ArticleBMC systems biology2010
Further developments towards a genome-scale metabolic model of yeast.
Article in BMC systems biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 113 citations in OpenAlex.
- Evolution and applications of genome-scale metabolic models in yeast systems biology studies.FEMS yeast research · 2025Review
- Auxotrophy-based curation improves the consensus genome-scale metabolic model of yeast.Synthetic and systems biotechnology · 2024Article
- Technologies for whole-cell modeling: Genome-wide reconstruction of a cell in silico.Development, growth & differentiation · 2023Review
- Standards, dissemination, and best practices in systems biology.Current opinion in biotechnology · 2023Review
- A Computational Toolbox to Investigate the Metabolic Potential and Resource Allocation in Fission Yeast.mSystems · 2022Article
- Genome-scale modeling of yeast metabolism: retrospectives and perspectives.FEMS yeast research · 2022Review
- From Petri Plates to Petri Nets, a revolution in yeast biology.FEMS yeast research · 2022Article
- Path to improving the life cycle and quality of genome-scale models of metabolism.Cell systems · 2021Review
- Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species.FEMS yeast research · 2021Article
- Genome-scale metabolic reconstruction of the non-model yeastMetabolic engineering communications · 2020Article
- Improvement of l-arginine production by in silico genome-scale metabolic network model guided genetic engineering.3 Biotech · 2020Article
- A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism.Nature communications · 2019Article
- Current status and applications of genome-scale metabolic models.Genome biology · 2019Review
- SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework.BMC systems biology · 2019Article
- Genome-Scale Metabolic Modeling from Yeast to Human Cell Models of Complex Diseases: Latest Advances and Challenges.Methods in molecular biology (Clifton, N.J.) · 2019Article
- Genome-scale modeling of yeast: chronology, applications and critical perspectives.FEMS yeast research · 2017Review
- IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models.Scientific reports · 2017Article
- The Pivotal Role of Protein Phosphorylation in the Control of Yeast Central Metabolism.G3 (Bethesda, Md.) · 2017Article
- Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli.PLoS computational biology · 2017Article
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Corrections and comments
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Authors and funding
19 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundTo date, several genome-scale network reconstructions have been used to describe the metabolism of the yeast Saccharomyces cerevisiae, each differing in scope and content. The recent community-driven reconstruction, while rigorously evidenced and well annotated, under-represented metabolite transport, lipid metabolism and other pathways, and was not amenable to constraint-based analyses because of lack of pathway connectivity.
resultsWe have expanded the yeast network reconstruction to incorporate many new reactions from the literature and represented these in a well-annotated and standards-compliant manner. The new reconstruction comprises 1102 unique metabolic reactions involving 924 unique metabolites--significantly larger in scope than any previous reconstruction. The representation of lipid metabolism in particular has improved, with 234 out of 268 enzymes linked to lipid metabolism now present in at least one reaction. Connectivity is emphatically improved, with more than 90% of metabolites now reachable from the growth medium constituents. The present updates allow constraint-based analyses to be performed; viability predictions of single knockouts are comparable to results from in vivo experiments and to those of previous reconstructions.
conclusionsWe report the development of the most complete reconstruction of yeast metabolism to date that is based upon reliable literature evidence and richly annotated according to MIRIAM standards. The reconstruction is available in the Systems Biology Markup Language (SBML) and via a publicly accessible database http://www.comp-sys-bio.org/yeastnet/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.