ReviewMicrobial genomics2023
Challenges in prokaryote pangenomics.
Review in Microbial genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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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
23 citing papers in PubMed.
- A reusable model of pangenome selection informs optimal surveillance strategies over vaccine introductions.Genome medicine · 2026Article
- How the social lives of bacteria affect their pangenome.Essays in biochemistry · 2026Review
- SURE-Pipe: a pipeline to compare genomes and extract shared and unique regions.NAR genomics and bioinformatics · 2026Article
- RefiningMicrobial genomics · 2026Article
- Pan-genome insights into genetic diversity, evolutionary dynamics, and pathogenic traits of Staphylococcus agnetis.BMC genomics · 2026Article
- Defining thebioRxiv : the preprint server for biology · 2026Article
- Tn-seq of Thermus thermophilus Genome Reveals Unexpected Tolerance to Insertions in Bacterial Common Essential Genes.MicrobiologyOpen · 2026Article
- PyamilySeq: exposing the fragility of conventional gene (re)clustering and prokaryotic pangenomic inference methods.NAR genomics and bioinformatics · 2026Article
- The pangenome: a statistical model, not a fixed biological property.Bioinformatics advances · 2026Review
- De novo origin of numerous microproteins in enterobacteria.Nucleic acids research · 2025Article
- De novo gene birth and the conundrum of ORFan genes in bacteria.Genome research · 2025Review
- Unveiling Genomic Islands Hosting Antibiotic Resistance Genes and Virulence Genes in Foodborne Multidrug-Resistant Patho-GenicBiology · 2025Article
- Linkage-based ortholog refinement in bacterial pangenomes with CLARC.Nucleic acids research · 2025Article
- Pitfalls of bacterial pan-genome analysis approaches: a case study of Mycobacterium tuberculosis and two less clonal bacterial species.Bioinformatics (Oxford, England) · 2025Article
- Rampant Interkingdom Horizontal Gene Transfer in Pezizomycotina? An Updated Inspection of Anomalous Phylogenies.International journal of molecular sciences · 2025Article
- Decoding EcuadorianBiomedicines · 2025Article
- Quantifying the Evolutionary Dynamics of Structure and Content in Closely Related E. coli Genomes.Molecular biology and evolution · 2025Article
- Unravelling Prokaryotic Codon Usage: Insights from Phylogeny, Influencing Factors and Pathogenicity.Current genomics · 2025Review
- A gentle introduction to pangenomics.Briefings in bioinformatics · 2024Review
- CELEBRIMBOR: core and accessory genes from metagenomes.Bioinformatics (Oxford, England) · 2024Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Horizontal gene transfer (HGT) and the resulting patterns of gene gain and loss are a fundamental part of bacterial evolution. Investigating these patterns can help us to understand the role of selection in the evolution of bacterial pangenomes and how bacteria adapt to a new niche. Predicting the presence or absence of genes can be a highly error-prone process that can confound efforts to understand the dynamics of horizontal gene transfer. This review discusses both the challenges in accurately constructing a pangenome and the potential consequences errors can have on downstream analyses. We hope that by summarizing these issues researchers will be able to avoid potential pitfalls, leading to improved bacterial pangenome analyses.
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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.