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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
Citation: 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.
URI: http://hdl.handle.net/1942/22562
DOI: 10.1093/nar/gkw437
ISI #: 000379786800048
ISSN: 0305-1048
Category: A1
Type: Journal Contribution
Validation: ecoom, 2017
Appears in Collections: Research publications

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