ArticleJournal of computational biology : a journal of computational molecular cell biology2022
Normalizing Metagenomic Hi-C Data and Detecting Spurious Contacts Using Zero-Inflated Negative Binomial Regression.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Host Range Breadth Correlates with Genic Diversity in Honeybee Phages.Genome biology and evolution · 2026Article
- Gut Hi-C metagenomes of severe COVID-19 patients: bacteria and yeast involved in gut-lung axis.mSphere · 2026Article
- Hi-C Links Reveal Viral Activity and Infection Within the Free-Living Microbial Community of a Secondary Chlorophyll Maximum in the Eastern Tropical North Pacific.Environmental microbiology · 2026Article
- Gut virome dynamics: from commensal to critical player in health and disease.Nature reviews. Gastroenterology & hepatology · 2026Review
- Benchmarking alignment strategies for Hi-C reads in metagenomic Hi-C data.Genome biology · 2026Article
- Article
- MetaHiCNet: a web server for normalizing and visualizing microbial Hi-C interaction networks.Nucleic acids research · 2025Article
- Understanding the transfer and persistence of antimicrobial resistance in aquaculture using a model teleost gut system.Animal microbiome · 2025Article
- Leveraging human microbiomes for disease prediction and treatment.Trends in pharmacological sciences · 2025Article
- MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data.Nature communications · 2023Article
- Noise reduction strategies in metagenomic chromosome confirmation capture to link antibiotic resistance genes to microbial hosts.Microbial genomics · 2023Article
- Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats.Nature microbiology · 2023Article
- ViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C data.Nature communications · 2023Article
- HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps.Genome biology · 2022Article
- A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data.Computational and structural biotechnology journal · 2021Review
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4 authors.
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Abstract
High-throughput chromosome conformation capture (Hi-C) has recently been applied to natural microbial communities and revealed great potential to study multiple genomes simultaneously. Several extraneous factors may influence chromosomal contacts rendering the normalization of Hi-C contact maps essential for downstream analyses. However, the current paucity of metagenomic Hi-C normalization methods and the ignorance for spurious interspecies contacts weaken the interpretability of the data. Here, we report on two types of biases in metagenomic Hi-C experiments: explicit biases and implicit biases, and introduce HiCzin, a parametric model to correct both types of biases and remove spurious interspecies contacts. We demonstrate that the normalized metagenomic Hi-C contact maps by HiCzin result in lower biases, higher capability to detect spurious contacts, and better performance in metagenomic contig clustering.
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