Current status and applications of genome-scale metabolic models
Abstract Genome-scale metabolic models (GEMs) computationally describe gene-protein-reaction associations for entire metabolic genes in an organism, and can be simulated to predict metabolic fluxes for various systems-level metabolic studies. Since the first GEM for Haemophilus influenzae was report...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-06-01
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| Series: | Genome Biology |
| Online Access: | http://link.springer.com/article/10.1186/s13059-019-1730-3 |
| _version_ | 1811218234705182720 |
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| author | Changdai Gu Gi Bae Kim Won Jun Kim Hyun Uk Kim Sang Yup Lee |
| author_facet | Changdai Gu Gi Bae Kim Won Jun Kim Hyun Uk Kim Sang Yup Lee |
| author_sort | Changdai Gu |
| collection | DOAJ |
| description | Abstract Genome-scale metabolic models (GEMs) computationally describe gene-protein-reaction associations for entire metabolic genes in an organism, and can be simulated to predict metabolic fluxes for various systems-level metabolic studies. Since the first GEM for Haemophilus influenzae was reported in 1999, advances have been made to develop and simulate GEMs for an increasing number of organisms across bacteria, archaea, and eukarya. Here, we review current reconstructed GEMs and discuss their applications, including strain development for chemicals and materials production, drug targeting in pathogens, prediction of enzyme functions, pan-reactome analysis, modeling interactions among multiple cells or organisms, and understanding human diseases. |
| first_indexed | 2024-04-12T07:07:38Z |
| format | Article |
| id | doaj.art-cfee059aa89f46b398a1fdccc2ecc339 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-04-12T07:07:38Z |
| publishDate | 2019-06-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-cfee059aa89f46b398a1fdccc2ecc3392022-12-22T03:42:45ZengBMCGenome Biology1474-760X2019-06-0120111810.1186/s13059-019-1730-3Current status and applications of genome-scale metabolic modelsChangdai Gu0Gi Bae Kim1Won Jun Kim2Hyun Uk Kim3Sang Yup Lee4Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Metabolic and Biomolecular Engineering National Research Laboratory, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST)Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Metabolic and Biomolecular Engineering National Research Laboratory, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST)Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Metabolic and Biomolecular Engineering National Research Laboratory, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST)Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Systems Biology and Medicine Laboratory, KAISTDepartment of Chemical and Biomolecular Engineering (BK21 Plus Program), Metabolic and Biomolecular Engineering National Research Laboratory, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST)Abstract Genome-scale metabolic models (GEMs) computationally describe gene-protein-reaction associations for entire metabolic genes in an organism, and can be simulated to predict metabolic fluxes for various systems-level metabolic studies. Since the first GEM for Haemophilus influenzae was reported in 1999, advances have been made to develop and simulate GEMs for an increasing number of organisms across bacteria, archaea, and eukarya. Here, we review current reconstructed GEMs and discuss their applications, including strain development for chemicals and materials production, drug targeting in pathogens, prediction of enzyme functions, pan-reactome analysis, modeling interactions among multiple cells or organisms, and understanding human diseases.http://link.springer.com/article/10.1186/s13059-019-1730-3 |
| spellingShingle | Changdai Gu Gi Bae Kim Won Jun Kim Hyun Uk Kim Sang Yup Lee Current status and applications of genome-scale metabolic models Genome Biology |
| title | Current status and applications of genome-scale metabolic models |
| title_full | Current status and applications of genome-scale metabolic models |
| title_fullStr | Current status and applications of genome-scale metabolic models |
| title_full_unstemmed | Current status and applications of genome-scale metabolic models |
| title_short | Current status and applications of genome-scale metabolic models |
| title_sort | current status and applications of genome scale metabolic models |
| url | http://link.springer.com/article/10.1186/s13059-019-1730-3 |
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