Context-Specific Genome-Scale Metabolic Modelling and Its Application to the Analysis of COVID-19 Metabolic Signatures
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...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-01-01
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| Series: | Metabolites |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2218-1989/13/1/126 |
| _version_ | 1827623264197804032 |
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| author | Miha Moškon Tadeja Režen |
| author_facet | Miha Moškon Tadeja Režen |
| author_sort | Miha Moškon |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T11:42:16Z |
| format | Article |
| id | doaj.art-2e80652899584622b9459c365e5dfe09 |
| institution | Directory Open Access Journal |
| issn | 2218-1989 |
| language | English |
| last_indexed | 2024-03-09T11:42:16Z |
| publishDate | 2023-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Metabolites |
| spelling | doaj.art-2e80652899584622b9459c365e5dfe092023-11-30T23:29:21ZengMDPI AGMetabolites2218-19892023-01-0113112610.3390/metabo13010126Context-Specific Genome-Scale Metabolic Modelling and Its Application to the Analysis of COVID-19 Metabolic SignaturesMiha Moškon0Tadeja Režen1Faculty of Computer and Information Science, University of Ljubljana, 1000 Ljubljana, SloveniaCentre for Functional Genomics and Bio-Chips, Institute for Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, SloveniaGenome-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.https://www.mdpi.com/2218-1989/13/1/126context-specific genome scale metabolic modellingconstraint-based modellingomics data integrationmodel extraction methodcomputational pipelinemetabolic fluxes |
| spellingShingle | Miha Moškon Tadeja Režen Context-Specific Genome-Scale Metabolic Modelling and Its Application to the Analysis of COVID-19 Metabolic Signatures Metabolites context-specific genome scale metabolic modelling constraint-based modelling omics data integration model extraction method computational pipeline metabolic fluxes |
| title | Context-Specific Genome-Scale Metabolic Modelling and Its Application to the Analysis of COVID-19 Metabolic Signatures |
| title_full | Context-Specific Genome-Scale Metabolic Modelling and Its Application to the Analysis of COVID-19 Metabolic Signatures |
| title_fullStr | Context-Specific Genome-Scale Metabolic Modelling and Its Application to the Analysis of COVID-19 Metabolic Signatures |
| title_full_unstemmed | Context-Specific Genome-Scale Metabolic Modelling and Its Application to the Analysis of COVID-19 Metabolic Signatures |
| title_short | Context-Specific Genome-Scale Metabolic Modelling and Its Application to the Analysis of COVID-19 Metabolic Signatures |
| title_sort | context specific genome scale metabolic modelling and its application to the analysis of covid 19 metabolic signatures |
| topic | context-specific genome scale metabolic modelling constraint-based modelling omics data integration model extraction method computational pipeline metabolic fluxes |
| url | https://www.mdpi.com/2218-1989/13/1/126 |
| work_keys_str_mv | AT mihamoskon contextspecificgenomescalemetabolicmodellinganditsapplicationtotheanalysisofcovid19metabolicsignatures AT tadejarezen contextspecificgenomescalemetabolicmodellinganditsapplicationtotheanalysisofcovid19metabolicsignatures |