Staff View: A non-dominated sorting differential search algorithm flux balance analysis (ndsDSAFBA) for in silico multiobjective optimization in identifying reactions knockout

A non-dominated sorting differential search algorithm flux balance analysis (ndsDSAFBA) for in silico multiobjective optimization in identifying reactions knockout

Metabolic engineering is defined as improving the cellular activities of an organism by manipulating the metabolic, signal or regulatory network. In silico reaction knockout simulation is one of the techniques applied to analyse the effects of genetic perturbations on metabolite production. Many met...

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Main Authors:	Mohd. Daud, Kauthar, Mohamad, Mohd. Saberi, Zakaria, Zalmiyah, Hassan, Rohayanti, Shah, Zuraini Ali, Deris, Safaai, Ibrahim, Zuwairie, Napis, Suhaimi, Sinnott, Richard O.
Format:	Article
Language:	English
Published:	Elsevier Ltd 2019
Subjects:	QA75 Electronic computers. Computer science
Online Access:	http://eprints.utm.my/id/eprint/89410/1/KautharMohdDaud2019_ANonDominatedSortingDifferentialSearchAlgorithm.pdf http://eprints.utm.my/id/eprint/89410/ http://dx.doi.org/10.1016/j.compbiomed.2019.103390
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spelling	my.utm.894102021-02-22T06:04:37Z http://eprints.utm.my/id/eprint/89410/ A non-dominated sorting differential search algorithm flux balance analysis (ndsDSAFBA) for in silico multiobjective optimization in identifying reactions knockout Mohd. Daud, Kauthar Mohamad, Mohd. Saberi Zakaria, Zalmiyah Hassan, Rohayanti Shah, Zuraini Ali Deris, Safaai Ibrahim, Zuwairie Napis, Suhaimi Sinnott, Richard O. QA75 Electronic computers. Computer science Metabolic engineering is defined as improving the cellular activities of an organism by manipulating the metabolic, signal or regulatory network. In silico reaction knockout simulation is one of the techniques applied to analyse the effects of genetic perturbations on metabolite production. Many methods consider growth coupling as the objective function, whereby it searches for mutants that maximise the growth and production rate. However, the final goal is to increase the production rate. Furthermore, they produce one single solution, though in reality, cells do not focus on one objective and they need to consider various different competing objectives. In this work, a method, termed ndsDSAFBA (non-dominated sorting Differential Search Algorithm and Flux Balance Analysis), has been developed to find the reaction knockouts involved in maximising the production rate and growth rate of the mutant, by incorporating Pareto dominance concepts. The proposed ndsDSAFBA method was validated using three genome-scale metabolic models. We obtained a set of non-dominated solutions, with each solution representing a different mutant strain. The results obtained were compared with the single objective optimisation (SOO) and multi-objective optimisation (MOO) methods. The results demonstrate that ndsDSAFBA is better than the other methods in terms of production rate and growth rate. Elsevier Ltd 2019-10 Article PeerReviewed application/pdf en http://eprints.utm.my/id/eprint/89410/1/KautharMohdDaud2019_ANonDominatedSortingDifferentialSearchAlgorithm.pdf Mohd. Daud, Kauthar and Mohamad, Mohd. Saberi and Zakaria, Zalmiyah and Hassan, Rohayanti and Shah, Zuraini Ali and Deris, Safaai and Ibrahim, Zuwairie and Napis, Suhaimi and Sinnott, Richard O. (2019) A non-dominated sorting differential search algorithm flux balance analysis (ndsDSAFBA) for in silico multiobjective optimization in identifying reactions knockout. Computers in Biology and Medicine, 113 . pp. 1-13. ISSN 0010-4825 http://dx.doi.org/10.1016/j.compbiomed.2019.103390 DOI:10.1016/j.compbiomed.2019.103390
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 Mohamad, Mohd. Saberi Zakaria, Zalmiyah Hassan, Rohayanti Shah, Zuraini Ali Deris, Safaai Ibrahim, Zuwairie Napis, Suhaimi Sinnott, Richard O. A non-dominated sorting differential search algorithm flux balance analysis (ndsDSAFBA) for in silico multiobjective optimization in identifying reactions knockout
description	Metabolic engineering is defined as improving the cellular activities of an organism by manipulating the metabolic, signal or regulatory network. In silico reaction knockout simulation is one of the techniques applied to analyse the effects of genetic perturbations on metabolite production. Many methods consider growth coupling as the objective function, whereby it searches for mutants that maximise the growth and production rate. However, the final goal is to increase the production rate. Furthermore, they produce one single solution, though in reality, cells do not focus on one objective and they need to consider various different competing objectives. In this work, a method, termed ndsDSAFBA (non-dominated sorting Differential Search Algorithm and Flux Balance Analysis), has been developed to find the reaction knockouts involved in maximising the production rate and growth rate of the mutant, by incorporating Pareto dominance concepts. The proposed ndsDSAFBA method was validated using three genome-scale metabolic models. We obtained a set of non-dominated solutions, with each solution representing a different mutant strain. The results obtained were compared with the single objective optimisation (SOO) and multi-objective optimisation (MOO) methods. The results demonstrate that ndsDSAFBA is better than the other methods in terms of production rate and growth rate.
format	Article
author	Mohd. Daud, Kauthar Mohamad, Mohd. Saberi Zakaria, Zalmiyah Hassan, Rohayanti Shah, Zuraini Ali Deris, Safaai Ibrahim, Zuwairie Napis, Suhaimi Sinnott, Richard O.
author_facet	Mohd. Daud, Kauthar Mohamad, Mohd. Saberi Zakaria, Zalmiyah Hassan, Rohayanti Shah, Zuraini Ali Deris, Safaai Ibrahim, Zuwairie Napis, Suhaimi Sinnott, Richard O.
author_sort	Mohd. Daud, Kauthar
title	A non-dominated sorting differential search algorithm flux balance analysis (ndsDSAFBA) for in silico multiobjective optimization in identifying reactions knockout
title_short	A non-dominated sorting differential search algorithm flux balance analysis (ndsDSAFBA) for in silico multiobjective optimization in identifying reactions knockout
title_full	A non-dominated sorting differential search algorithm flux balance analysis (ndsDSAFBA) for in silico multiobjective optimization in identifying reactions knockout
title_fullStr	A non-dominated sorting differential search algorithm flux balance analysis (ndsDSAFBA) for in silico multiobjective optimization in identifying reactions knockout
title_full_unstemmed	A non-dominated sorting differential search algorithm flux balance analysis (ndsDSAFBA) for in silico multiobjective optimization in identifying reactions knockout
title_sort	non-dominated sorting differential search algorithm flux balance analysis (ndsdsafba) for in silico multiobjective optimization in identifying reactions knockout
publisher	Elsevier Ltd
publishDate	2019
url	http://eprints.utm.my/id/eprint/89410/1/KautharMohdDaud2019_ANonDominatedSortingDifferentialSearchAlgorithm.pdf http://eprints.utm.my/id/eprint/89410/ http://dx.doi.org/10.1016/j.compbiomed.2019.103390
_version_	1692991779653025792
score	13.211869

A non-dominated sorting differential search algorithm flux balance analysis (ndsDSAFBA) for in silico multiobjective optimization in identifying reactions knockout

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