ArticleNature communications2025
Tensor-FLAMINGO unravels the complexity of single-cell spatial architectures of genomes at high-resolution.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Spatially resolved chromatin architectures in mammalian brain tissues.Nature methods · 2026Article
- Hi-Cformer enables multiscale chromatin contact map modeling for single-cell Hi-C data analysis.Science advances · 2026Article
- Physics-Based Modeling of Sparse Single-Cell Hi-C Uncovers Structural and Epigenetic Variability.International journal of molecular sciences · 2026Article
- SCW: building the whole-genome 3D structures based on extremely sparse single-cell Hi-C data.BMC bioinformatics · 2026Article
- FAIR sharing of Chromatin Tracing datasets using the newly developed 4DN FISH Omics Format.ArXiv · 2025Article
- geomeTriD: a Bioconductor package for interactive and integrative visualization of 3D structural model with multi-omics data.Bioinformatics advances · 2025Article
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6 authors.
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Abstract
The dynamic three-dimensional spatial conformations of chromosomes demonstrate complex structural variations across single cells, which plays pivotal roles in modulating single-cell specific transcription and epigenetics landscapes. The high rates of missing contacts in single-cell chromatin contact maps impose significant challenges to reconstruct high-resolution spatial chromatin configurations. We develop a data-driven algorithm, Tensor-FLAMINGO, based on a low-rank tensor completion strategy. Implemented on a diverse panel of single-cell chromatin datasets, Tensor-FLAMINGO generates 10kb- and 30kb-resolution spatial chromosomal architectures across individual cells. Tensor-FLAMINGO achieves superior accuracy in reconstructing 3D chromatin structures, recovering missing contacts, and delineating cell clusters. The unprecedented high-resolution characterization of single-cell genome folding enables expanded identification of single-cell specific long-range chromatin interactions, multi-way spatial hubs, and the mechanisms of disease-associated GWAS variants. Beyond the sparse 2D contact maps, the complete 3D chromatin conformations promote an avenue to understand the dynamics of spatially coordinated molecular processes across different cells.
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