ArticleProceedings of the National Academy of Sciences of the United States of America2024
Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed.
- Article
- Article
- Cooperation and the evolution of bacterial niche breadth.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Genomic perplexity and the evolution of context-dependent function.Molecular biology and evolution · 2026Article
- Genome-wide co-occurrence patterns link mobile genetic elements, antimicrobial resistance and defense systems in Pseudomonas aeruginosa.BMC genomics · 2026Article
- Genomic variants distinguish Pseudomonas aeruginosa from cystic fibrosis sputum and bloodstream infection.BMC infectious diseases · 2026Article
- PanForest: predicting genes in genomes using random forests.Bioinformatics (Oxford, England) · 2026Article
- Multi-scale ecological drivers shape the genome flexibility of soil-dwellingISME communications · 2026Article
- CORGIAS: identifying correlated gene pairs by considering evolutionary history in a large-scale prokaryotic genome dataset.NAR genomics and bioinformatics · 2025Article
- Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes.Molecular biology and evolution · 2025Article
- Machine learning and statistical inference in microbial population genomics.Genome biology · 2025Review
- MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis.Nucleic acids research · 2025Article
- A phylogenetic approach to comparative genomics.Nature reviews. Genetics · 2025Review
- Distribution of Polyphosphate Kinase 2 Genes in Bacteria Underscores a Dynamic Evolutionary History.Proteins · 2025Article
- Context matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution.mSystems · 2025Review
- Review
- Persistent, Private, and Mobile Genes: A Model for Gene Dynamics in Evolving Pangenomes.Molecular biology and evolution · 2025Article
- Chromosomal capture of beneficial genes drives plasmids toward ecological redundancy.The ISME journal · 2025Article
- Forecasting framework for dominant SARS-CoV-2 strains before clade replacement using phylogeny-informed genetic distances.Frontiers in microbiology · 2025Article
- Article
Corrections and comments
- Commented on by
Authors and funding
3 authors.
Funding
Abstract
Pangenomes exhibit remarkable variability in many prokaryotic species, much of which is maintained through the processes of horizontal gene transfer and gene loss. Repeated acquisitions of near-identical homologs can easily be observed across pangenomes, leading to the question of whether these parallel events potentiate similar evolutionary trajectories, or whether the remarkably different genetic backgrounds of the recipients mean that postacquisition evolutionary trajectories end up being quite different. In this study, we present a machine learning method that predicts the presence or absence of genes in the
Indexed as
Identifiers
What OpenQuestion holds
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.