Formulation, construction and analysis of kinetic models of metabolism: A review of modelling frameworks
Open accessAbstract
Kinetic models are critical to predict the dynamic behaviour of metabolic networks. Mechanistic kinetic models for large networks remain uncommon due to the difficulty of fitting their parameters. Recent modelling frameworks promise new ways to overcome this obstacle while retaining predictive capabilities. In this review, we present an overview of the relevant mathematical frameworks for kinetic formulation, construction and analysis. Starting with kinetic formalisms, we next review statistical methods for parameter inference, as well as recent computational frameworks applied to the construction and analysis of kinetic models. Finally, we discuss opportunities and limitations hindering the development of larger kinetic reconstructions.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In genome-scale kinetic models of cellular metabolism, missing kcat values are typically addressed by sampling or fitting them to large datasets.
“In genome-scale kinetic models of cellular metabolism, this issue is typically addressed by either sampling missing k cat values or fitting them to large datasets 7 , 8 , 12 , 13 .”
From Turnover number predictions for kinetically uncharacterized enzymes using machine and deep learning (2023) · cites this paper as [12]
The citation lists haven’t been fetched yet
References 230 · Cited by 166
- Authors
- Saa, P. A., & Nielsen, L. K.
- Affiliations
- The University of Queensland (AU)
- Corresponding author
- Nielsen, Lars K.
- Venue
- Biotechnology Advances
- Publisher
- Elsevier BV
- Published
- 2017-12
- Volume
- 35
- Issue
- 8
- Pages
- 981-1003
- ISSN
- 0734-9750 (ISSN-L)
- OpenAlex
- W2755275228
- Cited by
- 166
- References
- 230
- Citations by year
- 2026: 20 · 2025: 10 · 2024: 16 · 2023: 21 · 2022: 21 · 2021: 22 · 2020: 23 · 2019: 16 · 2018: 17
- FWCI
- 1.43
- Type
- journal article
- Language
- en
- Open access
- green
- orbit.dtu.dk
- Licence
- Locations
- Biotechnology Advances (publishedVersion)
- PubMed (publishedVersion)
- Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion, other-oa)
- Funders
- Novo Nordisk Fonden (NNF14OC0009473, NNF10CC1016517)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- metabolic networks, parameter inference, model reconstruction, metabolic engineering, parameter estimation, model analysis
- MeSH terms
- Kinetics, Models, Biological, Monte Carlo Method, Metabolic Networks and Pathways
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
