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

By Hongzhong Lu, Feiran Li, Benjamín J. Sánchez, Zhengming Zhu, Gang Li, Iván Domenzain, Simonas Marcišauskas, P. Anton, D. Lappa, Christian Lieven and 4 more. Nature Communications, 2019

318 citations recorded by the source corpus.

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. Genome-scale metabolic models provide a platform to study metabolism through simulations and analysis of omics data. Here the authors introduce Yeast8 with its model ecosystem, a comprehensive computational resource for simulating the metabolism of Saccharomyces cerevisiae.

Subfields: Biomedical Engineering, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/98b0c30f5210a8d2857bf82d0cfb686757c5641c

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Citations in the corpus

An atlas of human metabolism (2020, methodology): “On the basis of the approach applied for the Yeast8 GEM ( 27 ), we developed Human1 using a Git repository hosted on GitHub to establish a more systematic and community-driven development process.”