ArticleWellcome open research2020
High-resolution sweep metagenomics using fast probabilistic inference.
Article in Wellcome open research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 1 of them a synthesis that pooled it.
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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
32 citing papers in PubMed, 1 synthesis or guideline pooled it, 37 citations in OpenAlex.
- Genetic strategies for sex-biased persistence of gut microbes across human life.Nature communications · 2023Pooled it
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- Protocols for genomic epidemiology and source attribution of enteric bacteria causing diarrhoeal disease across Africa.BMJ open · 2026Article
- Exploring clonality ofMicrobiology spectrum · 2026Article
- A more complete picture: capturing single nucleotide variant diversity in extended-spectrum beta-lactamase producingMicrobial genomics · 2026Article
- Identification of transporter-dependent capsular loci associated with the invasive potential of Escherichia coli.Nature microbiology · 2026Article
- Sequence type and strain-level detection ofMicrobial genomics · 2026Article
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- Environmental surveillance of bacteria in a new intensive care unit using plate sweeps.Microbial genomics · 2026Article
- Within-host genetic diversity of pneumococcal serotype 3 during one-year prolonged carriage in a healthy adult.Nature communications · 2025Article
- Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment.Bioinformatics (Oxford, England) · 2025Article
- Co-carriage of diverse vancomycin-resistantJAC-antimicrobial resistance · 2025Article
- Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain.Nature microbiology · 2025Article
- Contaminated drinking water facilitates Escherichia coli strain-sharing within households in urban informal settlements.Nature microbiology · 2025Article
- Seamless, rapid, and accurate analyses of outbreak genomic data using splitGenome research · 2024Article
- Where the Patterns Are: Repetition-Aware Compression for Colored de Bruijn GraphsJournal of computational biology : a journal of computational molecular cell biology · 2024Article
- Bacterial strain sharing between humans, animals, and the environment among urban households.medRxiv : the preprint server for health sciences · 2024Article
- Evolution and host-specific adaptation ofScience (New York, N.Y.) · 2024Article
- Deep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan.Nature communications · 2024Article
- Article
Corrections and comments
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Authors and funding
13 authors at 5 institutions in 4 countries.
Funding
Abstract
Determining the composition of bacterial communities beyond the level of a genus or species is challenging because of the considerable overlap between genomes representing close relatives. Here, we present the mSWEEP pipeline for identifying and estimating the relative sequence abundances of bacterial lineages from plate sweeps of enrichment cultures. mSWEEP leverages biologically grouped sequence assembly databases, applying probabilistic modelling, and provides controls for false positive results. Using sequencing data from major pathogens, we demonstrate significant improvements in lineage quantification and detection accuracy. Our pipeline facilitates investigating cultures comprising mixtures of bacteria, and opens up a new field of plate sweep metagenomics.
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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.