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:	Kauthar, Mohd Daud, Mohd Saberi, Mohamad, Zalmiyah, Zakaria, Rohayanti, Hassan, Zuraini, Ali Shah, Safaai, Deris, Zuwairie, Ibrahim, Suhaimi, Napis, Sinnott, Richard O.
Format:	Article
Language:	English
Published:	Elsevier Ltd 2019
Subjects:	QA75 Electronic computers. Computer science TK Electrical engineering. Electronics Nuclear engineering
Online Access:	http://umpir.ump.edu.my/id/eprint/26602/ http://umpir.ump.edu.my/id/eprint/26602/ http://umpir.ump.edu.my/id/eprint/26602/ http://umpir.ump.edu.my/id/eprint/26602/1/A%20non-dominated%20sorting%20differential%20search%20algorithm%20flux%20balance.pdf

id	ump-26602
recordtype	eprints
spelling	ump-266022019-12-10T02:07:35Z http://umpir.ump.edu.my/id/eprint/26602/ A non-dominated sorting differential search algorithm flux balance analysis (ndsDSAFBA) for in silico multiobjective optimization in identifying reactions knockout Kauthar, Mohd Daud Mohd Saberi, Mohamad Zalmiyah, Zakaria Rohayanti, Hassan Zuraini, Ali Shah Safaai, Deris Zuwairie, Ibrahim Suhaimi, Napis Sinnott, Richard O. QA75 Electronic computers. Computer science TK Electrical engineering. Electronics Nuclear engineering 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 2019-11 Article PeerReviewed pdf en http://umpir.ump.edu.my/id/eprint/26602/1/A%20non-dominated%20sorting%20differential%20search%20algorithm%20flux%20balance.pdf Kauthar, Mohd Daud and Mohd Saberi, Mohamad and Zalmiyah, Zakaria and Rohayanti, Hassan and Zuraini, Ali Shah and Safaai, Deris and Zuwairie, Ibrahim and Suhaimi, Napis 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 (103390). pp. 1-2. ISSN 0010-4825 https://doi.org/10.1016/j.compbiomed.2019.103390 https://www.sciencedirect.com/science/article/pii/S0010482519302677?via%3Dihub#!
repository_type	Digital Repository
institution_category	Local University
institution	Universiti Malaysia Pahang
building	UMP Institutional Repository
collection	Online Access
language	English
topic	QA75 Electronic computers. Computer science TK Electrical engineering. Electronics Nuclear engineering
spellingShingle	QA75 Electronic computers. Computer science TK Electrical engineering. Electronics Nuclear engineering Kauthar, Mohd Daud Mohd Saberi, Mohamad Zalmiyah, Zakaria Rohayanti, Hassan Zuraini, Ali Shah Safaai, Deris Zuwairie, Ibrahim Suhaimi, Napis 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	Kauthar, Mohd Daud Mohd Saberi, Mohamad Zalmiyah, Zakaria Rohayanti, Hassan Zuraini, Ali Shah Safaai, Deris Zuwairie, Ibrahim Suhaimi, Napis Sinnott, Richard O.
author_facet	Kauthar, Mohd Daud Mohd Saberi, Mohamad Zalmiyah, Zakaria Rohayanti, Hassan Zuraini, Ali Shah Safaai, Deris Zuwairie, Ibrahim Suhaimi, Napis Sinnott, Richard O.
author_sort	Kauthar, Mohd Daud
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://umpir.ump.edu.my/id/eprint/26602/ http://umpir.ump.edu.my/id/eprint/26602/ http://umpir.ump.edu.my/id/eprint/26602/ http://umpir.ump.edu.my/id/eprint/26602/1/A%20non-dominated%20sorting%20differential%20search%20algorithm%20flux%20balance.pdf
first_indexed	2023-09-18T22:41:31Z
last_indexed	2023-09-18T22:41:31Z
_version_	1777416946361303040

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

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