ReviewBiophysical reviews2019
Hi-C analysis: from data generation to integration.
Review in Biophysical reviews, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 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
58 citing papers in PubMed, 110 citations in OpenAlex.
- CUT&RUN as a Powerful Tool for Chromatin Profiling: A Focus on Neuropsychiatric Disorders.Biological psychiatry · 2026Review
- Haplotype-resolved chromosomal-level genome assembly of Chrysaora achlyos (black sea nettle).Scientific data · 2026Article
- Real-Time and Spatially Resolved Epigenetic Dynamics Tracking Beyond DNA Methylation via Live-Cell Epigenetic Sensors in 3D Systems.Biosensors · 2026Review
- Chromosome-level genome assembly and Oligo-FISH confirmation of chromosome models for the Tasmanian snow skink Carinascincus ocellatus (Scincidae, Eugongylinae).BMC biology · 2025Article
- Loopsim: enrichment analysis of chromosome conformation capture with fast empirical distribution simulation.NAR genomics and bioinformatics · 2025Article
- HiC4D-SPOT: a spatiotemporal outlier detection tool for Hi-C data.Briefings in bioinformatics · 2025Article
- Review
- Leveraging Hi-C Data to Detect Chromosomal Reorganizations.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Genome Assembly, Polishing, and Analysis of the Chytrid Batrachochytrium salamandrivorans.Methods in molecular biology (Clifton, N.J.) · 2025Article
- An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes.Genome research · 2024Article
- Using paired-end read orientations to assess technical biases in capture Hi-C.NAR genomics and bioinformatics · 2024Article
- HiCDiff: single-cell Hi-C data denoising with diffusion models.Briefings in bioinformatics · 2024Article
- Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers.Epigenetics & chromatin · 2024Article
- Epigenetic programming of stochastic olfactory receptor choice.Genesis (New York, N.Y. : 2000) · 2024Review
- Reply to: Revisiting the use of structural similarity index in Hi-C.Nature genetics · 2023Article
- Contrasting new and available reference genomes to highlight uncertainties in assemblies and areas for future improvement: an example with monodontid species.BMC genomics · 2023Article
- The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data.Briefings in bioinformatics · 2023Review
- Spatial mapping of the DNA adducts in cancer.DNA repair · 2023Review
- Article
- ParticleChromo3D+: A Web Server for ParticleChromo3D Algorithm for 3D Chromosome Structure Reconstruction.Current issues in molecular biology · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
In the epigenetics field, large-scale functional genomics datasets of ever-increasing size and complexity have been produced using experimental techniques based on high-throughput sequencing. In particular, the study of the 3D organization of chromatin has raised increasing interest, thanks to the development of advanced experimental techniques. In this context, Hi-C has been widely adopted as a high-throughput method to measure pairwise contacts between virtually any pair of genomic loci, thus yielding unprecedented challenges for analyzing and handling the resulting complex datasets. In this review, we focus on the increasing complexity of available Hi-C datasets, which parallels the adoption of novel protocol variants. We also review the complexity of the multiple data analysis steps required to preprocess Hi-C sequencing reads and extract biologically meaningful information. Finally, we discuss solutions for handling and visualizing such large genomics datasets.
Indexed as
Identifiers
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.