Comparison of optimization-modelling methods for metabolites production in escherichia coli
The metabolic network is the reconstruction of the metabolic pathway of an organism that is used to represent the interaction between enzymes and metabolites in genome level. Meanwhile, metabolic engineering is a process that modifies the metabolic network of a cell to increase the production of met...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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De Gruyter
2020
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| Online Access: | http://umpir.ump.edu.my/id/eprint/31042/ http://umpir.ump.edu.my/id/eprint/31042/1/Comparison%20of%20optimization-modelling%20methods%20for%20metabolites%20production.pdf |
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| author | Lee, M. K. Mohd Saberi, Mohamad Choon, Yee Wen Kauthar, Mohd Daud Nurul Athirah, Nasarudin Mohd Arfian, Ismail Zuwairie, Ibrahim Suhaimi, Napis Sinnott, Richard O. |
| author_facet | Lee, M. K. Mohd Saberi, Mohamad Choon, Yee Wen Kauthar, Mohd Daud Nurul Athirah, Nasarudin Mohd Arfian, Ismail Zuwairie, Ibrahim Suhaimi, Napis Sinnott, Richard O. |
| author_sort | Lee, M. K. |
| building | UMP Institutional Repository |
| collection | Online Access |
| description | The metabolic network is the reconstruction of the metabolic pathway of an organism that is used to represent the interaction between enzymes and metabolites in genome level. Meanwhile, metabolic engineering is a process that modifies the metabolic network of a cell to increase the production of metabolites. However, the metabolic networks are too complex that cause problem in identifying near-optimal knockout genes/reactions for maximizing the metabolite’s production. Therefore, through constraint-based modelling, various metaheuristic algorithms have been improvised to optimize the desired phenotypes. In this paper, PSOMOMA was compared with CSMOMA and ABCMOMA for maximizing the production of succinic acid in E. coli. Furthermore, the results obtained from PSOMOMA were validated with results from the wet lab experiment. |
| first_indexed | 2025-11-15T03:00:46Z |
| format | Article |
| id | ump-31042 |
| institution | Universiti Malaysia Pahang |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T03:00:46Z |
| publishDate | 2020 |
| publisher | De Gruyter |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | ump-310422021-06-30T14:31:02Z http://umpir.ump.edu.my/id/eprint/31042/ Comparison of optimization-modelling methods for metabolites production in escherichia coli Lee, M. K. Mohd Saberi, Mohamad Choon, Yee Wen Kauthar, Mohd Daud Nurul Athirah, Nasarudin Mohd Arfian, Ismail Zuwairie, Ibrahim Suhaimi, Napis Sinnott, Richard O. QA76 Computer software The metabolic network is the reconstruction of the metabolic pathway of an organism that is used to represent the interaction between enzymes and metabolites in genome level. Meanwhile, metabolic engineering is a process that modifies the metabolic network of a cell to increase the production of metabolites. However, the metabolic networks are too complex that cause problem in identifying near-optimal knockout genes/reactions for maximizing the metabolite’s production. Therefore, through constraint-based modelling, various metaheuristic algorithms have been improvised to optimize the desired phenotypes. In this paper, PSOMOMA was compared with CSMOMA and ABCMOMA for maximizing the production of succinic acid in E. coli. Furthermore, the results obtained from PSOMOMA were validated with results from the wet lab experiment. De Gruyter 2020-05-06 Article PeerReviewed pdf en cc_by_nc_nd_4 http://umpir.ump.edu.my/id/eprint/31042/1/Comparison%20of%20optimization-modelling%20methods%20for%20metabolites%20production.pdf Lee, M. K. and Mohd Saberi, Mohamad and Choon, Yee Wen and Kauthar, Mohd Daud and Nurul Athirah, Nasarudin and Mohd Arfian, Ismail and Zuwairie, Ibrahim and Suhaimi, Napis and Sinnott, Richard O. (2020) Comparison of optimization-modelling methods for metabolites production in escherichia coli. Journal of integrative bioinformatics, 17 (1). pp. 1-7. ISSN 1613-4516. (Published) https://doi.org/10.1515/jib-2019-0073 https://doi.org/10.1515/jib-2019-0073 |
| spellingShingle | QA76 Computer software Lee, M. K. Mohd Saberi, Mohamad Choon, Yee Wen Kauthar, Mohd Daud Nurul Athirah, Nasarudin Mohd Arfian, Ismail Zuwairie, Ibrahim Suhaimi, Napis Sinnott, Richard O. Comparison of optimization-modelling methods for metabolites production in escherichia coli |
| title | Comparison of optimization-modelling methods for metabolites production in escherichia coli |
| title_full | Comparison of optimization-modelling methods for metabolites production in escherichia coli |
| title_fullStr | Comparison of optimization-modelling methods for metabolites production in escherichia coli |
| title_full_unstemmed | Comparison of optimization-modelling methods for metabolites production in escherichia coli |
| title_short | Comparison of optimization-modelling methods for metabolites production in escherichia coli |
| title_sort | comparison of optimization-modelling methods for metabolites production in escherichia coli |
| topic | QA76 Computer software |
| url | http://umpir.ump.edu.my/id/eprint/31042/ http://umpir.ump.edu.my/id/eprint/31042/ http://umpir.ump.edu.my/id/eprint/31042/ http://umpir.ump.edu.my/id/eprint/31042/1/Comparison%20of%20optimization-modelling%20methods%20for%20metabolites%20production.pdf |