ArticleMicrobial genomics2020
Hogwash: three methods for genome-wide association studies in bacteria.
Article in Microbial genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
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Who cites it
18 citing papers in PubMed.
- Variation in multiple classes of simple sequence repeats can alter drug susceptibility inbioRxiv : the preprint server for biology · 2026Article
- Resolving competing evolutionary histories in joint ancestral state reconstruction.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Uncertainty in joint Ancestral State Reconstruction: Improving accuracy and biological interpretability of ancestral state prediction.bioRxiv : the preprint server for biology · 2025Article
- Identifying drivers of β-lactam/β-lactamase inhibitor resistance emergence and spread before their clinical deployment.medRxiv : the preprint server for health sciences · 2025Article
- Bacterial genome-wide association studies: exploring the genetic variation underlying bacterial phenotypes.Applied and environmental microbiology · 2025Review
- aurora: a machine learning gwas tool for analyzing microbial habitat adaptation.Genome biology · 2025Article
- Metagenomic global survey and in-depth genomic analyses of Ruminococcus gnavus reveal differences across host lifestyle and health status.Nature communications · 2025Article
- Comparative genomic study of non-typeableiScience · 2024Article
- Review
- Use of whole genome sequencing for surveillance and control of foodborne diseases:Frontiers in microbiology · 2024Review
- Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes.BMC bioinformatics · 2023Article
- Article
- Genome-Wide Study of Drug ResistantMicroorganisms · 2022Article
- Using genomics to understand the mechanisms of virulence and drug resistance in fungal pathogens.Biochemical Society transactions · 2022Review
- Article
- Article
- Forest and Trees: Exploring Bacterial Virulence with Genome-wide Association Studies and Machine Learning.Trends in microbiology · 2021Review
- Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Bacterial genome-wide association studies (bGWAS) capture associations between genomic variation and phenotypic variation. Convergence-based bGWAS methods identify genomic mutations that occur independently multiple times on the phylogenetic tree in the presence of phenotypic variation more often than is expected by chance. This work introduces hogwash, an open source R package that implements three algorithms for convergence-based bGWAS. Hogwash additionally contains two burden testing approaches to perform gene or pathway analysis to improve power and increase convergence detection for related but weakly penetrant genotypes. To identify optimal use cases, we applied hogwash to data simulated with a variety of phylogenetic signals and convergence distributions. These simulated data are publicly available and contain the relevant metadata regarding convergence and phylogenetic signal for each phenotype and genotype. Hogwash is available for download from GitHub.
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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.