5: 721. https://doi.org/10.3390/biom12050721

APA Style

Bi, X., Liu, Y., Li, J., Du, G., Lv, X., & Liu, L. (2022). Construction of Multiscale Genome-Scale Metabolic Models: Frameworks and Challenges. Biomolecules, 12(5), 721. https://doi.org/10.3390/biom12050721

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