ArticleNature communications2024
A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Origins and consequences of oncogenic 3D chromatin remodelling.Nature reviews. Cancer · 2026Review
- TADShop: systematic benchmarking and identification of topologically associating domains.Nature methods · 2026Article
- Persistent homology-based multiscale Hi-C analysis uncovers TADs-mediated gene regulation.Scientific reports · 2026Article
- CT-TADB predicts TAD boundaries without Hi-C by integrating DNA sequences and epigenomic features.NPJ systems biology and applications · 2026Article
- BandHiC: a memory-efficient and user-friendly Python package for organizing and analyzing Hi-C matrices down to sub-kilobase resolution.BMC genomics · 2026Article
- A wavelet-based approach generates quantitative, scale-free and hierarchical descriptions of 3D genome structures and new biological insights.PLoS computational biology · 2026Article
- High-throughputbioRxiv : the preprint server for biology · 2025Article
- EmbedTAD Using Graph Embedding and Unsupervised Learning to Identify TADs from High-Resolution Hi-C Data.Communications biology · 2025Article
- Multiscale structure of chromatin condensates explains phase separation and material properties.Science (New York, N.Y.) · 2025Article
- 3D Genome Constrains Breakpoints of Inversions That Can Act as Barriers to Gene Flow in the Stickleback.Molecular ecology · 2025Article
- 3D Genome Architecture in Stem Cell Lineage Commitment: from Structural Organization to Precision Regulation.Advanced genetics (Hoboken, N.J.) · 2025Review
- MIA-Jet: Multi-scale Identification Algorithm of Chromatin Jets.bioRxiv : the preprint server for biology · 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
- Quantitative spatial analysis of chromatin biomolecular condensates using cryoelectron tomography.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A novel deep learning framework with dynamic tokenization for identifying chromatin interactions along with motif importance investigation.Briefings in bioinformatics · 2025Article
- Quantitative Spatial Analysis of Chromatin Biomolecular Condensates using Cryo-Electron Tomography.bioRxiv : the preprint server for biology · 2024Article
- A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains.Nature communications · 2024Article
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Authors and funding
14 authors.
Funding
Abstract
Topologically associating domains (TADs), megabase-scale features of chromatin spatial architecture, are organized in a domain-within-domain TAD hierarchy. Within TADs, the inner and smaller subTADs not only manifest cell-to-cell variability, but also precisely regulate transcription and differentiation. Although over 20 TAD callers are able to detect TAD, their usability in biomedicine is confined by a disagreement of outputs and a limit in understanding TAD hierarchy. We compare 13 computational tools across various conditions and develop a metric to evaluate the similarity of TAD hierarchy. Although outputs of TAD hierarchy at each level vary among callers, data resolutions, sequencing depths, and matrices normalization, they are more consistent when they have a higher similarity of larger TADs. We present comprehensive benchmarking of TAD hierarchy callers and operational guidance to researchers of life science researchers. Moreover, by simulating the mixing of different types of cells, we confirm that TAD hierarchy is generated not simply from stacking Hi-C heatmaps of heterogeneous cells. Finally, we propose an air conditioner model to decipher the role of TAD hierarchy in transcription.
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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.