Computational Methods for Modification of Metabolic Networks

Computational Methods for Modification of Metabolic Networks

In metabolic engineering, modification of metabolic networks is an important biotechnology and a challenging computational task. In the metabolic network modification, we should modify metabolic networks by newly adding enzymes or/and knocking-out genes to maximize the biomass production with minimu...

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Main Authors: Tamura, Takeyuki, Lu, Wei, Akutsu, Tatsuya
Format: Online
Language:English
Published: Research Network of Computational and Structural Biotechnology 2015
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477032/
id pubmed-4477032
recordtype oai_dc
spelling pubmed-44770322015-06-23 Computational Methods for Modification of Metabolic Networks Tamura, Takeyuki Lu, Wei Akutsu, Tatsuya Mini Review In metabolic engineering, modification of metabolic networks is an important biotechnology and a challenging computational task. In the metabolic network modification, we should modify metabolic networks by newly adding enzymes or/and knocking-out genes to maximize the biomass production with minimum side-effect. In this mini-review, we briefly review constraint-based formalizations for Minimum Reaction Cut (MRC) problem where the minimum set of reactions is deleted so that the target compound becomes non-producible from the view point of the flux balance analysis (FBA), elementary mode (EM), and Boolean models. Minimum Reaction Insertion (MRI) problem where the minimum set of reactions is added so that the target compound newly becomes producible is also explained with a similar formalization approach. The relation between the accuracy of the models and the risk of overfitting is also discussed. Research Network of Computational and Structural Biotechnology 2015-05-28 /pmc/articles/PMC4477032/ /pubmed/26106462 http://dx.doi.org/10.1016/j.csbj.2015.05.004 Text en © 2015 The Authors http://creativecommons.org/licenses/by/4.0/ This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
repository_type Open Access Journal
institution_category Foreign Institution
institution US National Center for Biotechnology Information
building NCBI PubMed
collection Online Access
language English
format Online
author Tamura, Takeyuki
Lu, Wei
Akutsu, Tatsuya
spellingShingle Tamura, Takeyuki
Lu, Wei
Akutsu, Tatsuya
Computational Methods for Modification of Metabolic Networks
author_facet Tamura, Takeyuki
Lu, Wei
Akutsu, Tatsuya
author_sort Tamura, Takeyuki
title Computational Methods for Modification of Metabolic Networks
title_short Computational Methods for Modification of Metabolic Networks
title_full Computational Methods for Modification of Metabolic Networks
title_fullStr Computational Methods for Modification of Metabolic Networks
title_full_unstemmed Computational Methods for Modification of Metabolic Networks
title_sort computational methods for modification of metabolic networks
description In metabolic engineering, modification of metabolic networks is an important biotechnology and a challenging computational task. In the metabolic network modification, we should modify metabolic networks by newly adding enzymes or/and knocking-out genes to maximize the biomass production with minimum side-effect. In this mini-review, we briefly review constraint-based formalizations for Minimum Reaction Cut (MRC) problem where the minimum set of reactions is deleted so that the target compound becomes non-producible from the view point of the flux balance analysis (FBA), elementary mode (EM), and Boolean models. Minimum Reaction Insertion (MRI) problem where the minimum set of reactions is added so that the target compound newly becomes producible is also explained with a similar formalization approach. The relation between the accuracy of the models and the risk of overfitting is also discussed.
publisher Research Network of Computational and Structural Biotechnology
publishDate 2015
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477032/
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