ArticleGenome biology2020
3DeFDR: statistical methods for identifying cell type-specific looping interactions in 5C and Hi-C data.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 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
13 citing papers in PubMed.
- Persistent chromatin alterations and gene expression reprogramming follow widespread DNA damage in glioblastoma.Nature communications · 2026Article
- Persistent chromatin loops shape gene expression plasticity upon stimulation and restimulation of human neurons.bioRxiv : the preprint server for biology · 2025Article
- Learning induces persistent chromatin loops underlying robust gene expression during memory recall.bioRxiv : the preprint server for biology · 2025Article
- Mosaic H3K9me3 at BREACHes predicts synaptic gene expression associated with fragile X syndrome cognitive severity.bioRxiv : the preprint server for biology · 2025Article
- Cell-type-specific loops linked to RNA polymerase II elongation in human neural differentiation.Cell genomics · 2024Article
- A multi-looping chromatin signature predicts dysregulated gene expression in neurons with familial Alzheimer's disease mutations.bioRxiv : the preprint server for biology · 2024Article
- Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome.Cell · 2023Article
- Cell type-specific loops linked to RNA polymerase II elongation in human neural differentiation.bioRxiv : the preprint server for biology · 2023Article
- A deep learning method for replicate-based analysis of chromosome conformation contacts using Siamese neural networks.Nature communications · 2023Article
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- Assessing Specific Networks of Chromatin Interactions with HiChIP.Methods in molecular biology (Clifton, N.J.) · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
An important unanswered question in chromatin biology is the extent to which long-range looping interactions change across developmental models, genetic perturbations, drug treatments, and disease states. Computational tools for rigorous assessment of cell type-specific loops across multiple biological conditions are needed. We present 3DeFDR, a simple and effective statistical tool for classifying dynamic loops across biological conditions from Chromosome-Conformation-Capture-Carbon-Copy (5C) and Hi-C data. Our work provides a statistical framework and open-source coding libraries for sensitive detection of cell type-specific loops in high-resolution 5C and Hi-C data from multiple cellular conditions.
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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.