A machine-learning algorithm to predict CTCF-mediated long-range chromatin interactions

Cross Team Collaboration Fun Times

7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

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Genomic coordinates of FIMO-predicted CTCF binding sites using JASPAR and other PWMs, human and mouse genome assemblies including mm39 and T2T. Also included experimentally derived ENCODE SCREEN CTCF-bound CREs.

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Analysis code repository for the paper "Spatial patterns of CTCF sites define the anatomy of TADs and their boundaries"

All codes used to generate results and figure that are reported in CTCF project.

DNA methylation regulates alternative polyadenylation via CTCF and the cohesin complex (2019 paper submission)

Quantitative modeling of CTCF-mediated loop anchors

CCIP is a software for the prediction of CTCF-mediated chromatin loops

Deep learning of CTCF-mediated chromatin loops in 3D genome organization

GILoop is a deep learning framework for detecting CTCF-mediated loops on Hi-C contact maps.

DeepLncCTCF for identification and analysis of consensus RNA motifs binding to the genome regulator CTCF

CLNN-loop: A deep learning model to predict chromatin loops in the different cell lines and CTCF-binding sites (CBS) pair types

Python tool to compute distribution of Loop's CTCF orientation in a pie chart format

It's a strong semantic segmentation network for building type classification from very high romte sensing images.

An analysis of CTCF binding and alternative splicing using ENCODE data.

Free energy based high-resolution modeling of CTCF-mediated chromatin loops for human genome

Deep Learning of Sequence Patterns for CTCF-Mediated Chromatin Loop Formation

Studying 3D genome evolution using genomic sequence

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Deep learning model built to quantitatively predict the binding affinities of DNA sequences to human CCCTC-binding factor(CTCF)

Analysis of directionality bias of CTCF motifs in Hi-C interactions.

code associated with Hafner 2022 paper on cohesin and ctcf degron lines

A reproducible Snakemake pipeline for end-to-end cell-free DNA (cfDNA) fragmentomics analysis (WPS, TSS, CTCF, motifs，MDS)).

We established the first global map of regulatory elements (15 chromatin states) and defined their coordinated activities in cattle, through genome-wide profiling for six histone modifications, RNA polymerase II, CTCF-binding sites, DNA accessibility, DNA methylation, and transcriptome in Rumen Epithelial Primary Cells (REPC), rumen tissues, and Madin-Darby Bovine Kidney Epithelial Cells (MDBK).

Predict potential binding sites for the CTCF (CCCTC-binding factor) transcription factor within DNA sequences

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