ArticleGenome biology2020
HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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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
25 citing papers in PubMed.
- A generalizable Hi-C foundation model for chromatin architecture, single-cell and multiomics analysis across species.Nature methods · 2026Article
- Annotating Interchromosomal Interactions at Sub-Megabase Resolution Using Network Clustering Coefficients.bioRxiv : the preprint server for biology · 2026Article
- BacPhase: Long-insert paired-end sequencing for bin marker construction and genome phasing.aBIOTECH · 2026Article
- Transcribing RNA polymerases: Dynamics of twin supercoiled domains.Biophysical journal · 2024Article
- ARGV: 3D genome structure exploration using augmented reality.BMC bioinformatics · 2024Article
- Enhancing Hi-C contact matrices for loop detection with Capricorn: a multiview diffusion model.Bioinformatics (Oxford, England) · 2024Article
- Matrin3 mediates differentiation through stabilizing chromatin loop-domain interactions and YY1 mediated enhancer-promoter interactions.Nature communications · 2024Article
- The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data.Briefings in bioinformatics · 2023Review
- Reference panel-guided super-resolution inference of Hi-C data.Bioinformatics (Oxford, England) · 2023Article
- 3D genomic organization in cancers.Quantitative biology (Beijing, China) · 2023Review
- Article
- Posterior inference of Hi-C contact frequency through sampling.Frontiers in bioinformatics · 2023Article
- HiC-GNN: A generalizable model for 3D chromosome reconstruction using graph convolutional neural networks.Computational and structural biotechnology journal · 2023Article
- Reference panel guided topological structure annotation of Hi-C data.Nature communications · 2022Article
- 3D chromatin remodeling potentiates transcriptional programs driving cell invasion.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Advances in profiling chromatin architecture shed light on the regulatory dynamics underlying brain disorders.Seminars in cell & developmental biology · 2022Review
- Mapping nucleosome and chromatin architectures: A survey of computational methods.Computational and structural biotechnology journal · 2022Review
- HiCORE: Hi-C Analysis for Identification of Core Chromatin Looping Regions with Higher Resolution.Molecules and cells · 2021Article
- Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture.Nature communications · 2021Article
- Computational methods for the prediction of chromatin interaction and organization using sequence and epigenomic profiles.Briefings in bioinformatics · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Hi-C is a popular technique to map three-dimensional chromosome conformation. In principle, Hi-C's resolution is only limited by the size of restriction fragments. However, insufficient sequencing depth forces researchers to artificially reduce the resolution of Hi-C matrices at a loss of biological interpretability. We present the Hi-C Interaction Frequency Inference (HIFI) algorithms that accurately estimate restriction-fragment resolution Hi-C matrices by exploiting dependencies between neighboring fragments. Cross-validation experiments and comparisons to 5C data and known regulatory interactions demonstrate HIFI's superiority to existing approaches. In addition, HIFI's restriction-fragment resolution reveals a new role for active regulatory regions in structuring topologically associating domains.
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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.