Utilize este identificador para referenciar este registo:
https://hdl.handle.net/1822/46347
Título: | Development of a framework for metabolic pathway analysis-driven strain optimization methods |
Autor(es): | Vieira, Vítor Maia, Paulo Rocha, Isabel Rocha, Miguel |
Palavras-chave: | Constraint-based modeling Metabolic engineering Pathway analysis Minimal cut sets Strain optimization |
Data: | Mar-2017 |
Editora: | Springer Nature |
Revista: | Interdisciplinary Sciences-Computational Life Sciences |
Citação: | Vieira, 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. |
Tipo: | Artigo |
URI: | https://hdl.handle.net/1822/46347 |
DOI: | 10.1007/s12539-017-0218-7 |
ISSN: | 19132751 |
e-ISSN: | 1867-1462 |
Versão da editora: | https://link.springer.com/journal/12539 |
Arbitragem científica: | yes |
Acesso: | Acesso aberto |
Aparece nas coleções: | CEB - Publicações em Revistas/Séries Internacionais / Publications in International Journals/Series |
Ficheiros deste registo:
Ficheiro | Descrição | Tamanho | Formato | |
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document_46696_1.pdf | 1,09 MB | Adobe PDF | Ver/Abrir |