Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/32865
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dc.contributor.authorWlasnowolski, Michal-
dc.contributor.authorSadowski, Michal-
dc.contributor.authorCzarnota, Tymon-
dc.contributor.authorJodkowska, Karolina-
dc.contributor.authorSZALAJ, Przemek-
dc.contributor.authorTang, Zhonghui-
dc.contributor.authorRuan, Yijun-
dc.contributor.authorPlewczynski, Dariusz-
dc.date.accessioned2020-12-10T14:38:02Z-
dc.date.available2020-12-10T14:38:02Z-
dc.date.issued2020-
dc.date.submitted2020-11-12T12:46:13Z-
dc.identifier.citationNUCLEIC ACIDS RESEARCH, 48 (W1) , p. W170 -W176-
dc.identifier.urihttp://hdl.handle.net/1942/32865-
dc.description.abstractStructural variants (SVs) that alter DNA sequence emerge as a driving force involved in the reorganisation of DNA spatial folding, thus affecting gene transcription. 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/.-
dc.description.sponsorshipPolish National Science Centre [2014/15/B/ST6/05082]; Foundation for Polish Science co-financed by the European Union under the European Regional Development Fund (TEAM to D.P.); 'Nucleome Positioning System for Spatiotemporal Genome Organization and Regulation' within the 4DNucleome National Institute of Health program, and by the European Commission as European Cooperation in Science and Technology COST actions: CA18127 'International Nucleome Consortium' (INC) [1U54DK107967-01]; 'Impact of Nuclear Domains On Gene Expression and Plant Traits' [CA16212]; Horizon 2020 Marie Sklodowska-Curie ITN Enhpathy grant 'Molecular Basis of Human enhanceropathies'; D.P. and M.W. were supported by the RENOIR Project from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie [691152]; Ministry of Science and Higher Education (Poland) [W34/H2020/2016, 329025/PnH/2016]. Funding for open access charge: Foundation for Polish Science co-financed by the European Union under the European Regional Development Fund (TEAM to DP). ACKNOWLEDGEMENTS We thank Veronika Mancikova for language editing and proofreading of the manuscript and Agnieszka Bucka and Agnes Alcantara Paculdar for critical reading of the text.-
dc.language.isoen-
dc.publisherOXFORD UNIV PRESS-
dc.rightsThe Author(s) 2020. 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 Non-Commercial 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-
dc.title3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome-
dc.typeJournal Contribution-
dc.identifier.epageW176-
dc.identifier.issueW1-
dc.identifier.spageW170-
dc.identifier.volume48-
local.format.pages7-
local.bibliographicCitation.jcatA1-
dc.description.notesPlewczynski, D (corresponding author), Univ Warsaw, Ctr New Technol, PL-02097 Warsaw, Poland.; Plewczynski, D (corresponding author), Warsaw Univ Technol, Fac Math & Informat Sci, PL-00662 Warsaw, Poland.; Plewczynski, D (corresponding author), Jackson Lab Genom Med, Farmington, CT 06032 USA.-
dc.description.notesd.plewczynski@cent.uw.edu.pl-
dc.description.otherPlewczynski, D (corresponding author), Univ Warsaw, Ctr New Technol, PL-02097 Warsaw, Poland ; Warsaw Univ Technol, Fac Math & Informat Sci, PL-00662 Warsaw, Poland ; Jackson Lab Genom Med, Farmington, CT 06032 USA. d.plewczynski@cent.uw.edu.pl-
local.publisher.placeGREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND-
local.type.refereedRefereed-
local.type.specifiedArticle-
dc.identifier.doi10.1093/nar/gkaa388-
dc.identifier.isiWOS:000562474100026-
dc.contributor.orcidPlewczynski, Dariusz/0000-0002-3840-7610-
dc.identifier.eissn-
dc.identifier.eissn1362-4962-
local.provider.typewosris-
local.uhasselt.uhpubyes-
local.description.affiliation[Wlasnowolski, Michal; Sadowski, Michal; Jodkowska, Karolina; Szalaj, Przemyslaw; Plewczynski, Dariusz] Univ Warsaw, Ctr New Technol, PL-02097 Warsaw, Poland.-
local.description.affiliation[Wlasnowolski, Michal; Czarnota, Tymon; Plewczynski, Dariusz] Warsaw Univ Technol, Fac Math & Informat Sci, PL-00662 Warsaw, Poland.-
local.description.affiliation[Szalaj, Przemyslaw] Med Univ Bialystok, Ctr Bioinformat & Data Anal, PL-15089 Bialystok, Poland.-
local.description.affiliation[Szalaj, Przemyslaw] Hasselt Univ, I BioStat, B-3500 Hasselt, Belgium.-
local.description.affiliation[Tang, Zhonghui; Ruan, Yijun; Plewczynski, Dariusz] Jackson Lab Genom Med, Farmington, CT 06032 USA.-
local.description.affiliation[Ruan, Yijun] UConn Hlth, Dept Genet & Genome Sci, Farmington, CT 06030 USA.-
local.uhasselt.internationalyes-
item.contributorWlasnowolski, Michal-
item.contributorSadowski, Michal-
item.contributorCzarnota, Tymon-
item.contributorJodkowska, Karolina-
item.contributorSZALAJ, Przemek-
item.contributorTang, Zhonghui-
item.contributorRuan, Yijun-
item.contributorPlewczynski, Dariusz-
item.accessRightsOpen Access-
item.fullcitationWlasnowolski, Michal; Sadowski, Michal; Czarnota, Tymon; Jodkowska, Karolina; SZALAJ, Przemek; Tang, Zhonghui; Ruan, Yijun & Plewczynski, Dariusz (2020) 3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome. In: NUCLEIC ACIDS RESEARCH, 48 (W1) , p. W170 -W176.-
item.validationecoom 2021-
item.fulltextWith Fulltext-
crisitem.journal.issn0305-1048-
crisitem.journal.eissn1362-4962-
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