Student or educator? Sign up with your school email and get 6 months of Pro free.
CoChat
Sign Up
Cited by 2,453

The DOI matches its Crossref record; 19 of the 19 references it cites were found in a registry or an index.

HiGlass: web-based visual exploration and analysis of genome interaction maps

Open access
Kerpedjiev, Peter, Abdennur, Nezar, Lekschas, Fritz, McCallum, Chuck, Dinkla, Kasper, Strobelt, Hendrik, Luber, Jacob M., Ouellette, Scott B., Azhir, Alaleh, Kumar, Nikhil, Hwang, Jeewon, Lee, Soohyun, Alver, Burak H., Pfister, Hanspeter, Mirny, Leonid A., Park, Peter J., Gehlenborg, Nils·2018·Genome Biology
DOI 10.1186/s13059-018-1486-1

Published version of a preprint

Open this paper in CoChat — free account

Abstract

We present HiGlass, an open source visualization tool built on web technologies that provides a rich interface for rapid, multiplex, and multiscale navigation of 2D genomic maps alongside 1D genomic tracks, allowing users to combine various data types, synchronize multiple visualization modalities, and share fully customizable views with others. We demonstrate its utility in exploring different experimental conditions, comparing the results of analyses, and creating interactive snapshots to share with collaborators and the broader public. HiGlass is accessible online at http://higlass.io and is also available as a containerized application that can be run on any platform.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1186/s13059-018-1486-1

Cites

19 of 19 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Show all 19 references

Research works printed but not linked: 31

  1. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326:289–93. · DOI · Paper page
  2. Rao SSP, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. Elsevier. 2014;159:1665–80.
  3. Seaman L, Chen H, Brown M, Wangsa D, Patterson G, Camps J, et al. Nucleome analysis reveals structure-function relationships for colon cancer. Mol Cancer Res. 2017. Available from: https://doi.org/10.1158/1541-7786.MCR-16-0374 · DOI
  4. Forcato M, Nicoletti C, Pal K, Livi CM, Ferrari F, Bicciato S. Comparison of computational methods for Hi-C data analysis. Nat Methods. 2017;14:679–85. · DOI · Paper page
  5. Gibcus JH, Samejima K, Goloborodko A, Samejima I, Naumova N, Kanemaki M, et al. A pathway for mitotic chromosome formation. Science. 2018;359.6376:eaao6135. · DOI · Paper page
  6. Durand NC, Robinson JT, Shamim MS, Machol I, Mesirov JP, Lander ES, et al. Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Cell Syst. 2016;3:99–101. · DOI · Paper page
  7. Lajoie BR, Dekker J, Kaplan N. The Hitchhiker’s guide to Hi-C analysis: practical guidelines. Methods. 2015;72:65–75. · DOI · Paper page
  8. Ay F, Noble WS. Analysis methods for studying the 3D architecture of the genome. Genome Biol. 2015;16:183. · DOI · Paper page
  9. Gehlenborg N, O’Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, et al. Visualization of omics data for systems biology. Nat Methods. 2010;7:S56–68. · DOI · Paper page
  10. Nielsen CB, Cantor M, Dubchak I, Gordon D, Wang T. Visualizing genomes: techniques and challenges. Nat Methods. 2010;7:S5–15. · DOI · Paper page
  11. Wang Y, Zhang B, Zhang L, An L, Xu J, Li D, et al. The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions. bioRxiv. 2017:112268. Available from: http://biorxiv.org/content/early/2017/02/27/112268 . Accessed 2 Mar 2017. · DOI
  12. Zhou X, Lowdon RF, Li D, Lawson HA, Madden PAF, Costello JF, et al. Exploring long-range genome interactions using the WashU Epigenome Browser. Nat Methods. 2013;10:375–6. · DOI · Paper page
  13. Akdemir KC, Chin L. HiCPlotter integrates genomic data with interaction matrices. Genome Biol. 2015;16:198. · DOI · Paper page
  14. Yardımcı GG, Noble WS. Software tools for visualizing Hi-C data. Genome Biol. 2017;18:26. · DOI
  15. Martin JS, Xu Z, Reiner AP, Mohlke KL, Sullivan P, Ren B, et al. HUGIn: Hi-C unifying genomic interrogator. Bioinformatics. 2017;33:3793–5. · DOI
  16. Calandrelli R, Wu Q, Guan J, Zhong S. GITAR: an open source tool for analysis and visualization of Hi-C data. bioRxiv. 2018:259515. Available from: https://www.biorxiv.org/content/early/2018/05/08/259515 . Accessed 24 May 2018.
  17. Kumar R, Sobhy H, Stenberg P, Lizana L. Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps. Nucleic Acids Res. 2017; Available from: https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx644 . Accessed 29 Aug 2017. · DOI
  18. Cockburn A, Karlson A, Bederson BB. A review of overview+detail, zooming, and focus+context interfaces. ACM Comput Surv. 2009;41:2:1–2:31. · DOI · Paper page
  19. Lekschas F, Bach B, Kerpedjiev P, Gehlenborg N, Pfister H. HiPiler: visual exploration of large genome interaction matrices with interactive small multiples. IEEE Trans Vis Comput Graph. 2017. Available from: https://doi.org/10.1109/TVCG.2017.2745978 · DOI
  20. Fudenberg G, Abdennur N, Imakaev M, Goloborodko A, Mirny LA. Emerging evidence of chromosome folding by loop extrusion. Cold Spring Harb Symp Quant Biol. 2018. Available from: https://doi.org/10.1101/sqb.2017.82.034710 · DOI · Paper page
  21. Lévy-Leduc C, Delattre M, Mary-Huard T, Robin S. Two-dimensional segmentation for analyzing Hi-C data. Bioinformatics. 2014;30:i386–92. · DOI
  22. Crane E, Bian Q, McCord RP, Lajoie BR, Wheeler BS, Ralston EJ, et al. Condensin-driven remodelling of X chromosome topology during dosage compensation. Nature. 2015;523:240–4. · DOI · Paper page
  23. Serra F, Baù D, Filion G, Marti-Renom MA. Structural features of the fly chromatin colors revealed by automatic three-dimensional modeling. bioRxiv. 2016:036764. Available from: https://www.biorxiv.org/content/early/2016/01/15/036764 . Accessed 26 Oct 2017. · DOI
  24. Weinreb C, Raphael BJ. Identification of hierarchical chromatin domains. Bioinformatics. 2016;32:1601–9. · DOI
  25. Filippova D, Patro R, Duggal G, Kingsford C. Identification of alternative topological domains in chromatin. Algorithms Mol Biol. 2014;9:14. · DOI · Paper page
  26. Gratzl S, Lex A, Gehlenborg N, Cosgrove N, Streit M. From visual exploration to storytelling and back again. Comput Graph Forum. 2016;35:491–500. · DOI
  27. Robinson JT, Turner D, Durand NC, Thorvaldsdóttir H, Mesirov JP, Aiden EL. Juicebox.js provides a cloud-based visualization system for Hi-C data. Cell Syst. 2018;6:256–8. e1. · DOI · Paper page
  28. Schwarzer W, Abdennur N, Goloborodko A, Pekowska A, Fudenberg G, Loe-Mie Y, et al. Two independent modes of chromatin organization revealed by cohesin removal. Nature. 2017;551:51–6. · DOI
  29. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29:24–6. · DOI · Paper page
  30. Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 2010;26:2204–7. · DOI · Paper page
  31. Liu Z, Heer J. The effects of interactive latency on exploratory visual analysis. IEEE Trans Vis Comput Graph. 2014;20:2122–31. · DOI · Paper page

