ArticleNature biotechnology2008
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.
Article in Nature biotechnology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 256 papers.
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Who cites it
256 citing papers in PubMed.
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- Metabolic adaptations of yeast cells to epigenetic modifiers: a comparative analysis of free amino acid profiles and key metabolites.World journal of microbiology & biotechnology · 2026Article
- Life beyond 6000 genes: from sequence to synthesis in a post-genomics era.FEMS yeast research · 2026Review
- Systems biology of yeast metabolism.FEMS yeast research · 2026Review
- Article
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- Evolution and applications of genome-scale metabolic models in yeast systems biology studies.FEMS yeast research · 2025Review
- CLAIRE: a contrastive learning-based predictor for EC number of chemical reactions.Journal of cheminformatics · 2025Article
- Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community.Molecular systems biology · 2024Article
- The Biology and Biochemistry of Kynurenic Acid, a Potential Nutraceutical with Multiple Biological Effects.International journal of molecular sciences · 2024Review
- Evidence for the Role of the Mitochondrial ABC Transporter MDL1 in the Uptake of Clozapine and Related Molecules into the YeastPharmaceuticals (Basel, Switzerland) · 2024Article
- Data integration strategies for whole-cell modeling.FEMS yeast research · 2024Review
- Cardinality optimization in constraint-based modelling: application to human metabolism.Bioinformatics (Oxford, England) · 2023Article
- Gear Shifting in Biological Energy Transduction.Entropy (Basel, Switzerland) · 2023Article
- Standards, dissemination, and best practices in systems biology.Current opinion in biotechnology · 2023Review
- Inducible Synthetic Growth Regulation Using the ClpXP Proteasome Enhances cis,cis-Muconic Acid and Glycolic Acid Yields inACS synthetic biology · 2023Article
- Plant and microbial sciences as key drivers in the development of metabolomics research.Proceedings of the National Academy of Sciences of the United States of America · 2023Review
- Using Kinetic Modelling to Infer Adaptations inMetabolites · 2023Article
196 more citing papers are in PubMed but not listed here.
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34 authors.
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Abstract
Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and content, and use different terminologies to describe the same chemical entities. This makes comparisons between them difficult and underscores the desirability of a consolidated metabolic network that collects and formalizes the 'community knowledge' of yeast metabolism. We describe how we have produced a consensus metabolic network reconstruction for S. cerevisiae. In drafting it, we placed special emphasis on referencing molecules to persistent databases or using database-independent forms, such as SMILES or InChI strings, as this permits their chemical structure to be represented unambiguously and in a manner that permits automated reasoning. The reconstruction is readily available via a publicly accessible database and in the Systems Biology Markup Language (http://www.comp-sys-bio.org/yeastnet). It can be maintained as a resource that serves as a common denominator for studying the systems biology of yeast. Similar strategies should benefit communities studying genome-scale metabolic networks of other organisms.
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