Biomolecules (May 2022)

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

  • Xinyu Bi,
  • Yanfeng Liu,
  • Jianghua Li,
  • Guocheng Du,
  • Xueqin Lv,
  • Long Liu

DOI
https://doi.org/10.3390/biom12050721
Journal volume & issue
Vol. 12, no. 5
p. 721

Abstract

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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.

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