ArticleBMC bioinformatics2022
A graph-based approach for the visualisation and analysis of bacterial pangenomes.
Article in BMC bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
14 citing papers in PubMed.
- PG2: algorithms and a web-based tool for effective layout and visual analysis of pangenome graphs.BMC bioinformatics · 2026Article
- Epistasis and co-adaptation in bacterial genome evolution.Nature reviews. Genetics · 2026Review
- Global emergence and evolution ofmSystems · 2026Article
- Pseudoalteromonas is a symbiont of marine invertebrates that exhibits broad patterns of phylosymbiosis.The ISME journal · 2026Article
- Pangenome-GWAS analysis ofCanadian journal of microbiology · 2026Article
- ntSynt: multi-genome synteny detection using minimizer graph mappings.BMC biology · 2025Article
- Emergence and regional evolution of Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae ST11 in China.BMC genomics · 2025Article
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- Article
- A gentle introduction to pangenomics.Briefings in bioinformatics · 2024Review
- Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Temporal dynamics of genetically heterogeneous extended-spectrum cephalosporin-resistantmSphere · 2023Article
- Protein structural insights into a rare PCSK9 gain-of-function variant (R496W) causing familial hypercholesterolemia in a Saudi family: whole exome sequencing and computational analysis.Frontiers in physiology · 2023Article
- Multiclonal human origin and global expansion of an endemic bacterial pathogen of livestock.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
backgroundThe advent of low cost, high throughput DNA sequencing has led to the availability of thousands of complete genome sequences for a wide variety of bacterial species. Examining and interpreting genetic variation on this scale represents a significant challenge to existing methods of data analysis and visualisation.
resultsStarting with the output of standard pangenome analysis tools, we describe the generation and analysis of interactive, 3D network graphs to explore the structure of bacterial populations, the distribution of genes across a population, and the syntenic order in which those genes occur, in the new open-source network analysis platform, Graphia. Both the analysis and the visualisation are scalable to datasets of thousands of genome sequences.
conclusionsWe anticipate that the approaches presented here will be of great utility to the microbial research community, allowing faster, more intuitive, and flexible interaction with pangenome datasets, thereby enhancing interpretation of these complex data.
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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.