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A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism.
Lu, Hongzhong; Li, Feiran; Sánchez, Benjamín J; Zhu, Zhengming; Li, Gang; Domenzain, Iván; Marcisauskas, Simonas; Anton, Petre Mihail; Lappa, Dimitra; Lieven, Christian; Beber, Moritz Emanuel; Sonnenschein, Nikolaus; Kerkhoven, Eduard J; Nielsen, Jens.
Afiliação
  • Lu H; Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden.
  • Li F; Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden.
  • Sánchez BJ; Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden.
  • Zhu Z; Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden.
  • Li G; School of Biotechnology, Jiangnan University, 1800 Lihu Road, 214122, Wuxi, Jiangsu, China.
  • Domenzain I; Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden.
  • Marcisauskas S; Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden.
  • Anton PM; Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden.
  • Lappa D; Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden.
  • Lieven C; Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden.
  • Beber ME; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark.
  • Sonnenschein N; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark.
  • Kerkhoven EJ; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark.
  • Nielsen J; Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden.
Nat Commun ; 10(1): 3586, 2019 08 08.
Article em En | MEDLINE | ID: mdl-31395883
ABSTRACT
Genome-scale metabolic models (GEMs) represent extensive knowledgebases that provide a platform for model simulations and integrative analysis of omics data. This study introduces Yeast8 and an associated ecosystem of models that represent a comprehensive computational resource for performing simulations of the metabolism of Saccharomyces cerevisiae--an important model organism and widely used cell-factory. Yeast8 tracks community development with version control, setting a standard for how GEMs can be continuously updated in a simple and reproducible way. We use Yeast8 to develop the derived models panYeast8 and coreYeast8, which in turn enable the reconstruction of GEMs for 1,011 different yeast strains. Through integration with enzyme constraints (ecYeast8) and protein 3D structures (proYeast8DB), Yeast8 further facilitates the exploration of yeast metabolism at a multi-scale level, enabling prediction of how single nucleotide variations translate to phenotypic traits.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Saccharomyces cerevisiae / Biologia Computacional / Metaboloma / Modelos Biológicos Tipo de estudo: Prognostic_studies Idioma: En Ano de publicação: 2019 Tipo de documento: Article
Texto completo
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Saccharomyces cerevisiae / Biologia Computacional / Metaboloma / Modelos Biológicos Tipo de estudo: Prognostic_studies Idioma: En Ano de publicação: 2019 Tipo de documento: Article