ArticleAdvanced science (Weinheim, Baden-Wurttemberg, Germany)2023
DeDoc2 Identifies and Characterizes the Hierarchy and Dynamics of Chromatin TAD-Like Domains in the Single Cells.
Article in Advanced science (Weinheim, Baden-Wurttemberg, Germany), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 22 citations in OpenAlex.
- Identification of differential topologically associating domains from low sequencing depth and pseudobulk chromatin contact maps.Genome research · 2026Article
- CTCF aligns single-cell TAD-like domain boundaries and stabilizes long-range active chromatin clusters.Science advances · 2026Article
- scDIAGRAM: detecting chromatin compartments from individual single-cell Hi-C matrix without imputation or reference features.Briefings in bioinformatics · 2026Article
- Navigating the 3D genome at single-cell resolution: techniques, computation, and mechanistic landscapes.Briefings in bioinformatics · 2025Review
- Unicorn: enhancing single-cell Hi-C data with blind super-resolution for 3D genome structure reconstruction.Bioinformatics (Oxford, England) · 2025Article
- The hierarchical folding dynamics of topologically associating domains during early embryo development.BMC biology · 2025Article
- Unveiling Multi-Scale Architectural Features in Single-Cell Hi-C Data Using scCAFE.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Novel AI-powered computational method using tensor decomposition for identification of common optimal bin sizes when integrating multiple Hi-C datasets.Scientific reports · 2025Article
- Single-Cell Hi-C Technologies and Computational Data Analysis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- Deciphering single-cell genomic architecture: insights into cellular heterogeneity and regulatory dynamics.Genomics & informatics · 2025Review
- Uncovering topologically associating domains from three-dimensional genome maps with TADGATE.Nucleic acids research · 2025Article
- Topologically associating domains of chromatin on single-cell Hi-C data: a survey of bioinformatic tools and applications in the light of artificial intelligence.Frontiers in genetics · 2025Review
- Topology entropy: Enhancing graph partitioning for TAD identification and single-cell clustering.Computational and structural biotechnology journal · 2025Article
- ScHiCAtt: Enhancing single-cell Hi-C data resolution using attention-based models.Computational and structural biotechnology journal · 2025Article
- DiffDomain enables identification of structurally reorganized topologically associating domains.Nature communications · 2024Article
- DeDoc2 Identifies and Characterizes the Hierarchy and Dynamics of Chromatin TAD-Like Domains in the Single Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
Topologically associating domains (TADs) are functional chromatin units with hierarchical structure. However, the existence, prevalence, and dynamics of such hierarchy in single cells remain unexplored. Here, a new generation TAD-like domain (TLD) detection algorithm, named deDoc2, to decode the hierarchy of TLDs in single cells, is reported. With dynamic programming, deDoc2 seeks genome partitions with global minimal structure entropy for both whole and local contact matrix. Notably, deDoc2 outperforms state-of-the-art tools and is one of only two tools able to identify the hierarchy of TLDs in single cells. By applying deDoc2, it is showed that the hierarchy of TLDs in single cells is highly dynamic during cell cycle, as well as among human brain cortex cells, and that it is associated with cellular identity and functions. Thus, the results demonstrate the abundance of information potentially encoded by TLD hierarchy for functional regulation. The deDoc2 can be freely accessed at https://github.com/zengguangjie/deDoc2.
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Registered trials
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