ArticleNature communications2022
Genome binning of viral entities from bulk metagenomics data.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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Who cites it
73 citing papers in PubMed.
- Ten quick tips for classifying unknown bacteriophage.PLoS computational biology · 2026Article
- Review
- Multi-kingdom profiling reveals altered gut phage-bacteria-metabolite interactions in MASLD.Nature communications · 2026Article
- Unveiling the biodiversity of large DNA viruses in intertidal mudflats via metagenomics.Nature communications · 2026Article
- Enhanced multi-omic viral profiling from microbial community sequencing with BAQLaVa.bioRxiv : the preprint server for biology · 2026Article
- Accurate plasmid reconstruction from metagenomics data using assembly-alignment graphs and contrastive learning.Nature biotechnology · 2026Article
- Viromics approaches for the study of viral diversity and ecology in microbiomes.Nature reviews. Genetics · 2026Review
- Computational Microbial and Viral Ecology Analysis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Article
- Prompt-based bioinformatic pipeline generation for a multi-step metaviral workflow.Bioinformatics advances · 2026Article
- Prophages and their interactions with lytic phages in the human gut microbiota and their impact on microbial diversity, gut health, and disease.Applied and environmental microbiology · 2025Review
- Phage diversity mirrors bacterial strain diversity in the honey bee gut microbiota.Nature communications · 2025Article
- Human immunodeficiency virus and antiretroviral therapies exert distinct influences across diverse gut microbiomes.Nature microbiology · 2025Article
- Phages with a broad host range are common across ecosystems.Nature microbiology · 2025Article
- Global biogeography of airborne viruses in public transit systems and their host interactions.Microbiome · 2025Article
- The genetic diversity and populational specificity of the human gut virome at single-nucleotide resolution.Microbiome · 2025Article
- Biases and complementarity in gut viromes obtained from bulk and virus-like particle-enriched metagenomic sequencing.Microbiology spectrum · 2025Article
- Population-scale sequencing resolves correlates and determinants of latent Epstein-Barr Virus infection.bioRxiv : the preprint server for biology · 2025Article
- Deep Learning Transforms Phage-Host Interaction Discovery from Metagenomic Data.bioRxiv : the preprint server for biology · 2025Article
- Genome-resolved metagenomics from short-read sequencing data in the era of artificial intelligence.Functional & integrative genomics · 2025Review
13 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite the accelerating number of uncultivated virus sequences discovered in metagenomics and their apparent importance for health and disease, the human gut virome and its interactions with bacteria in the gastrointestinal tract are not well understood. This is partly due to a paucity of whole-virome datasets and limitations in current approaches for identifying viral sequences in metagenomics data. Here, combining a deep-learning based metagenomics binning algorithm with paired metagenome and metavirome datasets, we develop Phages from Metagenomics Binning (PHAMB), an approach that allows the binning of thousands of viral genomes directly from bulk metagenomics data, while simultaneously enabling clustering of viral genomes into accurate taxonomic viral populations. When applied on the Human Microbiome Project 2 (HMP2) dataset, PHAMB recovered 6,077 high-quality genomes from 1,024 viral populations, and identified viral-microbial host interactions. PHAMB can be advantageously applied to existing and future metagenomes to illuminate viral ecological dynamics with other microbiome constituents.
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