ArticleNature methods2024
scGHOST: identifying single-cell 3D genome subcompartments.
Article in Nature methods, 2024. 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 19 papers.
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Who cites it
19 citing papers in PubMed.
- Foundation model reveals the shared organization of transcription and topologically associating domains.Cell systems · 2026Article
- Article
- Origins and consequences of oncogenic 3D chromatin remodelling.Nature reviews. Cancer · 2026Review
- Single-cell multiomics connects 3D genome and transcriptome alterations in Alzheimer's disease.Science (New York, N.Y.) · 2026Article
- Metadomain and metaloop genome interactions in mammalian T cells.Cell reports · 2026Article
- Kilobase-scale compartments enabled by CRUSH reveal regulatory programs across cell types, single-cells, and ancient mammoths.bioRxiv : the preprint server for biology · 2026Article
- CellLoop: Identifying single-cell 3D genome chromatin loops.Nature communications · 2026Article
- scDIAGRAM: detecting chromatin compartments from individual single-cell Hi-C matrix without imputation or reference features.Briefings in bioinformatics · 2026Article
- Recent advances in single-cell bioinformatics for inferring higher-order chromatin contact maps.BMB reports · 2025Review
- A comprehensive benchmark of single-cell Hi-C embedding tools.Nature communications · 2025Article
- Navigating the 3D genome at single-cell resolution: techniques, computation, and mechanistic landscapes.Briefings in bioinformatics · 2025Review
- MaxComp: Predicting single-cell chromatin compartments from 3D chromosome structures.PLoS computational biology · 2025Article
- Single-Cell Hi-C Technologies and Computational Data Analysis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- COCOA: A Framework for Fine-scale Mapping of Cell-type-specific Chromatin Compartments Using Epigenomic Information.Genomics, proteomics & bioinformatics · 2025Article
- Tumor suppressors RBL1 and PTEN are epigenetically silenced in IPF mesenchymal progenitor cells by a CD44/Brg1/PRMT5 regulatory complex.American journal of physiology. Lung cellular and molecular physiology · 2024Article
- Addressing scalability and managing sparsity and dropout events in single-cell representation identification with ZIGACL.Briefings in bioinformatics · 2024Article
- Breaking up the StayGold dimer yields three photostable monomers.Nature methods · 2024Article
- Computational methods for analysing multiscale 3D genome organization.Nature reviews. Genetics · 2024Review
- ChromaFactor: deconvolution of single-molecule chromatin organization with non-negative matrix factorization.bioRxiv : the preprint server for biology · 2023Article
Corrections and comments
- Erratum issued
- Update of
Authors and funding
3 authors.
Funding
Abstract
Single-cell Hi-C (scHi-C) technologies allow for probing of genome-wide cell-to-cell variability in three-dimensional (3D) genome organization from individual cells. Computational methods have been developed to reveal single-cell 3D genome features based on scHi-C, including A/B compartments, topologically associating domains and chromatin loops. However, no method exists for annotating single-cell subcompartments, which is important for understanding chromosome spatial localization in single cells. Here we present scGHOST, a single-cell subcompartment annotation method using graph embedding with constrained random walk sampling. Applications of scGHOST to scHi-C data and contact maps derived from single-cell 3D genome imaging demonstrate reliable identification of single-cell subcompartments, offering insights into cell-to-cell variability of nuclear subcompartments. Using scHi-C data from complex tissues, scGHOST identifies cell-type-specific or allele-specific subcompartments linked to gene transcription across various cell types and developmental stages, suggesting functional implications of single-cell subcompartments. scGHOST is an effective method for annotating single-cell 3D genome subcompartments in a broad range of biological contexts.
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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.