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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Research Network of Computational and Structural Biotechnology
2015
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477032/ https://www.ncbi.nlm.nih.gov/pubmed/26106462 http://dx.doi.org/10.1016/j.csbj.2015.05.004 |
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author | Tamura, Takeyuki Lu, Wei Akutsu, Tatsuya |
author_facet | Tamura, Takeyuki Lu, Wei Akutsu, Tatsuya |
author_sort | Tamura, Takeyuki |
collection | PubMed |
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. |
format | Online Article Text |
id | pubmed-4477032 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Research Network of Computational and Structural Biotechnology |
record_format | MEDLINE/PubMed |
spelling | pubmed-44770322015-06-23 Computational Methods for Modification of Metabolic Networks Tamura, Takeyuki Lu, Wei Akutsu, Tatsuya Comput Struct Biotechnol J 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/). |
spellingShingle | Mini Review Tamura, Takeyuki Lu, Wei Akutsu, Tatsuya Computational Methods for Modification of Metabolic Networks |
title | 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_short | Computational Methods for Modification of Metabolic Networks |
title_sort | computational methods for modification of metabolic networks |
topic | Mini Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477032/ https://www.ncbi.nlm.nih.gov/pubmed/26106462 http://dx.doi.org/10.1016/j.csbj.2015.05.004 |
work_keys_str_mv | AT tamuratakeyuki computationalmethodsformodificationofmetabolicnetworks AT luwei computationalmethodsformodificationofmetabolicnetworks AT akutsutatsuya computationalmethodsformodificationofmetabolicnetworks |