ArticleNucleic acids research2017
YMDB 2.0: a significantly expanded version of the yeast metabolome database.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
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Who cites it
87 citing papers in PubMed.
- DeepMASS v.2: An enhanced deep learning platform for large-scale discovery and structural annotation of unknown plant metabolites.Plant communications · 2026Article
- Towards the construction of a virtual yeast.Nature · 2026Review
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- MitoCommun: a database for decoding mitochondrial communication networks.BMC genomics · 2026Article
- Saccharomyces cerevisiae as a model for mammalian diseases.FEMS yeast research · 2026Review
- Systems biology of yeast metabolism.FEMS yeast research · 2026Review
- Flavorful Microbial Fermentation: Metabolic, Flavoromic, and Sensory Analysis Insights Into Probiotic-Enhanced Catharina Sour Beer WithInternational journal of microbiology · 2026Article
- Structural Isomer Cumulative molecular fingerprinting method (SIC) for standardizing structural isomeric relationships.Communications chemistry · 2025Article
- Recent Advances in Implementation of Machine Learning for Environmental Nontarget Identification.Environment & health (Washington, D.C.) · 2025Review
- Spatial quantitative metabolomics enables identification of remote and sustained ipsilateral cortical metabolic reprogramming after stroke.Nature metabolism · 2025Article
- What Happens Inside the Germinating Grain After Microbial Decontamination by Pulsed Electric Field? Data-Driven Multi-Omics Helps Find the Answer.Molecules (Basel, Switzerland) · 2025Article
- Coverage bias in small molecule machine learning.Nature communications · 2025Article
- Comprehensive Blood Metabolome and Exposome Analysis, Annotation, and Interpretation in E-Waste Workers.Metabolites · 2024Article
- Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community.Molecular systems biology · 2024Article
- Introducing 'identification probability' for automated and transferable assessment of metabolite identification confidence in metabolomics and related studies.bioRxiv : the preprint server for biology · 2024Article
- Chemical Composition of Commercial Cannabis.Journal of agricultural and food chemistry · 2024Article
- Perturbations in mitochondrial metabolism associated with defective cardiolipin biosynthesis: AnbioRxiv : the preprint server for biology · 2024Article
- Successful cultivation of edible fungi on textile waste offers a new avenue for bioremediation and potential food production.Scientific reports · 2024Article
- Accurate Prediction ofMetabolites · 2024Article
- Emergence of Orchestrated and Dynamic Metabolism ofACS synthetic biology · 2024Article
27 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
Funding
Abstract
YMDB or the Yeast Metabolome Database (http://www.ymdb.ca/) is a comprehensive database containing extensive information on the genome and metabolome of Saccharomyces cerevisiae Initially released in 2012, the YMDB has gone through a significant expansion and a number of improvements over the past 4 years. This manuscript describes the most recent version of YMDB (YMDB 2.0). More specifically, it provides an updated description of the database that was previously described in the 2012 NAR Database Issue and it details many of the additions and improvements made to the YMDB over that time. Some of the most important changes include a 7-fold increase in the number of compounds in the database (from 2007 to 16 042), a 430-fold increase in the number of metabolic and signaling pathway diagrams (from 66 to 28 734), a 16-fold increase in the number of compounds linked to pathways (from 742 to 12 733), a 17-fold increase in the numbers of compounds with nuclear magnetic resonance or MS spectra (from 783 to 13 173) and an increase in both the number of data fields and the number of links to external databases. In addition to these database expansions, a number of improvements to YMDB's web interface and its data visualization tools have been made. These additions and improvements should greatly improve the ease, the speed and the quantity of data that can be extracted, searched or viewed within YMDB. Overall, we believe these improvements should not only improve the understanding of the metabolism of S. cerevisiae, but also allow more in-depth exploration of its extensive metabolic networks, signaling pathways and biochemistry.
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