ArticlePLoS computational biology2018
A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination.
Article in PLoS computational biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 145 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
145 citing papers in PubMed, 277 citations in OpenAlex.
- Identification and characterization of non-canonical azole antifungal resistance pathways inmBio · 2026Article
- Genome-wide analyses of an avian herpesvirus identify 10 loci associated with tumorigenicity and vaccine escape.Science advances · 2026Article
- Integrated Genome-Wide Association Study and Machine Learning Approach for Characterizing the Determinants of Biofilm Formation in Staphylococcus aureus.Interdisciplinary sciences, computational life sciences · 2026Article
- Biosynthetic gene clusters inmSystems · 2026Article
- A robust, sensitive phylogenetic method enables gene-level metagenomic analyses.bioRxiv : the preprint server for biology · 2026Article
- High-precision binary trait association on phylogenetic trees.Microbial genomics · 2026Article
- Epistasis and co-adaptation in bacterial genome evolution.Nature reviews. Genetics · 2026Review
- GeneScanner: profiling genetic variation across bacterial populations.Microbial genomics · 2026Article
- A versatile multi-components mixed model for bacterial-Genome Wide association studies.Nature communications · 2026Article
- Climate-associated natural selection in the human mitochondrial genome.Molecular biology and evolution · 2026Article
- Resolving competing evolutionary histories in joint ancestral state reconstruction.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- BaGPipe: an automated, reproducible, and flexible pipeline for bacterial genome-wide association studies.BMC microbiology · 2026Article
- Comparative Analysis of Lineage Structure, Cellulose Locus Context, and Mobilome Diversity Across CompleteMicroorganisms · 2026Article
- Pathological convergence of a bacterial plant pathogen is associated with the horizontal transfer of an effector-containing mobile element.BMC genomics · 2026Article
- Article
- The unique role ofmBio · 2026Article
- Genome-Wide Association Reveals Signalling-Linked Infection Tolerance in Hibernating Bats.Pathogens (Basel, Switzerland) · 2026Article
- A Possible Recently Identified Evolutionary Strategy Using Membrane-Bound Vesicle Transfer of Genetic Material to Induce Bacterial Resistance, Virulence and Pathogenicity inInternational journal of molecular sciences · 2026Article
- Novel insights into the newly described Corynebacterium hesseae: first molecular and genomic characterization of a multidrug-resistant strain from blood culture.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2025Article
- CORGIAS: identifying correlated gene pairs by considering evolutionary history in a large-scale prokaryotic genome dataset.NAR genomics and bioinformatics · 2025Article
85 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Genome-Wide Association Studies (GWAS) in microbial organisms have the potential to vastly improve the way we understand, manage, and treat infectious diseases. Yet, microbial GWAS methods established thus far remain insufficiently able to capitalise on the growing wealth of bacterial and viral genetic sequence data. Facing clonal population structure and homologous recombination, existing GWAS methods struggle to achieve both the precision necessary to reject spurious findings and the power required to detect associations in microbes. In this paper, we introduce a novel phylogenetic approach that has been tailor-made for microbial GWAS, which is applicable to organisms ranging from purely clonal to frequently recombining, and to both binary and continuous phenotypes. Our approach is robust to the confounding effects of both population structure and recombination, while maintaining high statistical power to detect associations. Thorough testing via application to simulated data provides strong support for the power and specificity of our approach and demonstrates the advantages offered over alternative cluster-based and dimension-reduction methods. Two applications to Neisseria meningitidis illustrate the versatility and potential of our method, confirming previously-identified penicillin resistance loci and resulting in the identification of both well-characterised and novel drivers of invasive disease. Our method is implemented as an open-source R package called treeWAS which is freely available at https://github.com/caitiecollins/treeWAS.
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.