ArticleGenome research2023
Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe.
Article in Genome research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed.
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- Annotating the pangenome reveals the diversity in the genetic basis for metabolic enzymes.Science advances · 2026Article
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- Impact of selective digestive decontamination on the pangenome composition of ESBL-E. coli.The Journal of antimicrobial chemotherapy · 2026Article
- Global distribution, antimicrobial resistance, and virulence factors of Staphylococcus epidermidis revealed through population genomics.BMC 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
- Phenotypic and genomic characterization ofMicrobiology spectrum · 2026Article
- Complex temporal dynamics of phage-bacteria populations in an animal-associated marine system.Nature communications · 2026Article
- A widespread gut bacterial lineage distinguished by redox metabolism and phage defense.bioRxiv : the preprint server for biology · 2026Article
- Emergence and genomic adaptation of the globally disseminated ST2250 lineage within theAntimicrobial agents and chemotherapy · 2026Article
- Genomic and transcriptomic analyses reveal a Gifsy-1 prophage-encoded virulence module associated with enhanced epithelial adhesion ofFrontiers in cellular and infection microbiology · 2026Article
- De novo origin of numerous microproteins in enterobacteria.Nucleic acids research · 2025Article
- Genomic and spatial heterogeneity of Brucella melitensis underscores latent brucellosis risks in non-endemic zones in Southwest China.Communications biology · 2025Article
- TheeLife · 2025Article
- How to measure bacterial genome plasticity? A novel index helps gather insights on pathogens.Microbial genomics · 2025Article
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6 authors.
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Abstract
Horizontal gene transfer (HGT) plays a critical role in the evolution and diversification of many microbial species. The resulting dynamics of gene gain and loss can have important implications for the development of antibiotic resistance and the design of vaccine and drug interventions. Methods for the analysis of gene presence/absence patterns typically do not account for errors introduced in the automated annotation and clustering of gene sequences. In particular, methods adapted from ecological studies, including the pangenome gene accumulation curve, can be misleading as they may reflect the underlying diversity in the temporal sampling of genomes rather than a difference in the dynamics of HGT. Here, we introduce Panstripe, a method based on generalized linear regression that is robust to population structure, sampling bias, and errors in the predicted presence/absence of genes. We show using simulations that Panstripe can effectively identify differences in the rate and number of genes involved in HGT events, and illustrate its capability by analyzing several diverse bacterial genome data sets representing major human pathogens.
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