ArticlePhilosophical transactions of the Royal Society of London. Series B, Biological sciences2022
Mandrake: visualizing microbial population structure by embedding millions of genomes into a low-dimensional representation.
Article in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 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
10 citing papers in PubMed, 14 citations in OpenAlex.
- Life in sediments fosters 'sexual' speciation in the Shewanella baltica complex.PLoS genetics · 2026Article
- AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics.bioRxiv : the preprint server for biology · 2026Article
- Genomic epidemiology ofMicrobial genomics · 2026Article
- Machine learning and statistical inference in microbial population genomics.Genome biology · 2025Review
- Integrated population clustering and genomic epidemiology with PopPIPE.Microbial genomics · 2025Article
- Genomic Biosurveillance of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Biovar 3 Reveals Adaptation to Selective Pressures in New Zealand Orchards.Molecular plant pathology · 2025Article
- Development of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal population structure.Microbial genomics · 2024Article
- EnteroBase: hierarchical clustering of 100 000s of bacterial genomes into species/subspecies and populations.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
- Recent progress on methods for estimating and updating large phylogenies.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Review
- Genomic population structures of microbial pathogens.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 4 institutions in 10 countries.
Funding
Abstract
In less than a decade, population genomics of microbes has progressed from the effort of sequencing dozens of strains to thousands, or even tens of thousands of strains in a single study. There are now hundreds of thousands of genomes available even for a single bacterial species, and the number of genomes is expected to continue to increase at an accelerated pace given the advances in sequencing technology and widespread genomic surveillance initiatives. This explosion of data calls for innovative methods to enable rapid exploration of the structure of a population based on different data modalities, such as multiple sequence alignments, assemblies and estimates of gene content across different genomes. Here, we present Mandrake, an efficient implementation of a dimensional reduction method tailored for the needs of large-scale population genomics. Mandrake is capable of visualizing population structure from millions of whole genomes, and we illustrate its usefulness with several datasets representing major pathogens. Our method is freely available both as an analysis pipeline (https://github.com/johnlees/mandrake) and as a browser-based interactive application (https://gtonkinhill.github.io/mandrake-web/). This article is part of a discussion meeting issue 'Genomic population structures of microbial pathogens'.
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.