ArticleBioinformatics advances2022
CTCF: an R/bioconductor data package of human and mouse CTCF binding sites.
Article in Bioinformatics advances, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
18 citing papers in PubMed.
- Chromatin topology and distal elements underlie divergent cell-type-specific regulation of 9p21 locus cell cycle genes.Cell genomics · 2026Article
- CLASH (Chromatin Loop Across-sample Score Harmonizer) quantifies the relative contributions of genetic variation, methylation, and CTCF occupancy on chromatin loop strength across individuals.bioRxiv : the preprint server for biology · 2026Article
- Genome-Wide Annotation of Promoter-Enhancer Interactions via Chromatin Loops in the Hybrid Rat Diversity Panel.bioRxiv : the preprint server for biology · 2026Article
- Histone H4 acetyl-methyllysine marks accessible chromatin that resists compaction.bioRxiv : the preprint server for biology · 2026Article
- A Murine Database of Structural Variants Identifies A Candidate Gene for a Spontaneous Murine Lymphoma Model.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Novel insights into hypoxia-driven transcriptomic and epigenetic landscapes in grade 3 meningioma.Journal of translational medicine · 2025Article
- Unveiling Multi-Scale Architectural Features in Single-Cell Hi-C Data Using scCAFE.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion.Nature communications · 2025Article
- A Murine Database of Structural Variants Enables the Genetic Architecture of a Spontaneous Murine Lymphoma to be Characterized.bioRxiv : the preprint server for biology · 2025Article
- UV-induced reorganization of 3D genome mediates DNA damage response.Nature communications · 2025Article
- Multi-locus CRISPRi targeting with a single truncated guide RNA.Nature communications · 2025Article
- ChromaFold predicts the 3D contact map from single-cell chromatin accessibility.Nature communications · 2024Article
- Exploring the roles of RNAs in chromatin architecture using deep learning.Nature communications · 2024Article
- scGrapHiC: deep learning-based graph deconvolution for Hi-C using single cell gene expression.Bioinformatics (Oxford, England) · 2024Article
- A Lightweight Framework For Chromatin Loop Detection at the Single-Cell Level.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Exploring the Roles of RNAs in Chromatin Architecture Using Deep Learning.bioRxiv : the preprint server for biology · 2023Article
- DNA strand asymmetry generated by CpG hemimethylation has opposing effects on CTCF binding.Nucleic acids research · 2023Article
- Temporal analysis suggests a reciprocal relationship between 3D chromatin structure and transcription.Cell reports · 2022Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Summary: CTCF (CCCTC-binding factor) is an 11-zinc-finger DNA binding protein which regulates much of the eukaryotic genome's 3D structure and function. The diversity of CTCF binding motifs has led to a fragmented landscape of CTCF binding data. We collected position weight matrices of CTCF binding motifs and defined strand-oriented CTCF binding sites in the human and mouse genomes, including the recent Telomere to Telomere and mm39 assemblies. We included selected experimentally determined and predicted CTCF binding sites, such as CTCF-bound cis-regulatory elements from SCREEN ENCODE. We recommend filtering strategies for CTCF binding motifs and demonstrate that liftOver is a viable alternative to convert CTCF coordinates between assemblies. Our comprehensive data resource and usage recommendations can serve to harmonize and strengthen the reproducibility of genomic studies utilizing CTCF binding data. Availability and implementation: https://bioconductor.org/packages/CTCF. Companion website: https://dozmorovlab.github.io/CTCF/; Code to reproduce the analyses: https://github.com/dozmorovlab/CTCF.dev. Supplementary information: Supplementary data are available at
Identifiers
What OpenQuestion holds
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.