{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T04:57:30Z","timestamp":1775192250739,"version":"3.50.1"},"reference-count":42,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2016,3,3]],"date-time":"2016-03-03T00:00:00Z","timestamp":1456963200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1004780","type":"journal-article","created":{"date-parts":[[2016,3,3]],"date-time":"2016-03-03T13:59:22Z","timestamp":1457013562000},"page":"e1004780","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":94,"title":["4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments"],"prefix":"10.1371","volume":"12","author":[{"given":"Ramya","family":"Raviram","sequence":"first","affiliation":[]},{"given":"Pedro P.","family":"Rocha","sequence":"additional","affiliation":[]},{"given":"Christian L.","family":"M\u00fcller","sequence":"additional","affiliation":[]},{"given":"Emily R.","family":"Miraldi","sequence":"additional","affiliation":[]},{"given":"Sana","family":"Badri","sequence":"additional","affiliation":[]},{"given":"Yi","family":"Fu","sequence":"additional","affiliation":[]},{"given":"Emily","family":"Swanzey","sequence":"additional","affiliation":[]},{"given":"Charlotte","family":"Proudhon","sequence":"additional","affiliation":[]},{"given":"Valentina","family":"Snetkova","sequence":"additional","affiliation":[]},{"given":"Richard","family":"Bonneau","sequence":"additional","affiliation":[]},{"given":"Jane A.","family":"Skok","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2016,3,3]]},"reference":[{"issue":"6","key":"ref1","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1016\/j.stem.2014.05.017","article-title":"The 3D genome in transcriptional regulation and pluripotency","volume":"14","author":"DU Gorkin","year":"2014","journal-title":"Cell Stem Cell"},{"issue":"6","key":"ref2","doi-asserted-by":"crossref","first-page":"1270","DOI":"10.1016\/j.cell.2013.02.001","article-title":"Genome architecture: domain organization of interphase chromosomes","volume":"152","author":"WA Bickmore","year":"2013","journal-title":"Cell"},{"issue":"7143","key":"ref3","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1038\/nature05916","article-title":"Nuclear organization of the genome and the potential for gene regulation","volume":"447","author":"P Fraser","year":"2007","journal-title":"Nature"},{"issue":"3","key":"ref4","doi-asserted-by":"crossref","first-page":"a003889","DOI":"10.1101\/cshperspect.a003889","article-title":"Chromosome territories","volume":"2","author":"T Cremer","year":"2010","journal-title":"Cold Spring Harb Perspect Biol"},{"issue":"2","key":"ref5","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1016\/j.gde.2011.12.006","article-title":"Chromosome organization in the nucleus\u2014charting new territory across the Hi-Cs","volume":"22","author":"J Dostie","year":"2012","journal-title":"Curr Opin Genet Dev"},{"issue":"5950","key":"ref6","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1126\/science.1181369","article-title":"Comprehensive mapping of long-range interactions reveals folding principles of the human genome","volume":"326","author":"E Lieberman-Aiden","year":"2009","journal-title":"Science"},{"issue":"7398","key":"ref7","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/nature11049","article-title":"Spatial partitioning of the regulatory landscape of the X-inactivation centre","volume":"485","author":"EP Nora","year":"2012","journal-title":"Nature"},{"issue":"7398","key":"ref8","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature11082","article-title":"Topological domains in mammalian genomes identified by analysis of chromatin interactions","volume":"485","author":"JR Dixon","year":"2012","journal-title":"Nature"},{"issue":"3","key":"ref9","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1016\/j.cell.2012.01.010","article-title":"Three-dimensional folding and functional organization principles of the Drosophila genome","volume":"148","author":"T Sexton","year":"2012","journal-title":"Cell"},{"issue":"7","key":"ref10","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":"SS Rao","year":"2014","journal-title":"Cell"},{"issue":"6","key":"ref11","doi-asserted-by":"crossref","first-page":"1281","DOI":"10.1016\/j.cell.2013.04.053","article-title":"Architectural protein subclasses shape 3D organization of genomes during lineage commitment","volume":"153","author":"JE