ArticlePLoS computational biology2020
PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.
Article in PLoS computational biology, 2020. 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 167 papers.
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Who cites it
167 citing papers in PubMed.
- metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.Gut microbes · 2026Article
- BeyondEmerging microbes & infections · 2026Article
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- Comparative pangenomics unveils distinct host adaptation trends and conserved biosynthetic potential in microbiome Clostridia.Molecular biology and evolution · 2026Article
- Phylogeny-agnostic strain-level prediction of phage-host interactions from genomes using machine learning.Nature microbiology · 2026Article
- How the social lives of bacteria affect their pangenome.Essays in biochemistry · 2026Review
- Life in sediments fosters 'sexual' speciation in the Shewanella baltica complex.PLoS genetics · 2026Article
- PanDelos-plus: A parallel algorithm for computing sequence homology in pangenomic analysis.PLoS computational biology · 2026Article
- Integrated poultry production as a reservoir ofMicrobial genomics · 2026Article
- Comparative Genomic Analysis of Bovine and Publicly Available HumanAnimals : an open access journal from MDPI · 2026Article
- Phylogeny-aware comparative genomics ofmBio · 2026Article
- Genomic Insights Into Antimicrobial Resistance and Virulence of Enterococcus avium Strains From Bovine Mastitis in Some Selected Dairy Farms of Bangladesh.Veterinary medicine and science · 2026Article
- Panorama: A robust pangenome-based method for predicting and comparing biological systems across species.PLoS computational biology · 2026Article
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Kente: A Graph-based Pangenomic Approach for Horizontal Gene Transfer Detection in Microbiomes.bioRxiv : the preprint server for biology · 2026Article
- Depth-associated selection and drift shape persistent microbial populations in Holocene lake sediments.mSystems · 2026Article
- A syntenic pangenome of Gardnerella reveals novel plasmids and phage, taxonomic boundaries, and species-level stratification of metabolic and virulence potential.Nature communications · 2026Article
- Genome-based insights into metal co-resistance in Amazonian mercury-resistant bacteria: ecological lifestyle and biosafety implications for bioremediation.Microbiology spectrum · 2026Article
- Comparative genomics reveals high prophage diversity and horizontal gene transfer of effectors and phage defence systems in theMicrobial genomics · 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
107 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The use of comparative genomics for functional, evolutionary, and epidemiological studies requires methods to classify gene families in terms of occurrence in a given species. These methods usually lack multivariate statistical models to infer the partitions and the optimal number of classes and don't account for genome organization. We introduce a graph structure to model pangenomes in which nodes represent gene families and edges represent genomic neighborhood. Our method, named PPanGGOLiN, partitions nodes using an Expectation-Maximization algorithm based on multivariate Bernoulli Mixture Model coupled with a Markov Random Field. This approach takes into account the topology of the graph and the presence/absence of genes in pangenomes to classify gene families into persistent, cloud, and one or several shell partitions. By analyzing the partitioned pangenome graphs of isolate genomes from 439 species and metagenome-assembled genomes from 78 species, we demonstrate that our method is effective in estimating the persistent genome. Interestingly, it shows that the shell genome is a key element to understand genome dynamics, presumably because it reflects how genes present at intermediate frequencies drive adaptation of species, and its proportion in genomes is independent of genome size. The graph-based approach proposed by PPanGGOLiN is useful to depict the overall genomic diversity of thousands of strains in a compact structure and provides an effective basis for very large scale comparative genomics. The software is freely available at https://github.com/labgem/PPanGGOLiN.
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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.