ReviewNature reviews. Genetics2024
Computational methods for analysing multiscale 3D genome organization.
Review in Nature reviews. Genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
56 citing papers in PubMed.
- Foundation model reveals the shared organization of transcription and topologically associating domains.Cell systems · 2026Article
- Hi-Cformer enables multiscale chromatin contact map modeling for single-cell Hi-C data analysis.Science advances · 2026Article
- 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
- Article
- Metadomain and metaloop genome interactions in mammalian T cells.Cell reports · 2026Article
- Persistent homology-based multiscale Hi-C analysis uncovers TADs-mediated gene regulation.Scientific reports · 2026Article
- Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie.Genome research · 2026Article
- Jointly-hic: joint decomposition of contact frequency maps captures salient features of genome architecture across tissues and development.Genome biology · 2026Article
- szKendall: spatial-structural-zero-aware dissimilarity measures for subtype discovery using single cell Hi-C data.Nature communications · 2026Article
- CellLoop: Identifying single-cell 3D genome chromatin loops.Nature communications · 2026Article
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- scDIAGRAM: detecting chromatin compartments from individual single-cell Hi-C matrix without imputation or reference features.Briefings in bioinformatics · 2026Article
- HiCMamba: Enhancing Hi-C resolution and identifying 3D genome structures with state space modeling.PLoS computational biology · 2026Article
- A data-driven chromatin model reveals spatial and dynamic features of genome organization.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture.BMC bioinformatics · 2026Article
- ChromNet: A Multi-Task Learning Framework for Cross-Cell Type Prediction of 3D Chromatin Interactions Using Epigenetic Signals.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Accurate and robust 3D genome feature discovery from multiplexed DNA FISH.bioRxiv : the preprint server for biology · 2025Article
- DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks.Nature communications · 2025Article
- Structural variants in the 3D genome as drivers of disease.Nature reviews. Genetics · 2025Review
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Recent progress in whole-genome mapping and imaging technologies has enabled the characterization of the spatial organization and folding of the genome in the nucleus. In parallel, advanced computational methods have been developed to leverage these mapping data to reveal multiscale three-dimensional (3D) genome features and to provide a more complete view of genome structure and its connections to genome functions such as transcription. Here, we discuss how recently developed computational tools, including machine-learning-based methods and integrative structure-modelling frameworks, have led to a systematic, multiscale delineation of the connections among different scales of 3D genome organization, genomic and epigenomic features, functional nuclear components and genome function. However, approaches that more comprehensively integrate a wide variety of genomic and imaging datasets are still needed to uncover the functional role of 3D genome structure in defining cellular phenotypes in health and disease.
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What Socratic holds
Registered trials
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 Socratic graph.