Staff View: A hybrid of differential search algorithm and flux balance analysis to: Identify knockout strategies for in silico optimization of metabolites production

A hybrid of differential search algorithm and flux balance analysis to: Identify knockout strategies for in silico optimization of metabolites production

An increasing demand of naturally producing metabolites has gained the attention of researchers to develop better algorithms for predicting the effects of reaction knockouts. With the success of genome sequencing, in silico metabolic engineering has aided the researchers in modifying the genome-scal...

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Main Authors:	Mohd. Daud, Kauthar, Zakaria, Zalmiyah, Ali Shah, Zuraini, Mohamad, Mohd. Saberi, Deris, Safaai, Omatu, Sigeru, Corchado, Juan Manuel
Format:	Article
Language:	English
Published:	International Center for Scientific Research and Studies 2018
Subjects:	QA75 Electronic computers. Computer science
Online Access:	http://eprints.utm.my/id/eprint/84598/1/KautharMohdDaud2018_AHybridofDifferentialSearchAlgorithmandFlux.pdf http://eprints.utm.my/id/eprint/84598/ http://www.home.ijasca.com/article-in-press/volume-10-2018/vol-10-2/
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spelling	my.utm.845982020-02-27T03:20:43Z http://eprints.utm.my/id/eprint/84598/ A hybrid of differential search algorithm and flux balance analysis to: Identify knockout strategies for in silico optimization of metabolites production Mohd. Daud, Kauthar Zakaria, Zalmiyah Ali Shah, Zuraini Mohamad, Mohd. Saberi Deris, Safaai Omatu, Sigeru Corchado, Juan Manuel QA75 Electronic computers. Computer science An increasing demand of naturally producing metabolites has gained the attention of researchers to develop better algorithms for predicting the effects of reaction knockouts. With the success of genome sequencing, in silico metabolic engineering has aided the researchers in modifying the genome-scale metabolic network. However, the complexities of the metabolic networks, have led to difficulty in obtaining a set of knockout reactions, which eventually lead to increase in computational time. Hence, many computational algorithms have been developed. Nevertheless, most of these algorithms are hindered by the solution being trapped in the local optima. In this paper, we proposed a hybrid of Differential Search Algorithm (DSA) and Flux Balance Analysis (FBA), to identify knockout reactions for enhancing the production of desired metabolites. Two organisms namely Escherichia coli and Zymomonas mobilis were tested by targeting the production rate of succinic acid, acetic acid, and ethanol. From this experiment, we obtained the list of knockout reactions and production rate. The results show that our proposed hybrid algorithm is capable of identifying knockout reactions with above 70% of production rate from the wild-type. International Center for Scientific Research and Studies 2018-07 Article PeerReviewed application/pdf en http://eprints.utm.my/id/eprint/84598/1/KautharMohdDaud2018_AHybridofDifferentialSearchAlgorithmandFlux.pdf Mohd. Daud, Kauthar and Zakaria, Zalmiyah and Ali Shah, Zuraini and Mohamad, Mohd. Saberi and Deris, Safaai and Omatu, Sigeru and Corchado, Juan Manuel (2018) A hybrid of differential search algorithm and flux balance analysis to: Identify knockout strategies for in silico optimization of metabolites production. International Journal of Advances in Soft Computing and its Applications, 10 (2). pp. 84-107. ISSN 2074-8523 http://www.home.ijasca.com/article-in-press/volume-10-2018/vol-10-2/
institution	Universiti Teknologi Malaysia
building	UTM Library
collection	Institutional Repository
continent	Asia
country	Malaysia
content_provider	Universiti Teknologi Malaysia
content_source	UTM Institutional Repository
url_provider	http://eprints.utm.my/
language	English
topic	QA75 Electronic computers. Computer science
spellingShingle	QA75 Electronic computers. Computer science Mohd. Daud, Kauthar Zakaria, Zalmiyah Ali Shah, Zuraini Mohamad, Mohd. Saberi Deris, Safaai Omatu, Sigeru Corchado, Juan Manuel A hybrid of differential search algorithm and flux balance analysis to: Identify knockout strategies for in silico optimization of metabolites production
description	An increasing demand of naturally producing metabolites has gained the attention of researchers to develop better algorithms for predicting the effects of reaction knockouts. With the success of genome sequencing, in silico metabolic engineering has aided the researchers in modifying the genome-scale metabolic network. However, the complexities of the metabolic networks, have led to difficulty in obtaining a set of knockout reactions, which eventually lead to increase in computational time. Hence, many computational algorithms have been developed. Nevertheless, most of these algorithms are hindered by the solution being trapped in the local optima. In this paper, we proposed a hybrid of Differential Search Algorithm (DSA) and Flux Balance Analysis (FBA), to identify knockout reactions for enhancing the production of desired metabolites. Two organisms namely Escherichia coli and Zymomonas mobilis were tested by targeting the production rate of succinic acid, acetic acid, and ethanol. From this experiment, we obtained the list of knockout reactions and production rate. The results show that our proposed hybrid algorithm is capable of identifying knockout reactions with above 70% of production rate from the wild-type.
format	Article
author	Mohd. Daud, Kauthar Zakaria, Zalmiyah Ali Shah, Zuraini Mohamad, Mohd. Saberi Deris, Safaai Omatu, Sigeru Corchado, Juan Manuel
author_facet	Mohd. Daud, Kauthar Zakaria, Zalmiyah Ali Shah, Zuraini Mohamad, Mohd. Saberi Deris, Safaai Omatu, Sigeru Corchado, Juan Manuel
author_sort	Mohd. Daud, Kauthar
title	A hybrid of differential search algorithm and flux balance analysis to: Identify knockout strategies for in silico optimization of metabolites production
title_short	A hybrid of differential search algorithm and flux balance analysis to: Identify knockout strategies for in silico optimization of metabolites production
title_full	A hybrid of differential search algorithm and flux balance analysis to: Identify knockout strategies for in silico optimization of metabolites production
title_fullStr	A hybrid of differential search algorithm and flux balance analysis to: Identify knockout strategies for in silico optimization of metabolites production
title_full_unstemmed	A hybrid of differential search algorithm and flux balance analysis to: Identify knockout strategies for in silico optimization of metabolites production
title_sort	hybrid of differential search algorithm and flux balance analysis to: identify knockout strategies for in silico optimization of metabolites production
publisher	International Center for Scientific Research and Studies
publishDate	2018
url	http://eprints.utm.my/id/eprint/84598/1/KautharMohdDaud2018_AHybridofDifferentialSearchAlgorithmandFlux.pdf http://eprints.utm.my/id/eprint/84598/ http://www.home.ijasca.com/article-in-press/volume-10-2018/vol-10-2/
_version_	1662754280521596928
score	13.244368

A hybrid of differential search algorithm and flux balance analysis to: Identify knockout strategies for in silico optimization of metabolites production

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