ReviewNature methods2017
How best to identify chromosomal interactions: a comparison of approaches.
Review in Nature methods, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
91 citing papers in PubMed.
- Chromosomal inversions modulate 3D chromatin interactions and regulatory architecture inResearch square · 2026Article
- Dynamics and master transcription factors dependence of intestinal super-enhancers during differentiation and oncogenesis.Nucleic acids research · 2026Article
- Loop extrusion by cohesin plays a role in enhancer-activated gene expression early in differentiation.Nature communications · 2026Article
- GraphLooper: predicting chromatin loops based on hierarchical multi-view graph pooling method.Briefings in bioinformatics · 2026Article
- Differential analysis of image-based chromatin tracing data with Dory.bioRxiv : the preprint server for biology · 2026Article
- UniChrom: a universal deep learning architecture for cross-scale chromatin interaction prediction.BMC genomics · 2026Article
- Emerging insights into enhancer RNAs: biogenesis, function, mechanism, and disease implication.Briefings in bioinformatics · 2026Review
- Combination of 3D chromatin architecture and omics analysis provides insight into anthocyanin regulation inHorticulture research · 2025Article
- The role of multi-omics in biomarker discovery, diagnosis, prognosis, and therapeutic monitoring of tissue repair and regeneration processes.Journal of orthopaedic translation · 2025Review
- CTCF depletion decouples enhancer-mediated gene activation from chromatin hub formation.Nature structural & molecular biology · 2025Article
- Cardiac enhancers: Gateway to the regulatory mechanisms of heart regeneration.Seminars in cell & developmental biology · 2025Review
- Microscopy methods for the in vivo study of nanoscale nuclear organization.Biochemical Society transactions · 2025Review
- Functional associations of evolutionarily recent human genes exhibit sensitivity to the 3D genome landscape and disease.bioRxiv : the preprint server for biology · 2024Article
- Single-cell technologies meet Hi-C.Nature genetics · 2024Article
- BRCAness, DNA gaps, and gain and loss of PARP inhibitor-induced synthetic lethality.The Journal of clinical investigation · 2024Review
- Regulating epithelial-mesenchymal plasticity from 3D genome organization.Communications biology · 2024Review
- Removing unwanted variation between samples in Hi-C experiments.Briefings in bioinformatics · 2024Article
- MMCT-Loop: a mix model-based pipeline for calling targeted 3D chromatin loops.Nucleic acids research · 2024Article
- Ultrafine mapping of chromosome conformation at hundred basepair resolution reveals regulatory genome architecture.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Toward a comprehensive catalog of regulatory elements.Human genetics · 2023Review
31 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
4 authors.
Funding
Abstract
Chromosome conformation capture (3C) methods are central to understanding the link between nuclear structure and function, and the physical interactions between distal regulatory elements and promoters. However, no one method is appropriate to address all biological questions, as each variant differs markedly in resolution, reproducibility, throughput and biases. A thorough appreciation of the strengths and weaknesses of each technique is critical when choosing the correct method for a specific application or for gauging how best to interpret different sources of data. In addition, the analysis method must be carefully considered, as this choice can profoundly affect the output. In this Review, we describe and compare the different available 3C-based approaches, with a focus on the analysis of mammalian genomes.
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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.