Context-specific genome-scale metabolic modelling and its application to the analysis of COVID-19 metabolic signatures

Moškon, Miha (author), Režen, Tadeja (author)

Genome-scale metabolic models (GEMs) have found numerous applications in different domains, ranging from biotechnology to systems medicine. Herein, we overview the most popular algorithms for the automated reconstruction of context-specific GEMs using high-throughput experimental data. Moreover, we describe different datasets applied in the process, and protocols that can be used to further automate the model reconstruction and validation. Finally, we describe recent COVID-19 applications of context-specific GEMs, focusing on the analysis of metabolic implications, identification of biomarkers and potential drug targets.

• Language: English
• Keywords: context-specific genome scale metabolic modelling, constraint-based modelling, omics data integration, model extraction method, COVID-19, computational pipeline, metabolic fluxes, context-specific model
• Work type: Article
• Typology: 1.02 - Review Article
• Organization: FRI - Faculty of Computer and Information Science ; MF - Faculty of Medicine
• Publication status: Published
• Publication version: Version of Record
• Year: 2023
• Number of pages: 28 str.
• Numbering: Vol. 13, iss. 1, art. 126
• PID: 20.500.12556/RUL-166034
• UDC: 004:578.834
• ISSN on article: 2218-1989
• DOI: 10.3390/metabo13010126
• COBISS.SI-ID: 137763843
• Publication date in RUL: 18.12.2024

Record is a part of a journal

• Title: Metabolites
• Shortened title: Metabolites
• Publisher: MDPI
• ISSN: 2218-1989
• COBISS.SI-ID: 523274009

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: kontekstno specifično modeliranje metabolizma, modeliranje z omejitvami, integracija omskih podatkov, metode za ekstrakcijo modelov, COVID-19