ArticleMethods in molecular biology (Clifton, N.J.)2022
Analysis of Hi-C Data for Discovery of Structural Variations in Cancer.
Article in Methods in molecular biology (Clifton, N.J.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 24 citations in OpenAlex.
- Origins and consequences of oncogenic 3D chromatin remodelling.Nature reviews. Cancer · 2026Review
- map3C: a computational tool for processing multiomic single-cell Hi-C data.Bioinformatics (Oxford, England) · 2026Article
- Hi-C for genome-wide detection of enhancer-hijacking rearrangements in routine lymphoid cancer biopsies.Cell genomics · 2026Article
- A reduced TBX5-dependent gene regulatory network links atrial fibrillation and heart failure.Nature cardiovascular research · 2026Article
- The 3D Genome Browser 2.0: an enhanced online platform for visualizing and analyzing 3D genome architecture.Nucleic acids research · 2026Article
- Hi-C sequencing data from frontal cortex of laboratory rats.Scientific data · 2025Article
- Recent advances in single-cell bioinformatics for inferring higher-order chromatin contact maps.BMB reports · 2025Review
- Article
- Structural variants in the 3D genome as drivers of disease.Nature reviews. Genetics · 2025Review
- Enhancer activation from transposable elements in extrachromosomal DNA.Nature cell biology · 2025Article
- map3C: a computational tool for processing multiomic single-cell Hi-C data.bioRxiv : the preprint server for biology · 2025Article
- Article
- Enhancer activation from transposable elements in extrachromosomal DNA.bioRxiv : the preprint server for biology · 2025Article
- Genomic Evaluation of AML-Main Techniques and Novel Approaches.Journal of clinical medicine · 2025Review
- Review
- 3D chromatin hubs as regulatory units of identity and survival in human acute leukemia.Molecular cell · 2025Article
- Article
- Tbx5 maintains atrial identity in post-natal cardiomyocytes by regulating an atrial-specific enhancer network.Nature cardiovascular research · 2023Article
- Massively parallelbioRxiv : the preprint server for biology · 2023Article
- Dynamic changes in P300 enhancers and enhancer-promoter contacts control mouse cardiomyocyte maturation.Developmental cell · 2023Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Structural variations (SVs) are large genomic rearrangements that can be challenging to identify with current short read sequencing technology due to various confounding factors such as existence of genomic repeats and complex SV structures. Hi-C breakfinder is the first computational tool that utilizes the technology of high-throughput chromatin conformation capture assay (Hi-C) to systematically identify SVs, without being interfered by regular confounding factors. SVs change the spatial distance of genomic regions and cause discontinuous signals in Hi-C, which are difficult to analyze by routine informatics practice. Here we provide step-by-step guidance for how to identify SVs using Hi-C data and how to reconstruct Hi-C maps in the presence of SVs.
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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.