ArticleNature communications2023
SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 10 citations in OpenAlex.
- Differential analysis of image-based chromatin tracing data with Dory.bioRxiv : the preprint server for biology · 2026Article
- Accurate and robust 3D genome feature discovery from multiplexed DNA FISH.bioRxiv : the preprint server for biology · 2025Article
- FAIR sharing of Chromatin Tracing datasets using the newly developed 4DN FISH Omics Format.ArXiv · 2025Article
- ImputeHiFI: An Imputation Method for Multiplexed DNA FISH Data by Utilizing Single-Cell Hi-C and RNA FISH Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Spectral-based detection of chromatin loops in multiplexed super-resolution FISH data.Nature communications · 2024Article
- SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data.Communications biology · 2024Article
- SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data.bioRxiv : the preprint server for biology · 2024Article
- Image-based 3D genomics through chromatin tracing.Nature reviews. Methods primers · 2024Article
- SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data.Nature communications · 2023Article
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Authors and funding
15 authors at 8 institutions in 1 country.
Funding
Abstract
Multiplexed DNA fluorescence in situ hybridization (FISH) imaging technologies have been developed to map the folding of chromatin fibers at tens of nanometers and up to several kilobases in resolution in single cells. However, computational methods to reliably identify chromatin loops from such imaging datasets are still lacking. Here we present a Single-Nucleus Analysis Pipeline for multiplexed DNA FISH (SnapFISH), to process the multiplexed DNA FISH data and identify chromatin loops. SnapFISH can identify known chromatin loops from mouse embryonic stem cells with high sensitivity and accuracy. In addition, SnapFISH obtains comparable results of chromatin loops across datasets generated from diverse imaging technologies. SnapFISH is freely available at https://github.com/HuMingLab/SnapFISH .
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