title: 3D-GNOME: an integrated web service for structural modeling of the 3D genome.
abstract: Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C 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/.
authors.affiliation: Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland Center for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-089 Bialystok, Poland I-BioStat, Hasselt University, 3500 Hasselt, Belgium przemek.szalaj@uhasselt.be.
authors.forename: Przemyslaw
authors.initials: P
authors.lastname: Szalaj
authors.affiliation: The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA Paul.Michalski@jax.org.
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Michalski
authors.affiliation: Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland.
authors.forename: Przemysław
authors.initials: P
authors.lastname: Wróblewski
authors.affiliation: The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
authors.forename: Zhonghui
authors.initials: Z
authors.lastname: Tang
authors.affiliation: Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland.
authors.forename: Michal
authors.initials: M
authors.lastname: Kadlof
authors.affiliation: Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Mazzocco
authors.affiliation: The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030-6403, USA.
authors.forename: Yijun
authors.initials: Y
authors.lastname: Ruan
authors.affiliation: Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland Center for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-089 Bialystok, Poland Faculty of Pharmacy, Medical University of Warsaw, 02-097 Warsaw, Poland d.plewczynski@cent.uw.edu.pl.
authors.forename: Dariusz
authors.initials: D
authors.lastname: Plewczynski
mesh_terms: D002461:Cell Line, Transformed; D002875:Chromosomes; D003196:Computer Graphics; D003198:Computer Simulation; D015894:Genome, Human; D006801:Humans; D021621:Imaging, Three-Dimensional / Q000379:methods*; D016247:Information Storage and Retrieval; D020407:Internet; D008214:Lymphocytes / Q000378:metabolism / Q000473:pathology; D008954:Models, Biological; D014584:User-Computer Interface