{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:45Z","timestamp":1772138085805,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2017,10,3]],"date-time":"2017-10-03T00:00:00Z","timestamp":1506988800000},"content-version":"vor","delay-in-days":4,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["DGE1144152"],"award-info":[{"award-number":["DGE1144152"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>The 3D architecture of DNA within the nucleus is a key determinant of interactions between genes, regulatory elements, and transcriptional machinery. As a result, differences in DNA looping structure are associated with variation in gene expression and cell state. To systematically assess changes in DNA looping architecture between samples, we introduce diffloop, an R\/Bioconductor package that provides a suite of functions for the quality control, statistical testing, annotation, and visualization of DNA loops. We demonstrate this functionality by detecting differences between ENCODE ChIA-PET samples and relate looping to variability in epigenetic state.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Diffloop is implemented as an R\/Bioconductor package available at https:\/\/bioconductor.org\/packages\/release\/bioc\/html\/diffloop.html<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx623","type":"journal-article","created":{"date-parts":[[2017,9,27]],"date-time":"2017-09-27T23:12:40Z","timestamp":1506553960000},"page":"672-674","source":"Crossref","is-referenced-by-count":79,"title":["diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4179-4807","authenticated-orcid":false,"given":"Caleb A","family":"Lareau","sequence":"first","affiliation":[{"name":"Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"},{"name":"Department of Pathology, Harvard Medical School, Boston, MA, USA"}]},{"given":"Martin J","family":"Aryee","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"},{"name":"Department of Pathology, Harvard Medical School, Boston, MA, USA"},{"name":"Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,9,29]]},"reference":[{"key":"2023012712333071100_btx623-B1","doi-asserted-by":"crossref","first-page":"127.","DOI":"10.1186\/s13059-016-0992-2","article-title":"CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data","volume":"17","author":"Cairns","year":"2016","journal-title":"Genome Biol"},{"key":"2023012712333071100_btx623-B2","doi-asserted-by":"crossref","first-page":"1306","DOI":"10.1126\/science.1067799","article-title":"Capturing chromosome conformation","volume":"295","author":"Dekker","year":"2002","journal-title":"Science"},{"key":"2023012712333071100_btx623-B3","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","author":"ENCODE Project Consortium","year":"2012","journal-title":"Nature"},{"key":"2023012712333071100_btx623-B4","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1038\/nature16490","article-title":"Insulator dysfunction and oncogene activation in IDH mutant gliomas","volume":"529","author":"Flavahan","year":"2016","journal-title":"Nature"},{"key":"2023012712333071100_btx623-B5","doi-asserted-by":"crossref","first-page":"1454","DOI":"10.1126\/science.aad9024","article-title":"Activation of proto-oncogenes by disruption of chromosome neighborhoods","volume":"351","author":"Hnisz","year":"2016","journal-title":"Science"},{"key":"2023012712333071100_btx623-B6","doi-asserted-by":"crossref","first-page":"258.","DOI":"10.1186\/s12859-015-0683-0","article-title":"diffHiC: a Bioconductor package to detect differential genomic interactions in Hi-C data","volume":"16","author":"Lun","year":"2015","journal-title":"BMC Bioinformatics"},{"key":"2023012712333071100_btx623-B7","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1038\/ng.3286","article-title":"Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C","volume":"47","author":"Mifsud","year":"2015","journal-title":"Nat. Genet"},{"key":"2023012712333071100_btx623-B8","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1038\/nmeth.3999","article-title":"HiChIP: efficient and sensitive analysis of protein-directed genome architecture","volume":"13","author":"Mumbach","year":"2016","journal-title":"Nat. Methods"},{"key":"2023012712333071100_btx623-B9","doi-asserted-by":"crossref","first-page":"3092","DOI":"10.1093\/bioinformatics\/btv336","article-title":"Mango: a bias-correcting ChIA-PET analysis pipeline","volume":"31","author":"Phanstiel","year":"2015","journal-title":"Bioinformatics"},{"key":"2023012712333071100_btx623-B10","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1016\/j.cell.2014.11.021","article-title":"A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping","volume":"159","author":"Rao","year":"2014","journal-title":"Cell"},{"key":"2023012712333071100_btx623-B11","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012712333071100_btx623-B12","author":"Stark","year":"2015"},{"key":"2023012712333071100_btx623-B13","doi-asserted-by":"crossref","first-page":"1611","DOI":"10.1016\/j.cell.2015.11.024","article-title":"CTCF-mediated human 3D genome architecture reveals chromatin topology for transcription","volume":"163","author":"Tang","year":"2015","journal-title":"Cell"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/4\/672\/48914276\/bioinformatics_34_4_672.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/4\/672\/48914276\/bioinformatics_34_4_672.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T08:21:31Z","timestamp":1674807691000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/4\/672\/4282662"}},"subtitle":[],"editor":[{"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,9,29]]},"references-count":13,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2018,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx623","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/087338","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,2,15]]},"published":{"date-parts":[[2017,9,29]]}}}