ArticleNucleic acids research2017
Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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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.
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Who cites it
19 citing papers in PubMed.
- Understanding the physical processes behind DNA-DNA proximity ligation assays.Research square · 2025Article
- Understanding the physical processes behind DNA-DNA proximity ligation assays.bioRxiv : the preprint server for biology · 2025Article
- Sir2 is required for the quiescence-specific condensed three-dimensional chromatin structure of rDNA.bioRxiv : the preprint server for biology · 2024Article
- Recapitulation of patient-specific 3D chromatin conformation using machine learning.Cell reports methods · 2023Article
- Mapping the semi-nested community structure of 3D chromosome contact networks.PLoS computational biology · 2023Article
- 3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma.Nature communications · 2023Article
- Topological screen identifies hundreds of Cp190- and CTCF-dependentScience advances · 2023Article
- HiCmapTools: a tool to access HiC contact maps.BMC bioinformatics · 2022Article
- CoolBox: a flexible toolkit for visual analysis of genomics data.BMC bioinformatics · 2021Article
- EnHiC: learning fine-resolution Hi-C contact maps using a generative adversarial framework.Bioinformatics (Oxford, England) · 2021Article
- Molecular and computational approaches to map regulatory elements in 3D chromatin structure.Epigenetics & chromatin · 2021Review
- HCMB: A stable and efficient algorithm for processing the normalization of highly sparse Hi-C contact data.Computational and structural biotechnology journal · 2021Article
- LncRNA ROR1‑AS1 high expression and its prognostic significance in liver cancer.Oncology reports · 2020Article
- Cooler: scalable storage for Hi-C data and other genomically labeled arrays.Bioinformatics (Oxford, England) · 2020Article
- Highly interacting regions of the human genome are enriched with enhancers and bound by DNA repair proteins.Scientific reports · 2019Article
- Genomic 3D compartments emerge from unfolding mitotic chromosomes.Chromosoma · 2019Article
- Hi-C analysis: from data generation to integration.Biophysical reviews · 2019Review
- Histone supply: Multitiered regulation ensures chromatin dynamics throughout the cell cycle.The Journal of cell biology · 2019Review
- HiGlass: web-based visual exploration and analysis of genome interaction maps.Genome biology · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hi-C experiments generate data in form of large genome contact maps (Hi-C maps). These show that chromosomes are arranged in a hierarchy of three-dimensional compartments. But to understand how these compartments form and by how much they affect genetic processes such as gene regulation, biologists and bioinformaticians need efficient tools to visualize and analyze Hi-C data. However, this is technically challenging because these maps are big. In this paper, we remedied this problem, partly by implementing an efficient file format and developed the genome contact map explorer platform. Apart from tools to process Hi-C data, such as normalization methods and a programmable interface, we made a graphical interface that let users browse, scroll and zoom Hi-C maps to visually search for patterns in the Hi-C data. In the software, it is also possible to browse several maps simultaneously and plot related genomic data. The software is openly accessible to the scientific community.
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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.