{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T23:19:06Z","timestamp":1767914346704,"version":"3.49.0"},"reference-count":24,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,6,2]],"date-time":"2025-06-02T00:00:00Z","timestamp":1748822400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,6,2]],"date-time":"2025-06-02T00:00:00Z","timestamp":1748822400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/501100001459","name":"Ministry of Education - Singapore","doi-asserted-by":"publisher","award":["RT5\/22"],"award-info":[{"award-number":["RT5\/22"]}],"id":[{"id":"10.13039\/501100001459","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001459","name":"Ministry of Education - Singapore","doi-asserted-by":"publisher","award":["RT5\/22"],"award-info":[{"award-number":["RT5\/22"]}],"id":[{"id":"10.13039\/501100001459","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"DOI":"10.1186\/s12859-025-06176-3","type":"journal-article","created":{"date-parts":[[2025,6,2]],"date-time":"2025-06-02T15:58:57Z","timestamp":1748879937000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["MultiVis.js: a software tool for the visualization of multiway chromatin interactions and SPRITE data"],"prefix":"10.1186","volume":"26","author":[{"given":"Jes Hui Min","family":"Kwek","sequence":"first","affiliation":[]},{"given":"Melissa Jane","family":"Fullwood","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2025,6,2]]},"reference":[{"issue":"7","key":"6176_CR1","doi-asserted-by":"publisher","first-page":"1665","DOI":"10.1016\/j.cell.2014.11.021","volume":"159","author":"SSP Rao","year":"2014","unstructured":"Rao SSP, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014;159(7):1665\u201380. https:\/\/doi.org\/10.1016\/j.cell.2014.11.021.","journal-title":"Cell"},{"issue":"2","key":"6176_CR2","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1016\/j.tig.2018.11.007","volume":"35","author":"YX See","year":"2019","unstructured":"See YX, Wang BZ, Fullwood MJ. Chromatin interactions and regulatory elements in cancer: from bench to bedside. Trends Genet. 2019;35(2):145\u201358. https:\/\/doi.org\/10.1016\/j.tig.2018.11.007.","journal-title":"Trends Genet"},{"issue":"5950","key":"6176_CR3","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1126\/science.1181369","volume":"326","author":"E Lieberman-Aiden","year":"2009","unstructured":"Lieberman-Aiden E, van Berkum NL, Williams L, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326(5950):289\u201393. https:\/\/doi.org\/10.1126\/science.1181369.","journal-title":"Science"},{"issue":"7269","key":"6176_CR4","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1038\/nature08497","volume":"462","author":"MJ Fullwood","year":"2009","unstructured":"Fullwood MJ, Liu MH, Pan YF, et al. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature. 2009;462(7269):58\u201364. https:\/\/doi.org\/10.1038\/nature08497.","journal-title":"Nature"},{"issue":"1","key":"6176_CR5","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/0471142727.mb2115s89","volume":"21","author":"MJ Fullwood","year":"2010","unstructured":"Fullwood MJ, Han Y, Wei C-L, Ruan X, Ruan Y. Chromatin interaction analysis using paired-end tag sequencing. Curr Protoc Mol Biol. 2010;21(1):1\u201325. https:\/\/doi.org\/10.1002\/0471142727.mb2115s89.","journal-title":"Curr Protoc Mol Biol"},{"issue":"5","key":"6176_CR6","doi-asserted-by":"publisher","first-page":"1132","DOI":"10.1016\/j.cell.2011.10.023","volume":"147","author":"T Montavon","year":"2011","unstructured":"Montavon T, Soshnikova N, Mascrez B, Joye E, Thevenet L, Splinter E, et al. A regulatory archipelago controls Hox genes transcription in digits. Cell. 2011;147(5):1132\u201345. https:\/\/doi.org\/10.1016\/j.cell.2011.10.023.","journal-title":"Cell"},{"issue":"1\u20132","key":"6176_CR7","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1016\/j.cell.2011.12.014","volume":"148","author":"G Li","year":"2012","unstructured":"Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 2012;148(1\u20132):84\u201398. https:\/\/doi.org\/10.1016\/j.cell.2011.12.014.","journal-title":"Cell"},{"issue":"1","key":"6176_CR8","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-024-52375-6","volume":"15","author":"BS Perlman","year":"2024","unstructured":"Perlman BS, Burget N, Zhou Y, Schwartz GW, Petrovic J, Modrusan Z, et al. Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance. Nat Commun. 2024;15(1):1\u201321.","journal-title":"Nat Commun"},{"issue":"8","key":"6176_CR9","doi-asserted-by":"publisher","first-page":"1406","DOI":"10.1016\/j.molcel.2024.02.015","volume":"84","author":"D Lando","year":"2024","unstructured":"Lando D, Ma X, Cao Y, Jartseva A, Stevens TJ, Boucher W, et al. Enhancer-promoter interactions are reconfigured through the formation of long-range multiway hubs as mouse ES cells exit pluripotency. Mol Cell. 2024;84(8):1406-1421.e8. https:\/\/doi.org\/10.1016\/j.molcel.2024.02.015.","journal-title":"Mol Cell"},{"issue":"1","key":"6176_CR10","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1038\/s41587-021-00998-1","volume":"40","author":"MV Arrastia","year":"2022","unstructured":"Arrastia MV, Jachowicz JW, Ollikainen N, Curtis MS, Lai C, Quinodoz SA, et al. Single-cell measurement of higher-order 3D genome organization with scSPRITE. Nat Biotechnol. 2022;40(1):64\u201373.","journal-title":"Nat Biotechnol"},{"issue":"3","key":"6176_CR11","doi-asserted-by":"publisher","first-page":"744","DOI":"10.1016\/j.cell.2018.05.024","volume":"174","author":"SA Quinodoz","year":"2018","unstructured":"Quinodoz SA, Ollikainen N, Tabak B, Palla A, Schmidt JM, Detmar E, et al. Higher-order inter-chromosomal hubs shape 3D genome organization in the nucleus. Cell. 2018;174(3):744-757.e24. https:\/\/doi.org\/10.1016\/j.cell.2018.05.024.","journal-title":"Cell"},{"issue":"23","key":"6176_CR12","doi-asserted-by":"publisher","first-page":"5775","DOI":"10.1016\/j.cell.2021.10.014","volume":"184","author":"SA Quinodoz","year":"2021","unstructured":"Quinodoz SA, Jachowicz JW, Bhat P, Ollikainen N, Banerjee AK, Goronzy IN, et al. RNA promotes the formation of spatial compartments in the nucleus. Cell. 2021;184(23):5775-5790.e30. https:\/\/doi.org\/10.1016\/j.cell.2021.10.014.","journal-title":"Cell"},{"issue":"9","key":"6176_CR13","doi-asserted-by":"publisher","first-page":"111730","DOI":"10.1016\/j.celrep.2022.111730","volume":"41","author":"IN Goronzy","year":"2022","unstructured":"Goronzy IN, Quinodoz SA, Jachowicz JW, Ollikainen N, Bhat P, Guttman M. Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription. Cell Rep. 2022;41(9):111730. https:\/\/doi.org\/10.1016\/j.celrep.2022.111730.","journal-title":"Cell Rep"},{"issue":"31","key":"6176_CR14","doi-asserted-by":"publisher","first-page":"E4504","DOI":"10.1073\/pnas.1609643113","volume":"113","author":"EM Darrow","year":"2016","unstructured":"Darrow EM, Huntley MH, Dudchenko O, Stamenova EK, Durand NC, Sun Z, et al. Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture. Proc Natl Acad Sci USA. 2016;113(31):E4504\u201312. https:\/\/doi.org\/10.1073\/pnas.1609643113.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"1","key":"6176_CR15","doi-asserted-by":"publisher","first-page":"5498","DOI":"10.1038\/s41467-022-32980-z","volume":"13","author":"GA Dotson","year":"2022","unstructured":"Dotson GA, Chen C, Lindsly S, Cicalo A, Dilworth S, Ryan C, et al. Deciphering multi-way interactions in the human genome. Nat Commun. 2022;13(1):5498. https:\/\/doi.org\/10.1038\/s41467-022-32980-z.","journal-title":"Nat Commun"},{"key":"6176_CR16","doi-asserted-by":"publisher","first-page":"673530","DOI":"10.3389\/fgene.2021.673530","volume":"12","author":"S Animesh","year":"2021","unstructured":"Animesh S, Choudhary R, Wong BJH, Koh CTJ, Ng XY, Tay JKX, et al. Profiling of 3D genome organization in nasopharyngeal cancer needle biopsy patient samples by a modified Hi-C approach. Front Genet. 