Please use this identifier to cite or link to this item:
http://hdl.handle.net/1942/22562
Title: | 3D-GNOME: an integrated web service for structural modeling of the 3D genome | Authors: | SZALAJ, Przemek Michalski, Paul J. Wroblewski, Przemyslaw Tang, Zhonghui Kadlof, Michal Mazzocco, Giovanni Ruan, Yijun Plewczynski, Dariusz |
Issue Date: | 2016 | Publisher: | OXFORD UNIV PRESS | Source: | NUCLEIC ACIDS RESEARCH, 44(W1), p. W288-W293 | Abstract: | Recent advances in high-throughput chromosome conformation capture (3C) technology, such as HiC and ChIA-PET, have demonstrated the importance of 3D genome organization in development, cell differentiation and transcriptional regulation. There is now a widespread need for computational tools to generate and analyze 3D structural models from 3C data. Here we introduce our 3D GeNOme Modeling Engine (3D-GNOME), a web service which generates 3D structures from 3C data and provides tools to visually inspect and annotate the resulting structures, in addition to a variety of statistical plots and heatmaps which characterize the selected genomic region. Users submit a bedpe (paired-end BED format) file containing the locations and strengths of long range contact points, and 3D-GNOME simulates the structure and provides a convenient user interface for further analysis. Alternatively, a user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specifying a genomic region of interest. 3D-GNOME is freely available at http://3dgnome.cent.uw.edu.pl/. | Notes: | [Szalaj, Przemyslaw; Wroblewski, Przemyslaw; Kadlof, Michal; Mazzocco, Giovanni; Plewczynski, Dariusz] Univ Warsaw, Ctr New Technol, PL-02097 Warsaw, Poland. [Szalaj, Przemyslaw; Plewczynski, Dariusz] Med Univ Bialystok, Ctr Bioinformat & Data Anal, PL-15089 Bialystok, Poland. [Szalaj, Przemyslaw] Hasselt Univ, I BioStat, B-3500 Hasselt, Belgium. [Michalski, Paul J.; Tang, Zhonghui; Ruan, Yijun] Jackson Lab Genom Med, Farmington, CT 06032 USA. [Ruan, Yijun] UConn Hlth, Dept Genet & Genome Sci, Farmington, CT 06030 USA. [Plewczynski, Dariusz] Med Univ Warsaw, Fac Pharm, PL-02097 Warsaw, Poland. | Document URI: | http://hdl.handle.net/1942/22562 | ISSN: | 0305-1048 | e-ISSN: | 1362-4962 | DOI: | 10.1093/nar/gkw437 | ISI #: | 000379786800048 | Rights: | © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com | Category: | A1 | Type: | Journal Contribution | Validations: | ecoom 2017 |
Appears in Collections: | Research publications |
Files in This Item:
File | Description | Size | Format | |
---|---|---|---|---|
szalaj 1.pdf | Published version | 1.76 MB | Adobe PDF | View/Open |
SCOPUSTM
Citations
18
checked on Sep 2, 2020
WEB OF SCIENCETM
Citations
25
checked on Oct 18, 2024
Page view(s)
48
checked on Sep 7, 2022
Download(s)
104
checked on Sep 7, 2022
Google ScholarTM
Check
Altmetric
Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.