ArticleGenome biology2017
DESMAN: a new tool for de novo extraction of strains from metagenomes.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers, 1 of them a synthesis that pooled it.
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Who cites it
106 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Environmental palaeogenomic reconstruction of an Ice Age algal population.Communications biology · 2021Pooled it
- Benchmarking of Reference-Based Tools for Strain-Level Resolution of Plant Microbiome.Molecular ecology resources · 2026Article
- How the social lives of bacteria affect their pangenome.Essays in biochemistry · 2026Review
- Evidence tiers for strain-resolved long-read metagenomics.iMetaOmics · 2026Article
- ZILA-SRM: a probabilistic framework with zero-inflated latent models for robust strain reconstruction from metagenomes.Microbiology spectrum · 2026Article
- Transcriptomic detection of Candidatus Allocryptoplasma (Anaplasmataceae) in Galápagos marine iguanas (Amblyrhynchus cristatus, Iguanidae).Parasites & vectors · 2025Article
- Strainify: Strain-Level Microbiome Profiling for Low-Coverage Short-Read Metagenomic Datasets.bioRxiv : the preprint server for biology · 2025Article
- Contrasting Genomic Responses of Hydrothermal Vent Animals and Their Symbionts to Population Decline After the Hunga Volcanic Eruption.Molecular ecology · 2025Article
- Intraspecies associations from strain-rich metagenome samples.Cell reports · 2025Article
- Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC.Genome research · 2025Article
- Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain.Nature microbiology · 2025Article
- Article
- Methods for Chromosome-Scale Haplotype Reconstruction.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Sequencing-based analysis of microbiomes.Nature reviews. Genetics · 2024Review
- An integrated strain-level analytic pipeline utilizing longitudinal metagenomic data.Microbiology spectrum · 2024Article
- Floria: fast and accurate strain haplotyping in metagenomes.Bioinformatics (Oxford, England) · 2024Article
- SNP-slice resolves mixed infections: simultaneously unveiling strain haplotypes and linking them to hosts.Bioinformatics (Oxford, England) · 2024Article
- Benchmarking short-, long- and hybrid-read assemblers for metagenome sequencing of complex microbial communities.Microbiology (Reading, England) · 2024Article
- Current Trends and Challenges of Microbiome Research in Prostate Cancer.Current oncology reports · 2024Review
- Decoding populations in the ocean microbiome.Microbiome · 2024Article
46 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
Abstract
We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin contigs into metagenome-assembled genomes but are unable to resolve strain-level variation. DESMAN identifies variants in core genes and uses co-occurrence across samples to link variants into haplotypes and abundance profiles. These are then searched for against non-core genes to determine the accessory genome of each strain. We validated DESMAN on a complex 50-species 210-genome 96-sample synthetic mock data set and then applied it to the Tara Oceans microbiome.
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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.