A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

Hongzhong Lu, Feiran Li, Benjamín J Sánchez, Zhengming Zhu, Gang Li, Iván Domenzain, Simonas Marcišauskas, Petre Mihail Anton, Dimitra Lappa, Christian Lieven, Moritz Emanuel Beber, Nikolaus Sonnenschein, Eduard J Kerkhoven, Jens Nielsen*

*Corresponding author for this work

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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.
Original languageEnglish
JournalNature Communications
Volume10
Issue number1
Pages (from-to)3586
Number of pages13
ISSN2041-1723
DOIs
Publication statusPublished - 2019

Cite this

Lu, Hongzhong ; Li, Feiran ; Sánchez, Benjamín J ; Zhu, Zhengming ; Li, Gang ; Domenzain, Iván ; Marcišauskas, Simonas ; Anton, Petre Mihail ; Lappa, Dimitra ; Lieven, Christian ; Beber, Moritz Emanuel ; Sonnenschein, Nikolaus ; Kerkhoven, Eduard J ; Nielsen, Jens. / A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. In: Nature Communications. 2019 ; Vol. 10, No. 1. pp. 3586.
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title = "A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism",
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.",
author = "Hongzhong Lu and Feiran Li and S{\'a}nchez, {Benjam{\'i}n J} and Zhengming Zhu and Gang Li and Iv{\'a}n Domenzain and Simonas Marcišauskas and Anton, {Petre Mihail} and Dimitra Lappa and Christian Lieven and Beber, {Moritz Emanuel} and Nikolaus Sonnenschein and Kerkhoven, {Eduard J} and Jens Nielsen",
year = "2019",
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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; Marcišauskas, Simonas; Anton, Petre Mihail; Lappa, Dimitra; Lieven, Christian; Beber, Moritz Emanuel; Sonnenschein, Nikolaus; Kerkhoven, Eduard J; Nielsen, Jens.

In: Nature Communications, Vol. 10, No. 1, 2019, p. 3586.

Research output: Contribution to journalJournal articleResearchpeer-review

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T1 - A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

AU - Lu, Hongzhong

AU - Li, Feiran

AU - Sánchez, Benjamín J

AU - Zhu, Zhengming

AU - Li, Gang

AU - Domenzain, Iván

AU - Marcišauskas, Simonas

AU - Anton, Petre Mihail

AU - Lappa, Dimitra

AU - Lieven, Christian

AU - Beber, Moritz Emanuel

AU - Sonnenschein, Nikolaus

AU - Kerkhoven, Eduard J

AU - Nielsen, Jens

PY - 2019

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AB - 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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