Optimising the production of succinate and lactate in Escherichia coli using a hybrid of artificial bee colony algorithm and minimisation of metabolic adjustment
Metabolic engineering is a research field that focuses on the design of models for metabolism, and uses computational procedures to suggest genetic manipulation. It aims to improve the yield of particular chemical or biochemical products. Several traditional metabolic engineering methods are commonl...
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| Format: | Article |
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Society for Biotechnology
2015
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| _version_ | 1796972570347569152 |
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| author | Tang, Phooi Wah Choon, Yee Wen Mohamad, Mohd Saberi Deris, Safaai Napis, Suhaimi |
| author_facet | Tang, Phooi Wah Choon, Yee Wen Mohamad, Mohd Saberi Deris, Safaai Napis, Suhaimi |
| author_sort | Tang, Phooi Wah |
| collection | UPM |
| description | Metabolic engineering is a research field that focuses on the design of models for metabolism, and uses computational procedures to suggest genetic manipulation. It aims to improve the yield of particular chemical or biochemical products. Several traditional metabolic engineering methods are commonly used to increase the production of a desired target, but the products are always far below their theoretical maximums. Using numeral optimisation algorithms to identify gene knockouts may stall at a local minimum in a multivariable function. This paper proposes a hybrid of the artificial bee colony (ABC) algorithm and the minimisation of metabolic adjustment (MOMA) to predict an optimal set of solutions in order to optimise the production rate of succinate and lactate. The dataset used in this work was from the iJO1366 Escherichia coli metabolic network. The experimental results include the production rate, growth rate and a list of knockout genes. From the comparative analysis, ABCMOMA produced better results compared to previous works, showing potential for solving genetic engineering problems. |
| first_indexed | 2024-03-06T08:29:58Z |
| format | Article |
| id | upm.eprints-34762 |
| institution | Universiti Putra Malaysia |
| last_indexed | 2024-03-06T08:29:58Z |
| publishDate | 2015 |
| publisher | Society for Biotechnology |
| record_format | dspace |
| spelling | upm.eprints-347622015-12-22T08:55:34Z http://psasir.upm.edu.my/id/eprint/34762/ Optimising the production of succinate and lactate in Escherichia coli using a hybrid of artificial bee colony algorithm and minimisation of metabolic adjustment Tang, Phooi Wah Choon, Yee Wen Mohamad, Mohd Saberi Deris, Safaai Napis, Suhaimi Metabolic engineering is a research field that focuses on the design of models for metabolism, and uses computational procedures to suggest genetic manipulation. It aims to improve the yield of particular chemical or biochemical products. Several traditional metabolic engineering methods are commonly used to increase the production of a desired target, but the products are always far below their theoretical maximums. Using numeral optimisation algorithms to identify gene knockouts may stall at a local minimum in a multivariable function. This paper proposes a hybrid of the artificial bee colony (ABC) algorithm and the minimisation of metabolic adjustment (MOMA) to predict an optimal set of solutions in order to optimise the production rate of succinate and lactate. The dataset used in this work was from the iJO1366 Escherichia coli metabolic network. The experimental results include the production rate, growth rate and a list of knockout genes. From the comparative analysis, ABCMOMA produced better results compared to previous works, showing potential for solving genetic engineering problems. Society for Biotechnology 2015-03 Article PeerReviewed Tang, Phooi Wah and Choon, Yee Wen and Mohamad, Mohd Saberi and Deris, Safaai and Napis, Suhaimi (2015) Optimising the production of succinate and lactate in Escherichia coli using a hybrid of artificial bee colony algorithm and minimisation of metabolic adjustment. Journal of Bioscience and Bioengineering, 119 (3). pp. 363-368. ISSN 1389-1723; ESSN: 1347-4421 http://www.sciencedirect.com/science/article/pii/S138917231400293X 10.1016/j.jbiosc.2014.08.004 |
| spellingShingle | Tang, Phooi Wah Choon, Yee Wen Mohamad, Mohd Saberi Deris, Safaai Napis, Suhaimi Optimising the production of succinate and lactate in Escherichia coli using a hybrid of artificial bee colony algorithm and minimisation of metabolic adjustment |
| title | Optimising the production of succinate and lactate in Escherichia coli using a hybrid of artificial bee colony algorithm and minimisation of metabolic adjustment |
| title_full | Optimising the production of succinate and lactate in Escherichia coli using a hybrid of artificial bee colony algorithm and minimisation of metabolic adjustment |
| title_fullStr | Optimising the production of succinate and lactate in Escherichia coli using a hybrid of artificial bee colony algorithm and minimisation of metabolic adjustment |
| title_full_unstemmed | Optimising the production of succinate and lactate in Escherichia coli using a hybrid of artificial bee colony algorithm and minimisation of metabolic adjustment |
| title_short | Optimising the production of succinate and lactate in Escherichia coli using a hybrid of artificial bee colony algorithm and minimisation of metabolic adjustment |
| title_sort | optimising the production of succinate and lactate in escherichia coli using a hybrid of artificial bee colony algorithm and minimisation of metabolic adjustment |
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