Phillips-Cremins","year":"2013","journal-title":"Cell"},{"issue":"5","key":"ref12","doi-asserted-by":"crossref","first-page":"455","DOI":"10.2217\/epi.14.47","article-title":"Interpreting 4C-Seq data: how far can we go?","volume":"6","author":"R Raviram","year":"2014","journal-title":"Epigenomics"},{"issue":"10","key":"ref13","doi-asserted-by":"crossref","first-page":"969","DOI":"10.1038\/nmeth.2173","article-title":"Robust 4C-seq data analysis to screen for regulatory DNA interactions","volume":"9","author":"HJ van de Werken","year":"2012","journal-title":"Nat Methods"},{"issue":"6","key":"ref14","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1016\/j.molcel.2012.06.036","article-title":"Close proximity to Igh is a contributing factor to AID-mediated translocations","volume":"47","author":"PP Rocha","year":"2012","journal-title":"Mol Cell"},{"issue":"7466","key":"ref15","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1038\/nature12420","article-title":"The pluripotent genome in three dimensions is shaped around pluripotency factors","volume":"501","author":"E de Wit","year":"2013","journal-title":"Nature"},{"issue":"5","key":"ref16","doi-asserted-by":"crossref","first-page":"602","DOI":"10.1016\/j.stem.2013.08.013","article-title":"Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization","volume":"13","author":"M Denholtz","year":"2013","journal-title":"Cell Stem Cell"},{"issue":"12","key":"ref17","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"MI Love","year":"2014","journal-title":"Genome Biol"},{"issue":"10","key":"ref18","doi-asserted-by":"crossref","first-page":"969","DOI":"10.1038\/nmeth.2173","article-title":"Robust 4C-seq data analysis to screen for regulatory DNA interactions","volume":"9","author":"HJ van de Werken","year":"2012","journal-title":"Nat Methods"},{"issue":"8","key":"ref19","doi-asserted-by":"crossref","first-page":"e68","DOI":"10.1093\/nar\/gku156","article-title":"fourSig: a method for determining chromosomal interactions in 4C-Seq data","volume":"42","author":"RL Williams Jr.","year":"2014","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"ref20","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1016\/j.ymeth.2012.04.009","article-title":"Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: from fixation to computation","volume":"58","author":"E Splinter","year":"2012","journal-title":"Methods"},{"issue":"13","key":"ref21","doi-asserted-by":"crossref","first-page":"e132","DOI":"10.1093\/nar\/gkt373","article-title":"r3Cseq: an R\/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data","volume":"41","author":"S Thongjuea","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"ref22","article-title":"FourCSeq: Analysis of 4C sequencing data","author":"FA Klein","year":"2015","journal-title":"Bioinformatics"},{"issue":"6053","key":"ref23","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1126\/science.1207194","article-title":"The dynamic architecture of Hox gene clusters","volume":"334","author":"D Noordermeer","year":"2011","journal-title":"Science"},{"issue":"2","key":"ref24","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1016\/j.cell.2014.02.019","article-title":"A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in leukemia","volume":"157","author":"S Groschel","year":"2014","journal-title":"Cell"},{"issue":"4","key":"ref25","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1038\/ni1448","article-title":"Reversible contraction by looping of the Tcra and Tcrb loci in rearranging thymocytes","volume":"8","author":"JA Skok","year":"2007","journal-title":"Nat Immunol"},{"issue":"1","key":"ref26","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1038\/ng.496","article-title":"Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells","volume":"42","author":"S Schoenfelder","year":"2010","journal-title":"Nat Genet"},{"issue":"1","key":"ref27","doi-asserted-by":"crossref","first-page":"e1002465","DOI":"10.1371\/journal.pgen.1002465","article-title":"Progressive polycomb assembly on H3K27me3 compartments generates polycomb bodies with developmentally regulated motion","volume":"8","author":"T Cheutin","year":"2012","journal-title":"PLoS Genet"},{"issue":"24","key":"ref28","doi-asserted-by":"crossref","first-page":"2778","DOI":"10.1101\/gad.251694.114","article-title":"Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization","volume":"28","author":"I