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...

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Main Authors:	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
Format:	Article
Language:	English
Published:	Elsevier Ltd 2018
Subjects:	QA76 Computer software TK Electrical engineering. Electronics Nuclear engineering
Online Access:	http://umpir.ump.edu.my/id/eprint/22302/ http://umpir.ump.edu.my/id/eprint/22302/ http://umpir.ump.edu.my/id/eprint/22302/ 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

id	ump-22302
recordtype	eprints
spelling	ump-223022018-11-15T03:39:17Z 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 https://doi.org/10.1016/j.compbiomed.2018.09.015 10.1016/j.compbiomed.2018.09.015
repository_type	Digital Repository
institution_category	Local University
institution	Universiti Malaysia Pahang
building	UMP Institutional Repository
collection	Online Access
language	English
topic	QA76 Computer software TK Electrical engineering. Electronics Nuclear engineering
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
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.
format	Article
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
title	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_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_sort	hybrid of cuckoo search and minimization of metabolic adjustment to optimize metabolites production in genome-scale models
publisher	Elsevier Ltd
publishDate	2018
url	http://umpir.ump.edu.my/id/eprint/22302/ http://umpir.ump.edu.my/id/eprint/22302/ http://umpir.ump.edu.my/id/eprint/22302/ 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
first_indexed	2023-09-18T22:33:07Z
last_indexed	2023-09-18T22:33:07Z
_version_	1777416418235514880

A hybrid of Cuckoo Search and Minimization of Metabolic Adjustment to optimize metabolites production in genome-scale models

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