ArticleNAR genomics and bioinformatics2022
Identification of chromatin loops from Hi-C interaction matrices by CTCF-CTCF topology classification.
Article in NAR genomics and bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- GraphChIAr: genome-wide super-resolution reconstruction of protein-mediated remote chromatin interactions by augmenting hi-C interaction maps with multiple ChIP-seq profiles.Briefings in bioinformatics · 2026Article
- An experimentally-informed polymer model reveals high resolution organization of genomic loci.Nature communications · 2026Article
- Dynamic three-dimensional chromatin remodeling in lung disease: mechanistic principles, pathogenic regulatory networks, and translational challenges.Frontiers in cell and developmental biology · 2026Review
- Loopsim: enrichment analysis of chromosome conformation capture with fast empirical distribution simulation.NAR genomics and bioinformatics · 2025Article
- Comparative study on chromatin loop callers using Hi-C data reveals their effectiveness.BMC bioinformatics · 2024Article
- MMCT-Loop: a mix model-based pipeline for calling targeted 3D chromatin loops.Nucleic acids research · 2024Article
- Computational methods for analysing multiscale 3D genome organization.Nature reviews. Genetics · 2024Review
- A Bioconductor/R Workflow for the Detection and Visualization of Differential Chromatin Loops.F1000Research · 2024Article
- The PENGUIN approach to reconstruct protein interactions at enhancer-promoter regions and its application to prostate cancer.Nature communications · 2023Article
- The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data.Briefings in bioinformatics · 2023Review
- DeepChIA-PET: Accurately predicting ChIA-PET from Hi-C and ChIP-seq with deep dilated networks.PLoS computational biology · 2023Article
- Cohesin and CTCF complexes mediate contacts in chromatin loops depending on nucleosome positions.Biophysical journal · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Genome-wide profiling of long-range interactions has revealed that the CCCTC-Binding factor (CTCF) often anchors chromatin loops and is enriched at boundaries of the so-called Topologically Associating Domains, which suggests that CTCF is essential in the 3D organization of chromatin. However, the systematic topological classification of pairwise CTCF-CTCF interactions has not been yet explored. Here, we developed a computational pipeline able to classify all CTCF-CTCF pairs according to their chromatin interactions from Hi-C experiments. The interaction profiles of all CTCF-CTCF pairs were further structurally clustered using self-organizing feature maps and their functionality characterized by their epigenetic states. The resulting clusters were then input to a convolutional neural network aiming at the
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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.