ArticleNature biotechnology2021
Improved metagenome binning and assembly using deep variational autoencoders.
Article in Nature biotechnology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 336 papers.
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Who cites it
336 citing papers in PubMed.
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- Lactiplantibacillus plantarum P9 for chronic diarrhea in young adults: a large double-blind, randomized, placebo-controlled trial.Nature communications · 2024Trial
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- Catalog of metagenome-assembled genomes of prokaryotic communities from the Red Sea hydrothermal vents.Microbiology resource announcements · 2026Article
- DecBin: Bayesian-optimized deep clustering for long-read metagenomic binning.Briefings in bioinformatics · 2026Article
- The planktonic microbiome of the Great Barrier Reef.Nature · 2026Article
- MetaCAT enables reconstruction of high-quality microbial genomes and their association with host traits from metagenomic data.Nature microbiology · 2026Article
- Deployable high-fidelity metagenome binning at scale with QuickBin.Communications biology · 2026Article
- Metagenomic insights into mechanisms of coral larval settlement induction and inhibition by marine biofilms.Environmental microbiome · 2026Article
- Computational Genomics for Resistome Characterization: Current Advancements and Future Challenges Under a One Health Perspective.Antibiotics (Basel, Switzerland) · 2026Review
- Widespread horizontal transfer and strong selection enhance microbial adaptation in Antarctic soils.Nature communications · 2026Article
- Stop codon reassignment to tryptophan in members of the bacterial phylumMicrobial genomics · 2026Article
- Innovative technologies and future perspectives in tumor microbiomics.Science China. Life sciences · 2026Review
- OAPGC: a high-quality oral and airway prokaryotic genome catalog for enhanced ecological resolution and disease inference.NPJ biofilms and microbiomes · 2026Article
- Genome-resolved gut microbial guild and fecal metabolic signatures associated with post-weaning estrus return in sows.Animal microbiome · 2026Article
- Alginate foraging is conserved in geographically and taxonomically distinct ruminant microbiomes.Nature communications · 2026Article
- Article
276 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite recent advances in metagenomic binning, reconstruction of microbial species from metagenomics data remains challenging. Here we develop variational autoencoders for metagenomic binning (VAMB), a program that uses deep variational autoencoders to encode sequence coabundance and k-mer distribution information before clustering. We show that a variational autoencoder is able to integrate these two distinct data types without any previous knowledge of the datasets. VAMB outperforms existing state-of-the-art binners, reconstructing 29-98% and 45% more near-complete (NC) genomes on simulated and real data, respectively. Furthermore, VAMB is able to separate closely related strains up to 99.5% average nucleotide identity (ANI), and reconstructed 255 and 91 NC Bacteroides vulgatus and Bacteroides dorei sample-specific genomes as two distinct clusters from a dataset of 1,000 human gut microbiome samples. We use 2,606 NC bins from this dataset to show that species of the human gut microbiome have different geographical distribution patterns. VAMB can be run on standard hardware and is freely available at https://github.com/RasmussenLab/vamb .
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