ArticleBMC bioinformatics2015
micropan: an R-package for microbial pan-genomics.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 147 papers.
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Who cites it
147 citing papers in PubMed.
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- A dual-tier plasmid network model underpins the evolutionary success of pandemic Klebsiella pneumoniae ST11.Scientific reports · 2026Article
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- Impact of selective digestive decontamination on the pangenome composition of ESBL-E. coli.The Journal of antimicrobial chemotherapy · 2026Article
- Deciphering the pangenome of the shellfish pathogenMicrobial genomics · 2026Article
- Genome-Resolved in Silico Analysis of Poultry and Swine Lactobacillales Provides a Data-Driven Framework for Elucidating Metabolic Complementary interactions in Multi-Strain Probiotics.Probiotics and antimicrobial proteins · 2026Article
- Global multi-host genomic epidemiology of Acinetobacter baumannii reveals transmission at one health interfaces.Nature communications · 2026Article
- Comprehensive characterization and genome-resolved insights into the probiotic potential of Bacillus sp. KNSH39 isolated from Litopenaeus vannamei intestine.World journal of microbiology & biotechnology · 2026Article
- Phylogenomics of Asgard archaea reveals a unique blend of prokaryotic-like horizontal transfer and eukaryotic-like gene duplication.Nature communications · 2026Article
- Integrative phylogenomic and pangenome landscape of Bacillus: insights from 10,000 genomes into taxonomy, functional potential, and biotechnological applications.World journal of microbiology & biotechnology · 2026Article
- Phylogenomics and gene association analysis support probiotic potential in a subset ofMicrobial genomics · 2026Article
- A widespread gut bacterial lineage distinguished by redox metabolism and phage defense.bioRxiv : the preprint server for biology · 2026Article
- Reduced MGE burden, virulence optimization, and acid stress tolerance shape the clonal succession of MRSA ST59.Science advances · 2026Article
- Biogeographical and phylogenetic constraints on horizontal gene transfer and genome evolution inMicrobiology spectrum · 2026Article
- Genomic insights into the functional and metabolic versatility of gut microbiomeMicrobial genomics · 2026Article
87 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundA pan-genome is defined as the set of all unique gene families found in one or more strains of a prokaryotic species. Due to the extensive within-species diversity in the microbial world, the pan-genome is often many times larger than a single genome. Studies of pan-genomes have become popular due to the easy access to whole-genome sequence data for prokaryotes. A pan-genome study reveals species diversity and gene families that may be of special interest, e.g because of their role in bacterial survival or their ability to discriminate strains.
resultsWe present an R package for the study of prokaryotic pan-genomes. The R computing environment harbors endless possibilities with respect to statistical analyses and graphics. External free software is used for the heavy computations involved, and the R package provides functions for building a computational pipeline.
conclusionsWe demonstrate parts of the package on a data set for the gram positive bacterium Enterococcus faecalis. The package is free to download and install from The Comprehensive R Archive Network.
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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.