ArticleGenome biology2022
HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps.
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 33 papers.
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Who cites it
33 citing papers in PubMed.
- Plasmidomics: studying plasmids as ecological entities beyond their hosts.Microbial genomics · 2026Review
- VirBinn improves viral genome binning from metagenomic Hi-C through graph diffusion.Bioinformatics (Oxford, England) · 2026Article
- Host Range Breadth Correlates with Genic Diversity in Honeybee Phages.Genome biology and evolution · 2026Article
- DCVBin: a novel binning method for single-sample metagenomes based on DNA language model and variational autoencoder.Briefings in bioinformatics · 2026Article
- Benchmarking alignment strategies for Hi-C reads in metagenomic Hi-C data.Genome biology · 2026Article
- Review
- Assessing live microbial therapeutic transmission.Gut microbes · 2025Review
- Article
- Metagenomic Applications to Herbivore Gut Microbiomes: A Comprehensive Review of Microbial Diversity and Host Interactions.Animals : an open access journal from MDPI · 2025Review
- Phages with a broad host range are common across ecosystems.Nature microbiology · 2025Article
- Computational Tools and Resources for Long-read Metagenomic Sequencing Using Nanopore and PacBio.Genomics, proteomics & bioinformatics · 2025Review
- MetaHiCNet: a web server for normalizing and visualizing microbial Hi-C interaction networks.Nucleic acids research · 2025Article
- Benchmarking metagenomic binning tools on real datasets across sequencing platforms and binning modes.Nature communications · 2025Article
- Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives.Briefings in bioinformatics · 2025Review
- Analysis of metagenomic data.Nature reviews. Methods primers · 2025Article
- Leveraging human microbiomes for disease prediction and treatment.Trends in pharmacological sciences · 2025Article
- Sequencing-based analysis of microbiomes.Nature reviews. Genetics · 2024Review
- Solving genomic puzzles: computational methods for metagenomic binning.Briefings in bioinformatics · 2024Review
- Unraveling metagenomics through long-read sequencing: a comprehensive review.Journal of translational medicine · 2024Review
- MarkerScan: Separation and assembly of cobionts sequenced alongside target species in biodiversity genomics projects.Wellcome open research · 2024Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Recovering high-quality metagenome-assembled genomes (MAGs) from complex microbial ecosystems remains challenging. Recently, high-throughput chromosome conformation capture (Hi-C) has been applied to simultaneously study multiple genomes in natural microbial communities. We develop HiCBin, a novel open-source pipeline, to resolve high-quality MAGs utilizing Hi-C contact maps. HiCBin employs the HiCzin normalization method and the Leiden clustering algorithm and includes the spurious contact detection into binning pipelines for the first time. HiCBin is validated on one synthetic and two real metagenomic samples and is shown to outperform the existing Hi-C-based binning methods. HiCBin is available at https://github.com/dyxstat/HiCBin .
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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.