ArticleGenome biology2016
CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 285 papers, 5 of them syntheses that pooled it.
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Who cites it
285 citing papers in PubMed, 5 syntheses or guidelines pooled it.
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- A meta-analysis of genome-wide association studies of childhood wheezing phenotypes identifieseLife · 2023Pooled it
- Genetic variation in cis-regulatory domains suggests cell type-specific regulatory mechanisms in immunity.Communications biology · 2023Pooled it
- Identification of four novel associations for B-cell acute lymphoblastic leukaemia risk.Nature communications · 2019Pooled it
- An enhanced genetic model of relapsed IGH-translocated multiple myeloma evolutionary dynamics.Blood cancer journal · 2020Trial
- Deletion of a distal IRF4 element prevents inflammation-induced reprogramming of human regulatory T cell fate.Nature immunology · 2026Article
- p-LoopF is associated with chromatin looping in large introns of Ginkgo biloba.Cell research · 2026Article
- Functional characterization of the 9q34.13 locus identifies RAPGEF1 as a candidate gene modulating risk for melanoma and nevi via RAS activation.American journal of human genetics · 2026Article
- High-resolution promoter interaction analysis implicates genes involved in activation of type 3 innate lymphoid cells in immune disease risk.Nature genetics · 2026Article
- Multi-ancestry transcriptome-wide association study reveals shared and population-specific genetic effects in Alzheimer disease.American journal of human genetics · 2026Article
- Polycomb chromatin topology enables long-range enhancer recruitment during craniofacial development.Nature communications · 2026Article
- esBAF and INO80C fine-tune subcompartments and differentially regulate enhancer-promoter interactions.Genetics · 2026Article
- Pan-3D Genome Analysis Reveals the Roles of Structural Variation in Chicken Chromatin Architectures, Domestication and Production Traits.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Variant-to-gene mapping identifiesbioRxiv : the preprint server for biology · 2026Article
- Chromatin dynamics identifies 78 genes at loci associated with elevated intraocular pressure and primary open-angle glaucoma.bioRxiv : the preprint server for biology · 2026Article
- Extensive enhancer crosstalk controls PPARG2 activation during adipogenesis.Nature communications · 2026Article
- Functional characterization of the 9q34.13 locus identifiesbioRxiv : the preprint server for biology · 2026Article
- An EGR1-dependent cascade modulates genome architecture at the CSF1R locus.Nucleic acids research · 2026Article
- High-resolution promoter interaction analysis implicates genes involved in the activation of Type 3 Innate Lymphoid Cells in autoimmune disease risk.bioRxiv : the preprint server for biology · 2026Article
225 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors.
Funding
Abstract
Capture Hi-C (CHi-C) is a method for profiling chromosomal interactions involving targeted regions of interest, such as gene promoters, globally and at high resolution. Signal detection in CHi-C data involves a number of statistical challenges that are not observed when using other Hi-C-like techniques. We present a background model and algorithms for normalisation and multiple testing that are specifically adapted to CHi-C experiments. We implement these procedures in CHiCAGO ( http://regulatorygenomicsgroup.org/chicago ), an open-source package for robust interaction detection in CHi-C. We validate CHiCAGO by showing that promoter-interacting regions detected with this method are enriched for regulatory features and disease-associated SNPs.
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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.