Multilevel Metabolic Modelling Using Ordinary Differential Equations - mauriceling/mauriceling.github.io GitHub Wiki

Citation: Sim, BJH, Tan, NTF, Ling, MHT. 2025. Multilevel Metabolic Modelling Using Ordinary Differential Equations. In Ranganathan, S., Cannataro, M., and Khan, A. M. (eds), Encyclopedia of Bioinformatics and Computational Biology (2nd Edition) Volume 4, Pages 491-498. Oxford: Elsevier. ISBN 978-0-323-95503-4.

Link to [Abstract]

Mathematical modelling has the potential to predict biological phenotypes under metabolic perturbations, which can be used to guide engineering approaches. There are many levels of biological modelling – from genomics represented by DNA at the core, to transcriptomics represented by mRNA, to proteomics represented by peptides and enzymes, to metabolomics represented by metabolism, to fluxomics represented by changes in metabolite concentrations over time. In this article, the steps to model gene expressions and metabolic reactions independently are described, which can be extended to model entire transcriptome and metabolome, respectively. After which, the link between transcriptome and metabolome will be described; and ending off with a brief overview on recent applications of metabolic models.