Cited by

See all 2,453

Metadata

Authors
Kerpedjiev, P., Abdennur, N., Lekschas, F., McCallum, C., Dinkla, K., Strobelt, H., Luber, J. M., Ouellette, S. B., Azhir, A., Kumar, N., Hwang, J., Lee, S., Alver, B. H., Pfister, H., Mirny, L. A., Park, P. J., & Gehlenborg, N.
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2018-08-24
Volume
19
Issue
1
Pages
125-125
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
DOI
10.1186/s13059-018-1486-1
OpenAlex
W2888425844
Cited by
2,453
References
19
FWCI
15.30
Type
journal article
Language
en
Open access
gold
Licence
creativecommons.org/licenses/by/4.0/ (tdm)
Funders
  • National Human Genome Research Institute (R00 HG007583, U54 HG007963)
  • National Cancer Institute (U01 CA200059)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

How to cite

Cite CoChat for the checks on this page, and the paper for its own findings.

This page
CoChat. (2026). Citation check: HiGlass: web-based visual exploration and analysis of genome interaction maps. https://app.cochat.ai/papers/10.1186/s13059-018-1486-1
The paper
Kerpedjiev, P., Abdennur, N., Lekschas, F., McCallum, C., Dinkla, K., Strobelt, H., Luber, J. M., Ouellette, S. B., Azhir, A., Kumar, N., Hwang, J., Lee, S., Alver, B. H., Pfister, H., Mirny, L. A., Park, P. J., & Gehlenborg, N. (2018). HiGlass: web-based visual exploration and analysis of genome interaction maps. Genome Biology. https://doi.org/10.1186/s13059-018-1486-1

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.