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Accuracy assessment","volume":"8","author":"B Ewing","year":"1998","journal-title":"Genome Res"},{"issue":"4","key":"ref41","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1093\/biostatistics\/kxh008","article-title":"Circular binary segmentation for the analysis of array-based DNA copy number data","volume":"5","author":"AB Olshen","year":"2004","journal-title":"Biostatistics"},{"issue":"22","key":"ref42","doi-asserted-by":"crossref","first-page":"7802","DOI":"10.1073\/pnas.84.22.7802","article-title":"Chromatin higher-order structure studied by neutron scattering and scanning transmission electron microscopy","volume":"84","author":"SE Gerchman","year":"1987","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"8","key":"ref43","doi-asserted-by":"crossref","first-page":"a017780","DOI":"10.1101\/cshperspect.a017780","article-title":"Position-effect variegation, heterochromatin formation, and gene silencing in Drosophila","volume":"5","author":"SC Elgin","year":"2013","journal-title":"Cold Spring Harb Perspect Biol"},{"issue":"5","key":"ref44","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1093\/bib\/bbv085","article-title":"How computer science can help in understanding the 3D genome architecture","volume":"17","author":"Y Shavit","year":"2016","journal-title":"Brief Bioinform"},{"issue":"1","key":"ref45","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1186\/s12864-016-3387-6","article-title":"HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking","volume":"18","author":"C Lazaris","year":"2017","journal-title":"BMC Genomics"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1186\/s13059-015-0745-7","article-title":"Analysis methods for studying the 3D architecture of the genome","volume":"16","author":"F Ay","year":"2015","journal-title":"Genome Biol"},{"issue":"13","key":"ref47","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera\u2014a visualization system for exploratory research and analysis","volume":"25","author":"EF Pettersen","year":"2004","journal-title":"J Comput Chem"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1005665","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2017,8,2]],"date-time":"2017-08-02T00:00:00Z","timestamp":1501632000000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005665","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T03:54:05Z","timestamp":1588996445000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005665"}},"subtitle":[],"editor":[{"given":"Andreas","family":"Prlic","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,7,19]]},"references-count":47,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2017,7,19]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1005665","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1005665","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,7,19]]}}}