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Title: Computational Methods for Modification of Metabolic Networks.
Authors: Tamura, Takeyuki  kyouindb  KAKEN_id
Lu, Wei
Akutsu, Tatsuya  kyouindb  KAKEN_id
Author's alias: 阿久津, 達也
Keywords: Metabolic network
Constraint-based programming
Flux balance analysis
Elementary mode
Boolean model
Overfitting
Issue Date: 2015
Journal title: Computational and structural biotechnology journal
Volume: 13
Start page: 376
End page: 381
Abstract: 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.
Rights: ©2015 Tamura et al. Published by Elsevier B.V. on behalf of the Research Network of Computational and Structural Biotechnology. This is an open access article under the CC BY license(http://creativecommons.org/licenses/by/4.0/).
URI: http://hdl.handle.net/2433/207603
DOI(Published Version): 10.1016/j.csbj.2015.05.004
PubMed ID: 26106462
Appears in Collections:Journal Articles

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