ReviewGenome biology2017
Software tools for visualizing Hi-C data.
Review in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 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
36 citing papers in PubMed.
- Replication timing uncovers a two-compartment nuclear architecture of interphase euchromatin.The Plant cell · 2026Article
- A high-quality Chromosome-level reference genome assembly of white-lipped deer (Przewalskium albirostris).Scientific data · 2025Article
- Mapping the 3D genome architecture.Computational and structural biotechnology journal · 2025Review
- ppHiC: Interactive exploration of Hi-C results on the ProteinPaint web portal.Computational and structural biotechnology journal · 2024Article
- Smoother: on-the-fly processing of interactome data using prefix sums.Nucleic acids research · 2024Article
- Visualization and data exploration of chromosome conformation capture data using Voronoi diagrams with v3c-viz.Scientific reports · 2023Article
- 3D models of fungal chromosomes to enhance visual integration of omics data.NAR genomics and bioinformatics · 2023Article
- Case Report: Decrypting an interchromosomal insertion associated with Marfan's syndrome: how optical genome mapping emphasizes the morbid burden of copy-neutral variants.Frontiers in genetics · 2023Article
- Ten simple rules for developing visualization tools in genomics.PLoS computational biology · 2022Article
- Acetylated HOXB13 Regulated Super Enhancer Genes Define Therapeutic Vulnerabilities of Castration-Resistant Prostate Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2022Article
- Review
- An improved ovine reference genome assembly to facilitate in-depth functional annotation of the sheep genome.GigaScience · 2022Article
- Methods for the Differential Analysis of Hi-C Data.Methods in molecular biology (Clifton, N.J.) · 2022Article
- 3D genome organization links non-coding disease-associated variants to genes.Frontiers in cell and developmental biology · 2022Review
- Productive visualization of high-throughput sequencing data using the SeqCode open portable platform.Scientific reports · 2021Article
- FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data.Genome biology · 2020Article
- SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering.BMC bioinformatics · 2020Article
- Mechanisms of tissue and cell-type specificity in heritable traits and diseases.Nature reviews. Genetics · 2020Review
- DNA Rchitect: an R based visualizer for network analysis of chromatin interaction data.Bioinformatics (Oxford, England) · 2020Article
- Computational Oncology in the Multi-Omics Era: State of the Art.Frontiers in oncology · 2020Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
High-throughput assays for measuring the three-dimensional (3D) configuration of DNA have provided unprecedented insights into the relationship between DNA 3D configuration and function. Data interpretation from assays such as ChIA-PET and Hi-C is challenging because the data is large and cannot be easily rendered using standard genome browsers. An effective Hi-C visualization tool must provide several visualization modes and be capable of viewing the data in conjunction with existing, complementary data. We review five software tools that do not require programming expertise. We summarize their complementary functionalities, and highlight which tool is best equipped for specific tasks.
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.