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In this work, we describe an improved version of our integrated web service for structural modeling of three-dimensional genome (3D-GNOME), which now incorporates all types of SVs to model changes to the reference 3D conformation of chromatin. In 3D-GNOME 2.0, the default reference 3D genome structure is generated using ChIA-PET data from the GM12878 cell line and SVs data are sourced from the population-scale catalogue of SVs identified by the 1000 Genomes Consortium. However, users may also submit their own structural data to set a customized reference genome structure, and\/or a custom input list of SVs. 3D-GNOME 2.0 provides novel tools to inspect, visualize and compare 3D models for regions that differ in terms of their linear genomic sequence. Contact diagrams are displayed to compare the reference 3D structure with the one altered by SVs. In our opinion, 3D-GNOME 2.0 is a unique online tool for modeling and analyzing conformational changes to the human genome induced by SVs across populations. It can be freely accessed at https:\/\/3dgnome.cent.uw.edu.pl\/.<\/jats:p>","DOI":"10.1093\/nar\/gkaa388","type":"journal-article","created":{"date-parts":[[2020,5,5]],"date-time":"2020-05-05T19:12:36Z","timestamp":1588705956000},"page":"W170-W176","source":"Crossref","is-referenced-by-count":22,"title":["3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome"],"prefix":"10.1093","volume":"48","author":[{"given":"Michal","family":"Wlasnowolski","sequence":"first","affiliation":[{"name":"Centre of New Technologies, University of Warsaw, Warsaw\u00a002-097, Poland"},{"name":"Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw\u00a000-662, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michal","family":"Sadowski","sequence":"first","affiliation":[{"name":"Centre of New Technologies, University of Warsaw, Warsaw\u00a002-097, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tymon","family":"Czarnota","sequence":"first","affiliation":[{"name":"Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw\u00a000-662, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karolina","family":"Jodkowska","sequence":"first","affiliation":[{"name":"Centre of New Technologies, University of Warsaw, Warsaw\u00a002-097, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Przemyslaw","family":"Szalaj","sequence":"first","affiliation":[{"name":"Centre of New Technologies, University of Warsaw, Warsaw\u00a002-097, Poland"},{"name":"Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok\u00a015-089, Poland"},{"name":"I-BioStat, Hasselt University, 3500 Hasselt, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhonghui","family":"Tang","sequence":"first","affiliation":[{"name":"The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3840-7610","authenticated-orcid":false,"given":"Yijun","family":"Ruan","sequence":"first","affiliation":[{"name":"The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA"},{"name":"Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030-6403, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dariusz","family":"Plewczynski","sequence":"first","affiliation":[{"name":"Centre of New Technologies, University of Warsaw, Warsaw\u00a002-097, Poland"},{"name":"Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw\u00a000-662, Poland"},{"name":"The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,5,22]]},"reference":[{"key":"2020062614044063800_B1","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1038\/s41576-018-0007-0","article-title":"Structural variation in the 3D genome","volume":"19","author":"Spielmann","year":"2018","journal-title":"Nat. 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