ArticleMicrobial genomics2019
PANINI: Pangenome Neighbour Identification for Bacterial Populations.
Article in Microbial genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
17 citing papers in PubMed.
- Genomic epidemiology of extended-spectrum beta-lactamase-producingMicrobial genomics · 2025Article
- Pan-genomics: Insight into the Functional Genome, Applications, Advancements, and Challenges.Current genomics · 2025Review
- Comparative pangenome analysis of Enterococcus faecium and Enterococcus lactis provides new insights into the adaptive evolution by horizontal gene acquisitions.BMC genomics · 2024Article
- Staphylococcus aureus populations from the gut and the blood are not distinguished by virulence traits-a critical role of host barrier integrity.Microbiome · 2022Article
- Dynamics of extended-spectrum cephalosporin resistance genes in Escherichia coli from Europe and North America.Nature communications · 2022Article
- Whole-Genome Sequence Comparisons ofMicroorganisms · 2022Article
- Mandrake: visualizing microbial population structure by embedding millions of genomes into a low-dimensional representation.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
- A graph-based approach for the visualisation and analysis of bacterial pangenomes.BMC bioinformatics · 2022Article
- Review
- Article
- Diversity of carbapenem-resistantMicrobial genomics · 2022Article
- Population Genomics ofmSystems · 2021Article
- Phylogeography and resistome of pneumococcal meningitis in West Africa before and after vaccine introduction.Microbial genomics · 2021Article
- Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era.Nature communications · 2021Article
- PanACoTA: a modular tool for massive microbial comparative genomics.NAR genomics and bioinformatics · 2021Article
- Article
- Fast and flexible bacterial genomic epidemiology with PopPUNK.Genome research · 2019Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
The standard workhorse for genomic analysis of the evolution of bacterial populations is phylogenetic modelling of mutations in the core genome. However, a notable amount of information about evolutionary and transmission processes in diverse populations can be lost unless the accessory genome is also taken into consideration. Here, we introduce panini (Pangenome Neighbour Identification for Bacterial Populations), a computationally scalable method for identifying the neighbours for each isolate in a data set using unsupervised machine learning with stochastic neighbour embedding based on the t-SNE (t-distributed stochastic neighbour embedding) algorithm. panini is browser-based and integrates with the Microreact platform for rapid online visualization and exploration of both core and accessory genome evolutionary signals, together with relevant epidemiological, geographical, temporal and other metadata. Several case studies with single- and multi-clone pneumococcal populations are presented to demonstrate the ability to identify biologically important signals from gene content data. panini is available at http://panini.pathogen.watch and code at http://gitlab.com/cgps/panini.
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Registered trials
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