ArticleNature communications2024
Effective binning of metagenomic contigs using contrastive multi-view representation learning.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed, 57 citations in OpenAlex.
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- Community-driven updates for comprehensive long-read metagenomics and enhanced binning in nf-core/mag v5.Bioinformatics (Oxford, England) · 2026Article
- Deployable high-fidelity metagenome binning at scale with QuickBin.Communications biology · 2026Article
- Large language models enhance annotation of enzymes in metagenomes.Science advances · 2026Article
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- Gut microbial community of patients with Parkinson's disease analyzed using metagenome-assembled genomes.Neural regeneration research · 2026Article
- MeioBIOME: A snakemake workflow for the parallel analysis of meiofaunal genomes and host-associated bacteria/archaea.bioRxiv : the preprint server for biology · 2026Article
- Chromid-like secondary replicons as predicted key sites of biosynthetic gene clusters inmSystems · 2026Article
- TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive.Nature communications · 2026Article
- Shared biosynthetic architectures generate diverse β-amino polyketide residues in cyanobacterial peptides.bioRxiv : the preprint server for biology · 2026Article
- Highly biased DNA sequence reconstruction in DNA storage with multi-scale attention mechanism and contrast learning.Synthetic and systems biotechnology · 2026Article
- A review of computational approaches for metagenomics by long-read sequencing.Science China. Life sciences · 2026Review
- Improving metagenome binning by integrating intrinsic features and taxonomy.Nature biotechnology · 2026Article
- The naked mole-rat microbiome is associated with healthy aging and social structure.Cell reports · 2026Article
- Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery.Nature communications · 2026Article
- End-to-end evaluation of pipelines for metagenome-assembled genomes reveals hidden performance gaps.bioRxiv : the preprint server for biology · 2026Article
- ChloroScan: Recovering Plastid Genome Bins From Metagenomic Data.Molecular ecology resources · 2026Article
- Metagenome Sequencing and Recovery of 52 Microbial Genomes from Plastic-Polluted Coastal Sediment.Scientific data · 2026Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
Contig binning plays a crucial role in metagenomic data analysis by grouping contigs from the same or closely related genomes. However, existing binning methods face challenges in practical applications due to the diversity of data types and the difficulties in efficiently integrating heterogeneous information. Here, we introduce COMEBin, a binning method based on contrastive multi-view representation learning. COMEBin utilizes data augmentation to generate multiple fragments (views) of each contig and obtains high-quality embeddings of heterogeneous features (sequence coverage and k-mer distribution) through contrastive learning. Experimental results on multiple simulated and real datasets demonstrate that COMEBin outperforms state-of-the-art binning methods, particularly in recovering near-complete genomes from real environmental samples. COMEBin outperforms other binning methods remarkably when integrated into metagenomic analysis pipelines, including the recovery of potentially pathogenic antibiotic-resistant bacteria (PARB) and moderate or higher quality bins containing potential biosynthetic gene clusters (BGCs).
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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.