ArticleNucleic acids research2023
proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
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- Linkage of nucleotide and functional diversity varies across gut bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Unbinned contigs expand known diversity in the global microbiome.Nature microbiology · 2026Article
- Cross-continental venom narratives: proteo-transcriptomic insights into Hydrophis cyanocinctus of India and China.Archives of toxicology · 2026Article
- A bifidobacterial enzyme orchestrates ecology and function of infant gut bacterial community.bioRxiv : the preprint server for biology · 2026Article
- Bacterial genomic structural variations in children with autism serve as diagnostic biomarkers.Gut · 2026Article
- bifidoAnnotator: fine-grained annotation of bifidobacterial glycoside hydrolases for human milk glycan utilization.Microbial genomics · 2026Article
- Unique ecology of co-occurring functionally and phylogenetically undescribed species in the infant oral microbiome.PLoS computational biology · 2026Article
- Community conservatism is widespread across microbial phyla and environments.Nature ecology & evolution · 2026Article
- Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny.The ISME journal · 2026Article
- Widespread marine and freshwater distributions of active sulfoquinovose-degrading bacteria.The ISME journal · 2026Article
- Conserved differential expression of DDX helicase and CPEB genes in skeletal muscles potentially influences neuromuscular junctions during aging: a computational analysis.Biogerontology · 2026Article
- proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes.Nucleic acids research · 2026Article
- VIRE: a metagenome-derived, planetary-scale virome resource with environmental context.Nucleic acids research · 2026Article
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21 authors.
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Abstract
The interpretation of genomic, transcriptomic and other microbial 'omics data is highly dependent on the availability of well-annotated genomes. As the number of publicly available microbial genomes continues to increase exponentially, the need for quality control and consistent annotation is becoming critical. We present proGenomes3, a database of 907 388 high-quality genomes containing 4 billion genes that passed stringent criteria and have been consistently annotated using multiple functional and taxonomic databases including mobile genetic elements and biosynthetic gene clusters. proGenomes3 encompasses 41 171 species-level clusters, defined based on universal single copy marker genes, for which pan-genomes and contextual habitat annotations are provided. The database is available at http://progenomes.embl.de/.
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