ArticleNature communications2022
Deciphering multi-way interactions in the human genome.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 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.
The trial behind it
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
27 citing papers in PubMed, 48 citations in OpenAlex.
- Transcription clusters and developmental pathways - nature, nurture, noise.Journal of cell science · 2026Review
- Connecting multiway enhancer-promoter interactions to changes in gene expression in cancer.bioRxiv : the preprint server for biology · 2026Article
- On the molecular basis of enduring memory in neurons, and cell fate in fibroblasts.Nucleic acids research · 2026Review
- HyperDeepTAD: a topologically associated domains detection method based on multiway chromatin interaction data and deep learning.BMC genomics · 2026Article
- Interplay between cohesin and RNA polymerase II in regulating chromatin interactions and gene transcription.Nature structural & molecular biology · 2026Article
- Pore-C Pipeline-Toolbox: a comprehensive pipeline for Pore-C data analysis.Briefings in bioinformatics · 2025Article
- MultiVis.js: a software tool for the visualization of multiway chromatin interactions and SPRITE data.BMC bioinformatics · 2025Article
- Ultrastable and versatile multimeric ensembles of FoxP3 on microsatellites.Molecular cell · 2025Article
- Profiling the epigenome using long-read sequencing.Nature genetics · 2025Review
- Article
- Node features of chromosome structure networks and their connections to genome annotation.Computational and structural biotechnology journal · 2024Article
- In silico and cheminformatics prediction with experimental validation of an adipogenesis cocktail, sorafenib with rosiglitazone for HCC dedifferentiation.Journal, genetic engineering & biotechnology · 2024Article
- Inter-chromosomal contacts demarcate genome topology along a spatial gradient.Nature communications · 2024Article
- A Survey on Hyperlink Prediction.IEEE transactions on neural networks and learning systems · 2024Article
- Stability of Ecological Systems: A Theoretical Review.Physics reports · 2024Article
- Advances in computational and experimental approaches for deciphering transcriptional regulatory networks: Understanding the roles of cis-regulatory elements is essential, and recent research utilizing MPRAs, STARR-seq, CRISPR-Cas9, and machine learning has yielded valuable insights.BioEssays : news and reviews in molecular, cellular and developmental biology · 2024Review
- Statistical modeling and significance estimation of multi-way chromatin contacts with HyperloopFinder.Briefings in bioinformatics · 2024Article
- Computational methods for analysing multiscale 3D genome organization.Nature reviews. Genetics · 2024Review
- KRONECKER PRODUCT OF TENSORS AND HYPERGRAPHS: STRUCTURE AND DYNAMICS.SIAM journal on matrix analysis and applications : a publication of the Society for Industrial and Applied Mathematics · 2024Article
- 'Bingo'-a large language model- and graph neural network-based workflow for the prediction of essential genes from protein data.Briefings in bioinformatics · 2023Article
Corrections and comments
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Authors and funding
15 authors at 4 institutions in 2 countries.
Funding
Abstract
Chromatin architecture, a key regulator of gene expression, can be inferred using chromatin contact data from chromosome conformation capture, or Hi-C. However, classical Hi-C does not preserve multi-way contacts. Here we use long sequencing reads to map genome-wide multi-way contacts and investigate higher order chromatin organization in the human genome. We use hypergraph theory for data representation and analysis, and quantify higher order structures in neonatal fibroblasts, biopsied adult fibroblasts, and B lymphocytes. By integrating multi-way contacts with chromatin accessibility, gene expression, and transcription factor binding, we introduce a data-driven method to identify cell type-specific transcription clusters. We provide transcription factor-mediated functional building blocks for cell identity that serve as a global signature for cell types.
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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 OpenQuestion graph.