ArticleMolecular systems biology2024
Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community.
Article in Molecular systems biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Thermo-flux: generation and analysis of thermodynamic-stoichiometric metabolic network models.Molecular systems biology · 2026Article
- Yeast species resource exploration and application in cell factories.Synthetic and systems biotechnology · 2026Review
- The shape of fitness functions and the distribution of mutational effect sizes jointly limit adaptation by regulatory mutations.Nature ecology & evolution · 2026Article
- AlphaGEM enables precise genome-scale metabolic modelling by integrating protein structure alignment with deep-learning-based dark metabolism mining.Nature communications · 2026Article
- Towards the construction of a virtual yeast.Nature · 2026Review
- Metabolic robustness is an emergent property of hierarchical network organization in yeast.mSystems · 2026Article
- EnzymeTuning improves enzyme-constrained metabolic modeling and proteome abundance prediction through deep learning.Nature communications · 2026Article
- Synthesis of Amines for Active Pharmaceutical Ingredients Using the Whole-Cell Factory Saccharomyces Cerevisae.Chembiochem : a European journal of chemical biology · 2026Review
- Reconstruction of human metabolic models with large language models.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Accurate prediction of flux distributions compatible with metabolite concentration effects in genome-scale metabolic networks.PLoS computational biology · 2026Article
- Advances in genome-scale metabolic modeling of Bacillus subtilis.Biotechnology letters · 2026Review
- Flux sampling and context-specific genome-scale metabolic models for biotechnological applications.Trends in biotechnology · 2026Review
- Systems biology of yeast metabolism.FEMS yeast research · 2026Review
- Uncovering coordinated pathway interactions through gene co-differential expression in yeast.Nucleic acids research · 2026Article
- Article
- Genome-scale metabolic modelling of the priority fungal pathogenmicroLife · 2026Article
- From Genome to Function: Metabolism-Wide Models of Lifecycle Stages of Parasites.Methods in molecular biology (Clifton, N.J.) · 2026Article
- From static definitions to dynamic landscapes: physiological states in yeast.Frontiers in microbiology · 2026Article
- Article
- The Power of Yeast.Yeast (Chichester, England) · 2025Review
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15 authors.
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Abstract
Genome-scale metabolic models (GEMs) can facilitate metabolism-focused multi-omics integrative analysis. Since Yeast8, the yeast-GEM of Saccharomyces cerevisiae, published in 2019, has been continuously updated by the community. This has increased the quality and scope of the model, culminating now in Yeast9. To evaluate its predictive performance, we generated 163 condition-specific GEMs constrained by single-cell transcriptomics from osmotic pressure or reference conditions. Comparative flux analysis showed that yeast adapting to high osmotic pressure benefits from upregulating fluxes through central carbon metabolism. Furthermore, combining Yeast9 with proteomics revealed metabolic rewiring underlying its preference for nitrogen sources. Lastly, we created strain-specific GEMs (ssGEMs) constrained by transcriptomics for 1229 mutant strains. Well able to predict the strains' growth rates, fluxomics from those large-scale ssGEMs outperformed transcriptomics in predicting functional categories for all studied genes in machine learning models. Based on those findings we anticipate that Yeast9 will continue to empower systems biology studies of yeast metabolism.
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