The DOI matches its Crossref record; 83 of the 83 references it cites were found in a registry or an index.
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism
Open accessAbstract
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 (proYeast8 DB), 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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Cited by
Robinson, J. L., Kocabaş, P., Wang, H., Cholley, P.-E., Cook, D., Nilsson, A., Anton, M., Ferreira, R., Domenzain, I., Billa, V., et al. (2020) · Science Signaling · doi:10.1126/scisignal.aaz1482 · Cited by 442
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Deep learning allows genome-scale prediction of Michaelis constants from structural features
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Metadata
- Authors
- Lu, H., Li, F., Sánchez, B. J., Zhu, Z., Li, G., Domenzain, I., Marcišauskas, S., Anton, P. M., Lappa, D., Lieven, C., Beber, M. E., Sonnenschein, N., Kerkhoven, E. J., & Nielsen, J.
- Venue
- Nature Communications
- Published
- 2019-08-08
- Volume
- 10
- Issue
- 1
- Pages
- 3586-3586
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W2965590414
- Cited by
- 361
- References
- 83
- FWCI
- 10.46
- Type
- journal article
- Language
- en
- Update notices
- correction (2020-10-22)
- Open access
- gold
- Licence
- creativecommons.org/licenses/by/4.0 (tdm)
- creativecommons.org/licenses/by/4.0 (vor)
- Funders
- Novo Nordisk Fonden (NNF10CC1016517)
- EC | Horizon 2020 Framework Programme (686070, 720824)
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- Lu, H., Li, F., Sánchez, B. J., Zhu, Z., Li, G., Domenzain, I., Marcišauskas, S., Anton, P. M., Lappa, D., Lieven, C., Beber, M. E., Sonnenschein, N., Kerkhoven, E. J., & Nielsen, J. (2019). A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nature Communications. https://doi.org/10.1038/s41467-019-11581-3
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