Williamson","year":"2014","journal-title":"Genes Dev"},{"issue":"2","key":"ref29","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1016\/j.celrep.2013.01.024","article-title":"Higher-order looping and nuclear organization of Tcra facilitate targeted rag cleavage and regulated rearrangement in recombination centers","volume":"3","author":"J Chaumeil","year":"2013","journal-title":"Cell Rep"},{"issue":"2","key":"ref30","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1038\/ng.2871","article-title":"Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment","volume":"46","author":"JR Hughes","year":"2014","journal-title":"Nat Genet"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/1756-8935-7-10","article-title":"Targeted Chromatin Capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements","volume":"7","author":"P Kolovos","year":"2014","journal-title":"Epigenetics Chromatin"},{"issue":"11","key":"ref32","doi-asserted-by":"crossref","first-page":"1854","DOI":"10.1101\/gr.175034.114","article-title":"Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C","volume":"24","author":"NH Dryden","year":"2014","journal-title":"Genome Res"},{"issue":"7","key":"ref33","article-title":"depmixS4: An R Package for Hidden Markov Models","volume":"36","author":"MS Ingmar Visser","year":"2010","journal-title":"Journal of Statistical Software"},{"issue":"1","key":"ref34","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1098\/rsbl.2006.0553","article-title":"A multiple-site similarity measure","volume":"3","author":"OH Diserud","year":"2007","journal-title":"Biol Lett"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/B978-0-12-391938-0.00004-5","article-title":"4C technology: protocols and data analysis","volume":"513","author":"HJ van de Werken","year":"2012","journal-title":"Methods Enzymol"},{"issue":"4","key":"ref36","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1038\/ni1567","article-title":"Association between the Igk and Igh immunoglobulin loci mediated by the 3' Igk enhancer induces 'decontraction' of the Igh locus in pre-B cells","volume":"9","author":"SL Hewitt","year":"2008","journal-title":"Nat Immunol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"2231","DOI":"10.1038\/ncomms3231","article-title":"The RAG2 C-terminus and ATM protect genome integrity by controlling antigen receptor gene cleavage","volume":"4","author":"J Chaumeil","year":"2013","journal-title":"Nat Commun"},{"issue":"12","key":"ref38","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.1038\/nmeth.2688","article-title":"Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position","volume":"10","author":"JD Buenrostro","year":"2013","journal-title":"Nat Methods"},{"issue":"9","key":"ref39","doi-asserted-by":"crossref","first-page":"1302","DOI":"10.1093\/bioinformatics\/btt774","article-title":"PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data","volume":"30","author":"O McCarthy MT","year":"2014","journal-title":"Bioinformatics"},{"issue":"3","key":"ref40","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1016\/j.cell.2014.05.049","article-title":"Genome-wide mapping and characterization of Notch-regulated long noncoding RNAs in acute leukemia","volume":"158","author":"T Trimarchi","year":"2014","journal-title":"Cell"},{"issue":"4","key":"ref41","doi-asserted-by":"crossref","first-page":"R36","DOI":"10.1186\/gb-2013-14-4-r36","article-title":"TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions","volume":"14","author":"D Kim","year":"2013","journal-title":"Genome Biol"},{"issue":"2","key":"ref42","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq\u2014a Python framework to work with high-throughput sequencing data","volume":"31","author":"S Anders","year":"2015","journal-title":"Bioinformatics"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004780","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,5]],"date-time":"2019-09-05T02:31:45Z","timestamp":1567650705000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004780"}},"subtitle":[],"editor":[{"given":"Alexandre V","family":"Morozov","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2016,3,3]]},"references-count":42,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2016,3,3]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1004780","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/030569","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,3,3]]}}}