2021;12:673530. https:\/\/doi.org\/10.3389\/fgene.2021.673530.","journal-title":"Front Genet"},{"issue":"4","key":"6176_CR17","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1101\/gr.276313.121","volume":"32","author":"YX See","year":"2022","unstructured":"See YX, Chen K, Fullwood MJ. MYC overexpression leads to increased chromatin interactions at super-enhancers and MYC binding sites. Genome Res. 2022;32(4):629\u201342.","journal-title":"Genome Res"},{"issue":"12","key":"6176_CR18","doi-asserted-by":"publisher","first-page":"810","DOI":"10.1016\/j.trecan.2018.10.003","volume":"4","author":"O Lancho","year":"2018","unstructured":"Lancho O, Herranz D. The MYC enhancer-ome: Long-range transcriptional regulation of MYC in cancer. Trends Cancer. 2018;4(12):810\u201322. https:\/\/doi.org\/10.1016\/j.trecan.2018.10.003.","journal-title":"Trends Cancer."},{"issue":"6","key":"6176_CR19","doi-asserted-by":"publisher","first-page":"a014241","DOI":"10.1101\/cshperspect.a014241","volume":"4","author":"M Gabay","year":"2014","unstructured":"Gabay M, Li Y, Felsher DW. MYC activation is a hallmark of cancer initiation and maintenance. Cold Spring Harb Perspect Med. 2014;4(6):a014241\u2013a014241. https:\/\/doi.org\/10.1101\/cshperspect.a014241.","journal-title":"Cold Spring Harb Perspect Med"},{"issue":"7646","key":"6176_CR20","doi-asserted-by":"publisher","first-page":"519","DOI":"10.1038\/nature21411","volume":"543","author":"RA Beagrie","year":"2017","unstructured":"Beagrie RA, Scialdone A, Schueler M, Kraemer DCA, Chotalia M, Xie SQ, et al. Complex multi-enhancer contacts captured by genome architecture mapping. Nature. 2017;543(7646):519\u201324.","journal-title":"Nature"},{"issue":"10","key":"6176_CR21","doi-asserted-by":"publisher","first-page":"1488","DOI":"10.1038\/s41587-022-01289-z","volume":"40","author":"AS Deshpande","year":"2022","unstructured":"Deshpande AS, Ulahannan N, Pendleton M, Dai X, Ly L, Behr JM, et al. Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing. Nat Biotechnol. 2022;40(10):1488\u201399.","journal-title":"Nat Biotechnol"},{"issue":"6","key":"6176_CR22","doi-asserted-by":"publisher","first-page":"1641","DOI":"10.1016\/j.cell.2020.07.032","volume":"182","author":"J-H Su","year":"2020","unstructured":"Su J-H, Zheng P, Kinrot SS, Bintu B, Zhuang X. Genome-scale imaging of the 3D organization and transcriptional activity of chromatin. Cell. 2020;182(6):1641-1659.e26. https:\/\/doi.org\/10.1016\/j.cell.2020.07.032.","journal-title":"Cell"},{"issue":"7398","key":"6176_CR23","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1038\/nature11082","volume":"485","author":"JR Dixon","year":"2012","unstructured":"Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485(7398):376\u201380. https:\/\/doi.org\/10.1038\/nature11082.","journal-title":"Nature"},{"issue":"6","key":"6176_CR24","doi-asserted-by":"publisher","first-page":"1281","DOI":"10.1016\/j.cell.2013.04.053","volume":"153","author":"JE Phillips-Cremins","year":"2013","unstructured":"Phillips-Cremins JE, Sauria MEG, Sanyal A, Gerasimova TI, Lajoie BR, Bell JSK, et al. Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell. 2013;153(6):1281\u201395. https:\/\/doi.org\/10.1016\/j.cell.2013.04.053.","journal-title":"Cell"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-025-06176-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-025-06176-3\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-025-06176-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,2]],"date-time":"2025-06-02T15:58:57Z","timestamp":1748879937000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-025-06176-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,6,2]]},"references-count":24,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["6176"],"URL":"https:\/\/doi.org\/10.1186\/s12859-025-06176-3","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,6,2]]},"assertion":[{"value":"27 February 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 May 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 June 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"M.J.F declares seven patents related to ChIA-PET. No other conflicts of interest are declared.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"144"}}