ArticleGenome biology2016
Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 468 papers.
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Who cites it
468 citing papers in PubMed.
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- A bacterial pangenome association study identifies a role for polyamine metabolism and alkaline tolerance in middle ear infections.PLoS pathogens · 2026Article
- Recombination and accessory genome turnover shaped the rise and decline of vanA Enterococcus faecium ST80 in Denmark.Genome medicine · 2026Article
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- Integrated Genome-Wide Association Study and Machine Learning Approach for Characterizing the Determinants of Biofilm Formation in Staphylococcus aureus.Interdisciplinary sciences, computational life sciences · 2026Article
- Global phylogenomics of Bordetella pertussis ST2 reveals regional heterogeneity in China and lineage-specific genome evolution.BMC genomics · 2026Article
- Plasmids of co-circulating Staphylococcus aureus serve as vehicles for antimicrobial resistance sharing across diseased host-species at short timescales.BMC microbiology · 2026Article
- Phylogeny-aware comparative genomics ofmBio · 2026Article
- High-precision binary trait association on phylogenetic trees.Microbial genomics · 2026Article
- Genomic analysis identifies candidate SOS-associated and EPS/envelope-remodeling islands in a drinking-water Stenotrophomonas maltophilia complex isolate.Scientific reports · 2026Article
- Role of Households with Children in Community Spread of Multidrug-Resistant Enterobacterales, St. Louis, Missouri, USA.Emerging infectious diseases · 2026Article
- Genomic diversity and virulence ofMicrobial genomics · 2026Article
- A versatile multi-components mixed model for bacterial-Genome Wide association studies.Nature communications · 2026Article
- Isolation and characterization of broad-rangeMicrobiology (Reading, England) · 2026Article
408 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome-wide association studies (GWAS) have become indispensable in human medicine and genomics, but very few have been carried out on bacteria. Here we introduce Scoary, an ultra-fast, easy-to-use, and widely applicable software tool that scores the components of the pan-genome for associations to observed phenotypic traits while accounting for population stratification, with minimal assumptions about evolutionary processes. We call our approach pan-GWAS to distinguish it from traditional, single nucleotide polymorphism (SNP)-based GWAS. Scoary is implemented in Python and is available under an open source GPLv3 license at https://github.com/AdmiralenOla/Scoary .
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