ArticleNature communications2016
Constructing 3D interaction maps from 1D epigenomes.
Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 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
90 citing papers in PubMed, 179 citations in OpenAlex.
- GraphLooper: predicting chromatin loops based on hierarchical multi-view graph pooling method.Briefings in bioinformatics · 2026Article
- Prenatal and postnatal effects of gestational immune activation on synaptic and neurodevelopmental pathways via epigenetic mechanisms.Translational psychiatry · 2026Article
- Techniques to detect physical interactions between genomic regions.Epigenomics · 2025Review
- Foxo1 regulates intestinal tissue-resident memory CD8 T cell biology in an anatomic compartment- and context-specific manner.Science immunology · 2025Article
- Comprehensive multimodal and multiomic profiling reveals epigenetic and transcriptional reprogramming in lung tumors.Communications biology · 2025Article
- Machine and Deep Learning Methods for Predicting 3D Genome Organization.Methods in molecular biology (Clifton, N.J.) · 2025Review
- GATv2EPI: Predicting Enhancer-Promoter Interactions with a Dynamic Graph Attention Network.Genes · 2024Article
- Differential impact of quiescent non-coding loci on chromatin entropy.Nucleic acids research · 2024Article
- The structure is the message: Preserving experimental context through tensor decomposition.Cell systems · 2024Review
- Non-Coding RNAs Extended Omnigenic Module of Cancers.Entropy (Basel, Switzerland) · 2024Article
- Joint-specific rheumatoid arthritis fibroblast-like synoviocyte regulation identified by integration of chromatin access and transcriptional activity.JCI insight · 2024Article
- Antipsychotic-induced epigenomic reorganization in frontal cortex of individuals with schizophrenia.eLife · 2024Article
- Article
- From bench to bedside via bytes: Multi-omic immunoprofiling and integration using machine learning and network approaches.Human vaccines & immunotherapeutics · 2023Review
- Recapitulation of patient-specific 3D chromatin conformation using machine learning.Cell reports methods · 2023Article
- An unsupervised deep learning framework for predicting human essential genes from population and functional genomic data.BMC bioinformatics · 2023Article
- Article
- Leveraging epigenomes and three-dimensional genome organization for interpreting regulatory variation.PLoS computational biology · 2023Article
- Computational methods for identifying enhancer-promoter interactions.Quantitative biology (Beijing, China) · 2023Review
- InferLoop: leveraging single-cell chromatin accessibility for the signal of chromatin loop.Briefings in bioinformatics · 2023Article
30 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 1 institution in 1 country.
Funding
Abstract
The human genome is tightly packaged into chromatin whose functional output depends on both one-dimensional (1D) local chromatin states and three-dimensional (3D) genome organization. Currently, chromatin modifications and 3D genome organization are measured by distinct assays. An emerging question is whether it is possible to deduce 3D interactions by integrative analysis of 1D epigenomic data and associate 3D contacts to functionality of the interacting loci. Here we present EpiTensor, an algorithm to identify 3D spatial associations within topologically associating domains (TADs) from 1D maps of histone modifications, chromatin accessibility and RNA-seq. We demonstrate that active promoter-promoter, promoter-enhancer and enhancer-enhancer associations identified by EpiTensor are highly concordant with those detected by Hi-C, ChIA-PET and eQTL analyses at 200 bp resolution. Moreover, EpiTensor has identified a set of interaction hotspots, characterized by higher chromatin and transcriptional activity as well as enriched TF and ncRNA binding across diverse cell types, which may be critical for stabilizing the local 3D interactions.
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What OpenQuestion 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 OpenQuestion graph.