ArticleComputational and structural biotechnology journal2021
FIREcaller: Detecting frequently interacting regions from Hi-C data.
Article in Computational and structural biotechnology journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 45 citations in OpenAlex.
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- Mega-enhancers compartmentalize transcriptionally active long genes in the brain.Nature cell biology · 2026Article
- MECP2 mutations disrupt pluripotent stem cell fate through remodeling of the three-dimensional genome.Cell death & disease · 2026Article
- Beyond blacklists: a critical assessment of exclusion set generation strategies and alternative approaches.Bioinformatics (Oxford, England) · 2026Article
- iceDP: identifying inter-chromatin engagement via density peaks clustering algorithm.Briefings in bioinformatics · 2026Article
- Analysis of chromatin structure reveals the connection between sQTLs and the splicing of distant genes.Scientific reports · 2025Article
- Joint analysis of sQTL and Hi-C reveals spatial proximity between sQTLs and target genes in cancer tissues.Scientific reports · 2025Article
- Beyond Blacklists: A Critical Assessment of Exclusion Set Generation Strategies and Alternative Approaches.bioRxiv : the preprint server for biology · 2025Article
- Comparative study on chromatin loop callers using Hi-C data reveals their effectiveness.BMC bioinformatics · 2024Article
- SATB2 organizes the 3D genome architecture of cognition in cortical neurons.Molecular cell · 2024Article
- A Bioconductor/R Workflow for the Detection and Visualization of Differential Chromatin Loops.F1000Research · 2024Article
- Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program.Nature communications · 2022Article
- Understanding Regulatory Mechanisms of Brain Function and Disease through 3D Genome Organization.Genes · 2022Review
- Innovative computational approaches shed light on genetic mechanisms underlying cognitive impairment among children born extremely preterm.Journal of neurodevelopmental disorders · 2022Article
- TADreg: a versatile regression framework for TAD identification, differential analysis and rearranged 3D genome prediction.BMC bioinformatics · 2022Article
- THUNDER: A reference-free deconvolution method to infer cell type proportions from bulk Hi-C data.PLoS genetics · 2022Article
- Parallel analysis of transcription, integration, and sequence of single HIV-1 proviruses.Cell · 2022Article
- From GWAS variant to function: A study of ∼148,000 variants for blood cell traits.HGG advances · 2022Article
- Advances in profiling chromatin architecture shed light on the regulatory dynamics underlying brain disorders.Seminars in cell & developmental biology · 2022Review
- Understanding the function of regulatory DNA interactions in the interpretation of non-coding GWAS variants.Frontiers in cell and developmental biology · 2022Review
Corrections and comments
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Authors and funding
12 authors at 4 institutions in 2 countries.
Funding
Abstract
Hi-C experiments have been widely adopted to study chromatin spatial organization, which plays an essential role in genome function. We have recently identified frequently interacting regions (FIREs) and found that they are closely associated with cell-type-specific gene regulation. However, computational tools for detecting FIREs from Hi-C data are still lacking. In this work, we present FIREcaller, a stand-alone, user-friendly R package for detecting FIREs from Hi-C data. FIREcaller takes raw Hi-C contact matrices as input, performs within-sample and cross-sample normalization, and outputs continuous FIRE scores, dichotomous FIREs, and super-FIREs. Applying FIREcaller to Hi-C data from various human tissues, we demonstrate that FIREs and super-FIREs identified, in a tissue-specific manner, are closely related to gene regulation, are enriched for enhancer-promoter (E-P) interactions, tend to overlap with regions exhibiting epigenomic signatures of
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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.