Utilize este identificador para referenciar este registo: http://hdl.handle.net/1822/46347

TítuloDevelopment of a framework for metabolic pathway analysis-driven strain optimization methods
Autor(es)Vieira, Vítor
Maia, Paulo
Rocha, Isabel
Rocha, Miguel
DataMar-2017
EditoraSpringer Nature
RevistaInterdisciplinary Sciences-Computational Life Sciences
CitaçãoVieira, Vítor; Maia, Paulo; Rocha, Isabel; Rocha, Miguel, Development of a framework for metabolic pathway analysis-driven strain optimization methods. Interdisciplinary Sciences-Computational Life Sciences, 9(1), 46-55, 2017
Resumo(s)Genome-scale metabolic models (GSMMs) have become important assets for rational design of compound overproduction using microbial cell factories. Most computational strain optimization methods (CSOM) using GSMMs, while useful in metabolic engineering, rely on the definition of questionable cell objectives, leading to some bias. Metabolic pathway analysis approaches do not require an objective function. Though their use brings immediate advantages, it has mostly been restricted to small scale models due to computational demands. Additionally, their complex parameterization and lack of intuitive tools pose an important challenge towards making these widely available to the community. Recently, MCSEnumerator has extended the scale of these methods, namely regarding enumeration of minimal cut sets, now able to handle GSMMs. This work proposes a tool implementing this method as a Java library and a plugin within the OptFlux metabolic engineering platform providing a friendly user interface. A standard enumeration problem and pipeline applicable to GSMMs is proposed, making use by the community simpler. To highlight the potential of these approaches, we devised a case study for overproduction of succinate, providing a phenotype analysis of a selected strategy and comparing robustness with a selected solution from a bi-level CSOM.
Tipoarticle
URIhttp://hdl.handle.net/1822/46347
DOI10.1007/s12539-017-0218-7
ISSN19132751
e-ISSN1867-1462
Versão da editorahttps://link.springer.com/journal/12539
Arbitragem científicayes
AcessoopenAccess
Aparece nas coleções:CEB - Publicações em Revistas/Séries Internacionais / Publications in International Journals/Series

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