ArticleGenome biology2022
StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers, 1 of them a synthesis that pooled it.
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Who cites it
77 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Genetic strategies for sex-biased persistence of gut microbes across human life.Nature communications · 2023Pooled it
- Fecal microbiota transplantation promotes reduction of antimicrobial resistance by strain replacement.Science translational medicine · 2023Trial
- Benchmarking of Reference-Based Tools for Strain-Level Resolution of Plant Microbiome.Molecular ecology resources · 2026Article
- Safety, tolerability, and gastrointestinal effect of a Bifidobacterium-based synergistic synbiotic in infants and toddlers.Pediatric research · 2026Article
- ZILA-SRM: a probabilistic framework with zero-inflated latent models for robust strain reconstruction from metagenomes.Microbiology spectrum · 2026Article
- Multi-strain Clostridioides difficile infection: Increased detection and clinical implications.The Journal of infection · 2026Article
- Culture-enriched metagenomic sequencing reveals within-patient diversity and transmission of vancomycin-resistantMicrobial genomics · 2026Article
- Strain sharing and persistence of microbial pathogens colonizing the skin of residents in a regional nursing home network.Nature communications · 2026Article
- Strain-level transmission inference across multi-kingdom metagenomic data using TRACS.Nature microbiology · 2026Article
- A WGS workflow for identifying genetically modified and foodborne-pathogenicFood chemistry. Molecular sciences · 2026Article
- Strain-level analyses of public sequencing data to characterizeOne health (Amsterdam, Netherlands) · 2026Article
- Unmasking pathogen traits for chronic colonization in neurogenic bladder.Cell reports · 2026Article
- Benchmarking the impact of reference genome selection on taxonomic profiling accuracy.BMC genomics · 2026Article
- Metabolic reprogramming of the infant gut by bifidobacteria-based probiotics drives exclusion of antibiotic-resistant pathobionts.Cell reports. Medicine · 2026Article
- Strain Diversity in the Human Microbiome: Personal Variation, Pathobionts, Therapeutics, and Methodological Challenges.Microorganisms · 2026Review
- Culture-enriched metagenomic sequencing reveals within-patient diversity and transmission of vancomycin-resistantmedRxiv : the preprint server for health sciences · 2026Article
- Efagins - engineerable agents that evolved independently to target the enterococcal cell wall.bioRxiv : the preprint server for biology · 2026Article
- Metagenomic strain tracking reveals patterns of bacterial spread and the impact of water chlorination.medRxiv : the preprint server for health sciences · 2026Article
- Strain-level metagenomic profiling using pangenome graphs with PanTax.Genome research · 2026Article
- Sequence type and strain-level detection ofMicrobial genomics · 2026Article
17 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors.
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Abstract
Human-associated microbial communities comprise not only complex mixtures of bacterial species, but also mixtures of conspecific strains, the implications of which are mostly unknown since strain level dynamics are underexplored due to the difficulties of studying them. We introduce the Strain Genome Explorer (StrainGE) toolkit, which deconvolves strain mixtures and characterizes component strains at the nucleotide level from short-read metagenomic sequencing with higher sensitivity and resolution than other tools. StrainGE is able to identify strains at 0.1x coverage and detect variants for multiple conspecific strains within a sample from coverages as low as 0.5x.
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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.