ArticleGenome biology2024
ChIPr: accurate prediction of cohesin-mediated 3D genome organization from 2D chromatin features.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 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
- Accurate prediction of cohesin and RNA Polymerase II-associated chromatin interactions using convolutional neural networks.Nucleic acids research · 2026Article
- Structural variants in the 3D genome as drivers of disease.Nature reviews. Genetics · 2025Review
- A distinct mechanism of epigenetic reprogramming silences PAX2 and initiates endometrial carcinogenesis.The Journal of clinical investigation · 2025Article
- Microbial cancer immunotherapy reprograms hematopoiesis to enhance myeloid-driven anti-tumor immunity.Cancer cell · 2025Article
- A review of deep learning models for the prediction of chromatin interactions with DNA and epigenomic profiles.Briefings in bioinformatics · 2024Review
- ChIPr: accurate prediction of cohesin-mediated 3D genome organization from 2D chromatin features.Genome biology · 2024Article
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Authors and funding
6 authors.
Funding
Abstract
The three-dimensional genome organization influences diverse nuclear processes. Here we present Chromatin Interaction Predictor (ChIPr), a suite of regression models based on deep neural networks, random forest, and gradient boosting to predict cohesin-mediated chromatin interaction strength between any two loci in the genome. The predictions of ChIPr correlate well with ChIA-PET data in four cell lines. The standard ChIPr model requires three experimental inputs: ChIP-Seq signals for RAD21, H3K27ac, and H3K27me3 but works well with just RAD21 signal. Integrative analysis reveals novel insights into the role of CTCF motif, its orientation, and CTCF binding on cohesin-mediated chromatin interactions.
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Registered trials
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