ArticleNature biotechnology2023
A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH.
Article in Nature biotechnology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 38 citations in OpenAlex.
- Differential analysis of image-based chromatin tracing data with Dory.bioRxiv : the preprint server for biology · 2026Article
- Reconstructing the three-dimensional architecture of extrachromosomal DNA with ec3D.Nature communications · 2025Article
- A methodology to reduce the localization error in multi-loci microscopy provides new insights into enhancer biology.PLoS computational biology · 2025Article
- Accurate and robust 3D genome feature discovery from multiplexed DNA FISH.bioRxiv : the preprint server for biology · 2025Article
- Article
- FAIR sharing of Chromatin Tracing datasets using the newly developed 4DN FISH Omics Format.ArXiv · 2025Article
- Nanoscale 3D DNA tracing in non-denatured cells resolves the Cohesin-dependent loop architecture of the genome in situ.Nature communications · 2025Article
- Emerging Techniques in Spatial Multiomics: Fundamental Principles and Applications to Dermatology.The Journal of investigative dermatology · 2025Review
- Cell type-specific 3D-genome organization and transcription regulation in the brain.Science advances · 2025Article
- Image Analysis Protocol for DNA/RNA/Immunofluorescence (IF)-seqFISH Data.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Measurement of Spatial Contact Map Using Sequential FISH.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Transcription-coupled changes in genomic region proximities during transcriptional bursting.Science advances · 2024Article
- Epigenetics and the timing of neuronal differentiation.Current opinion in neurobiology · 2024Review
- 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
- SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data.Communications biology · 2024Article
- Multiplex DNA fluorescence in situ hybridization to analyze maternal vs. paternal C. elegans chromosomes.Genome biology · 2024Article
- Polycomb repression of Hox genes involves spatial feedback but not domain compaction or phase transition.Nature genetics · 2024Article
- pyHiM: a new open-source, multi-platform software package for spatial genomics based on multiplexed DNA-FISH imaging.Genome biology · 2024Article
- Computational methods for analysing multiscale 3D genome organization.Nature reviews. Genetics · 2024Review
- SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Multiplexed fluorescence in situ hybridization (FISH) is a widely used approach for analyzing three-dimensional genome organization, but it is challenging to derive chromosomal conformations from noisy fluorescence signals, and tracing chromatin is not straightforward. Here we report a spatial genome aligner that parses true chromatin signal from noise by aligning signals to a DNA polymer model. Using genomic distances separating imaged loci, our aligner estimates spatial distances expected to separate loci on a polymer in three-dimensional space. Our aligner then evaluates the physical probability observed signals belonging to these loci are connected, thereby tracing chromatin structures. We demonstrate that this spatial genome aligner can efficiently model chromosome architectures from DNA FISH data across multiple scales and be used to predict chromosome ploidies de novo in interphase cells. Reprocessing of previous whole-genome chromosome tracing data with this method indicates the spatial aggregation of sister chromatids in S/G2 phase cells in asynchronous mouse embryonic stem cells and provides evidence for extranumerary chromosomes that remain tightly paired in postmitotic neurons of the adult mouse cortex.
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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.