A hybrid of Cuckoo Search and Minimization of Metabolic Adjustment to optimize metabolites production in genome-scale models
Metabolic engineering involves the modification and alteration of metabolic pathways to improve the production of desired substance. The modification can be made using in silicogene knockout simulation that is able to predict and analyse the disrupted genes which may enhance the metabolites producti...
| Autors principals: | , , , , , , , , |
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| Format: | Article |
| Idioma: | English |
| Publicat: |
Elsevier Ltd
2018
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| Matèries: | |
| Accés en línia: | http://umpir.ump.edu.my/id/eprint/22302/1/A%20hybrid%20of%20Cuckoo%20Search%20and%20Minimization%20of%20Metabolic%20Adjustment%20to%20optimize%20metabolites%20production%20in%20genome.pdf |
| _version_ | 1825812271429844992 |
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| author | Muhammad Azharuddin, Arif Mohd Saberi, Mohamad Muhammad Shafie, Abd Latif Safaai, Deris Muhammad Akmal, Remli Kauthar, Mohd Daud Zuwairie, Ibrahim Omatu, Sigeru Corchado, Juan Manuel |
| author_facet | Muhammad Azharuddin, Arif Mohd Saberi, Mohamad Muhammad Shafie, Abd Latif Safaai, Deris Muhammad Akmal, Remli Kauthar, Mohd Daud Zuwairie, Ibrahim Omatu, Sigeru Corchado, Juan Manuel |
| author_sort | Muhammad Azharuddin, Arif |
| collection | UMP |
| description | Metabolic engineering involves the modification and alteration of metabolic pathways to improve the production of desired substance. The modification can be made using in silicogene knockout simulation that is able to predict and analyse the disrupted genes which may enhance the metabolites production. Global optimization algorithms have been widely used for identifying gene knockout strategies. However, their productions were less than theoretical maximum and the algorithms are easily trapped into local optima. These algorithms also require a very large computation time to obtain acceptable results. This is due to the complexity of the metabolic models which are high dimensional and contain thousands of reactions. In this paper, a hybrid algorithm of Cuckoo Search and Minimization of Metabolic Adjustment is proposed to overcome the aforementioned problems. The hybrid algorithm searches for the near-optimal set of gene knockouts that leads to the overproduction of metabolites. Computational experiments on two sets of genome-scale metabolic models demonstrate that the proposed algorithm is better than the previous works in terms of growth rate, Biomass Product Couple Yield, and computation time. |
| first_indexed | 2024-03-06T12:26:42Z |
| format | Article |
| id | UMPir22302 |
| institution | Universiti Malaysia Pahang |
| language | English |
| last_indexed | 2024-03-06T12:26:42Z |
| publishDate | 2018 |
| publisher | Elsevier Ltd |
| record_format | dspace |
| spelling | UMPir223022018-11-15T03:39:17Z http://umpir.ump.edu.my/id/eprint/22302/ A hybrid of Cuckoo Search and Minimization of Metabolic Adjustment to optimize metabolites production in genome-scale models Muhammad Azharuddin, Arif Mohd Saberi, Mohamad Muhammad Shafie, Abd Latif Safaai, Deris Muhammad Akmal, Remli Kauthar, Mohd Daud Zuwairie, Ibrahim Omatu, Sigeru Corchado, Juan Manuel QA76 Computer software TK Electrical engineering. Electronics Nuclear engineering Metabolic engineering involves the modification and alteration of metabolic pathways to improve the production of desired substance. The modification can be made using in silicogene knockout simulation that is able to predict and analyse the disrupted genes which may enhance the metabolites production. Global optimization algorithms have been widely used for identifying gene knockout strategies. However, their productions were less than theoretical maximum and the algorithms are easily trapped into local optima. These algorithms also require a very large computation time to obtain acceptable results. This is due to the complexity of the metabolic models which are high dimensional and contain thousands of reactions. In this paper, a hybrid algorithm of Cuckoo Search and Minimization of Metabolic Adjustment is proposed to overcome the aforementioned problems. The hybrid algorithm searches for the near-optimal set of gene knockouts that leads to the overproduction of metabolites. Computational experiments on two sets of genome-scale metabolic models demonstrate that the proposed algorithm is better than the previous works in terms of growth rate, Biomass Product Couple Yield, and computation time. Elsevier Ltd 2018 Article PeerReviewed pdf en http://umpir.ump.edu.my/id/eprint/22302/1/A%20hybrid%20of%20Cuckoo%20Search%20and%20Minimization%20of%20Metabolic%20Adjustment%20to%20optimize%20metabolites%20production%20in%20genome.pdf Muhammad Azharuddin, Arif and Mohd Saberi, Mohamad and Muhammad Shafie, Abd Latif and Safaai, Deris and Muhammad Akmal, Remli and Kauthar, Mohd Daud and Zuwairie, Ibrahim and Omatu, Sigeru and Corchado, Juan Manuel (2018) A hybrid of Cuckoo Search and Minimization of Metabolic Adjustment to optimize metabolites production in genome-scale models. Computers in Biology and Medicine, 102. pp. 112-119. ISSN 0010-4825. (Published) https://doi.org/10.1016/j.compbiomed.2018.09.015 10.1016/j.compbiomed.2018.09.015 |
| spellingShingle | QA76 Computer software TK Electrical engineering. Electronics Nuclear engineering Muhammad Azharuddin, Arif Mohd Saberi, Mohamad Muhammad Shafie, Abd Latif Safaai, Deris Muhammad Akmal, Remli Kauthar, Mohd Daud Zuwairie, Ibrahim Omatu, Sigeru Corchado, Juan Manuel A hybrid of Cuckoo Search and Minimization of Metabolic Adjustment to optimize metabolites production in genome-scale models |
| title | A hybrid of Cuckoo Search and Minimization of Metabolic Adjustment to optimize metabolites production in genome-scale models |
| title_full | A hybrid of Cuckoo Search and Minimization of Metabolic Adjustment to optimize metabolites production in genome-scale models |
| title_fullStr | A hybrid of Cuckoo Search and Minimization of Metabolic Adjustment to optimize metabolites production in genome-scale models |
| title_full_unstemmed | A hybrid of Cuckoo Search and Minimization of Metabolic Adjustment to optimize metabolites production in genome-scale models |
| title_short | A hybrid of Cuckoo Search and Minimization of Metabolic Adjustment to optimize metabolites production in genome-scale models |
| title_sort | hybrid of cuckoo search and minimization of metabolic adjustment to optimize metabolites production in genome scale models |
| topic | QA76 Computer software TK Electrical engineering. Electronics Nuclear engineering |
| url | http://umpir.ump.edu.my/id/eprint/22302/1/A%20hybrid%20of%20Cuckoo%20Search%20and%20Minimization%20of%20Metabolic%20Adjustment%20to%20optimize%20metabolites%20production%20in%20genome.pdf |
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