ArticleBriefings in bioinformatics2024
Removing unwanted variation between samples in Hi-C experiments.
Article in Briefings in bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Multi-Omics Insights Into the Mechanisms of Early Muscle Fiber Difference and Transformation Between Lean-Type and Chinese Indigenous Pigs.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- A high-resolution 3D genome map of kiwifruit provides insights into chromatin architecture and transcriptional activity.Horticulture research · 2026Article
- SCUDDO: an unsupervised clustering algorithm for single-cell Hi-C maps using diagonal diffusion operators.Bioinformatics (Oxford, England) · 2026Article
- A compendium of chromatin interaction maps in the Giant Panda genome.Communications biology · 2026Article
- Examining the dynamics of three-dimensional genome organization with multitask matrix factorization.Genome research · 2025Article
- Comparing chromatin contact maps at scale: methods and insights.Nature methods · 2025Article
- Mapping the 3D genome architecture.Computational and structural biotechnology journal · 2025Review
- Haplotype-resolved 3D chromatin architecture of the hybrid pig.Genome research · 2024Article
- Dynamic chromatin architecture of the porcine adipose tissues with weight gain and loss.Nature communications · 2023Article
- Spatio-temporal transcriptome dynamics coordinate rapid transition of core crop functions in 'lactating' pigeon.PLoS genetics · 2023Article
- Comparative three-dimensional genome architectures of adipose tissues provide insight into human-specific regulation of metabolic homeostasis.The Journal of biological chemistry · 2023Article
- Normalization and de-noising of single-cell Hi-C data with BandNorm and scVI-3D.Genome biology · 2022Article
- The 3D architecture of the pepper genome and its relationship to function and evolution.Nature communications · 2022Article
- Comparative 3D genome architecture in vertebrates.BMC biology · 2022Article
- Reorganization of 3D genome architecture across wild boar and Bama pig adipose tissues.Journal of animal science and biotechnology · 2022Article
- Integrating Hi-C links with assembly graphs for chromosome-scale assembly.PLoS computational biology · 2019Article
- R Tutorial: Detection of Differentially Interacting Chromatin Regions From Multiple Hi-C Datasets.Current protocols in bioinformatics · 2019Article
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Authors and funding
5 authors.
Funding
Abstract
Hi-C data are commonly normalized using single sample processing methods, with focus on comparisons between regions within a given contact map. Here, we aim to compare contact maps across different samples. We demonstrate that unwanted variation, of likely technical origin, is present in Hi-C data with replicates from different individuals, and that properties of this unwanted variation change across the contact map. We present band-wise normalization and batch correction, a method for normalization and batch correction of Hi-C data and show that it substantially improves comparisons across samples, including in a quantitative trait loci analysis as well as differential enrichment across cell types.
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