ArticleNucleic acids research2022
HiCRes: a computational method to estimate and predict the genomic resolution of Hi-C libraries.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Enhanced chromatin compaction is associated with de novo expression of a nuclear microprotein, global loss of H3 acetylation and local transcriptional changes in retinal rod photoreceptors.Research square · 2026Article
- How human-derived brain organoids are built differently from brain organoids derived from genetically-close relatives: a multi-scale hypothesis.Soft matter · 2026Article
- Elucidating photoreceptor gene function with in-vivo CRISPR knock-out perturbation assay.Research square · 2025Article
- Topologically associating domains and the evolution of three-dimensional genome architecture in rice.The Plant journal : for cell and molecular biology · 2025Article
- Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon.Cell genomics · 2025Article
- Integrating Single-Molecule Sequencing and Deep Learning to Predict Haplotype-Specific 3D Chromatin Organization in a Mendelian Condition.bioRxiv : the preprint server for biology · 2025Article
- CWL-Based Analysis Pipeline for Hi-C Data: From FASTQ Files to Matrices.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Mapping the 3D genome architecture.Computational and structural biotechnology journal · 2025Review
- Epigenomic and 3D genomic mapping reveals developmental dynamics and subgenomic asymmetry of transcriptional regulatory architecture in allotetraploid cotton.Nature communications · 2024Article
- Single cell variant to enhancer to gene map for coronary artery disease.medRxiv : the preprint server for health sciences · 2024Article
- Crosslinking intensity modulates the reliability and sensitivity of chromatin conformation detection at different structural levels.Communications biology · 2024Article
- Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon.bioRxiv : the preprint server for biology · 2024Article
- Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers.Epigenetics & chromatin · 2024Article
- A commoneLife · 2024Article
- Stage-specific dynamic reorganization of genome topology shapes transcriptional neighborhoods in developing human retinal organoids.Cell reports · 2023Article
- TAD evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function.Nature communications · 2023Article
- High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon.BMC plant biology · 2023Article
- Three amphioxus reference genomes reveal gene and chromosome evolution of chordates.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- High-resolution genome topology of human retina uncovers super enhancer-promoter interactions at tissue-specific and multifactorial disease loci.Nature communications · 2022Article
- Nucleome programming is required for the foundation of totipotency in mammalian germline development.The EMBO journal · 2022Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Three-dimensional (3D) conformation of the chromatin is crucial to stringently regulate gene expression patterns and DNA replication in a cell-type specific manner. Hi-C is a key technique for measuring 3D chromatin interactions genome wide. Estimating and predicting the resolution of a library is an essential step in any Hi-C experimental design. Here, we present the mathematical concepts to estimate the resolution of a dataset and predict whether deeper sequencing would enhance the resolution. We have developed HiCRes, a docker pipeline, by applying these concepts to several Hi-C libraries.
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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 Socratic graph.