ArticleGenome research2019
Fast and flexible bacterial genomic epidemiology with PopPUNK.
Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 292 papers.
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Who cites it
292 citing papers in PubMed.
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- Performance of the IR Biotyper, Nanopore, and Illumina sequencing to discriminateMicrobiology spectrum · 2026Article
- ZPY-CpG-Ch, a broad coverage vaccine againstScience advances · 2026Article
- Phenotypic and genotypic characterization ofJAC-antimicrobial resistance · 2026Article
- Genomic and socioeconomic drivers of antimicrobial resistance forecast to 2050.Cell genomics · 2026Article
- Translation accuracy in E. coli.Nucleic acids research · 2026Article
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- Genomic analysis of intrahospital transmission of carbapenem-resistant Gram-negative bacteria: a multicentre study in Japan.Microbial genomics · 2026Article
- National genomic surveillance reveals global plasmid and chromosomal dissemination routes of blanpj antimicrobials and resistance · 2026Article
- Impact of selective digestive decontamination on the pangenome composition of ESBL-E. coli.The Journal of antimicrobial chemotherapy · 2026Article
- Translation Inhibiting Antibiotics Induce an asRNA Regulating Purine Metabolism inbioRxiv : the preprint server for biology · 2026Article
- A more complete picture: capturing single nucleotide variant diversity in extended-spectrum beta-lactamase producingMicrobial genomics · 2026Article
- Genomic surveillance of post-immunization pneumococcal carriage in Ghana.Microbial genomics · 2026Article
- Life Identification Numbers: A strain nomenclature approach to aid epidemiological surveillance of bacterial pathogens.PLoS biology · 2026Article
- Reference-free clustering as an epidemiological tool forMicrobial genomics · 2026Article
- Clonal expansion of global pneumococcal sequence cluster 3 within serotype 8 after 13-valent pneumococcal conjugate vaccine introduction, South Africa.Microbial genomics · 2026Article
232 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
The routine use of genomics for disease surveillance provides the opportunity for high-resolution bacterial epidemiology. Current whole-genome clustering and multilocus typing approaches do not fully exploit core and accessory genomic variation, and they cannot both automatically identify, and subsequently expand, clusters of significantly similar isolates in large data sets spanning entire species. Here, we describe PopPUNK (
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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.