{"id":"https://openalex.org/W2310342073","doi":"https://doi.org/10.1093/bioinformatics/btv485","title":"Identification of hierarchical chromatin domains","display_name":"Identification of hierarchical chromatin domains","publication_year":2015,"publication_date":"2015-08-26","ids":{"openalex":"https://openalex.org/W2310342073","doi":"https://doi.org/10.1093/bioinformatics/btv485","mag":"2310342073","pmid":"https://pubmed.ncbi.nlm.nih.gov/26315910"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv485","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv485","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/11/1601/22643996/btv485.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/11/1601/22643996/btv485.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047450437","display_name":"Caleb Weinreb","orcid":"https://orcid.org/0000-0001-6100-6084"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Caleb Weinreb","raw_affiliation_strings":["1 Center for Computational Molecular Biology and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Computational Molecular Biology and","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025899028","display_name":"Benjamin J. Raphael","orcid":"https://orcid.org/0000-0003-1274-048X"},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Benjamin J. Raphael","raw_affiliation_strings":["1 Center for Computational Molecular Biology and","2 Department of Computer Science, Brown University, Providence, RI 02912, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Computational Molecular Biology and","institution_ids":[]},{"raw_affiliation_string":"2 Department of Computer Science, Brown University, Providence, RI 02912, USA","institution_ids":["https://openalex.org/I27804330"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5025899028"],"corresponding_institution_ids":["https://openalex.org/I27804330"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":7.5666,"has_fulltext":true,"cited_by_count":181,"citation_normalized_percentile":{"value":0.98093503,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"32","issue":"11","first_page":"1601","last_page":"1609"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9932000041007996,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9932000041007996,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.0010999999940395355,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0010000000474974513,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/hierarchy","display_name":"Hierarchy","score":0.6129191517829895},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6043044924736023},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.6039186120033264},{"id":"https://openalex.org/keywords/ctcf","display_name":"CTCF","score":0.5354922413825989},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5173339247703552},{"id":"https://openalex.org/keywords/chromosome-conformation-capture","display_name":"Chromosome conformation capture","score":0.5043231248855591},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4478267431259155},{"id":"https://openalex.org/keywords/disk-formatting","display_name":"Disk formatting","score":0.4166390299797058},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3564136326313019},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3237009346485138},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2887915372848511},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24656417965888977},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.21478083729743958},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1702350378036499}],"concepts":[{"id":"https://openalex.org/C31170391","wikidata":"https://www.wikidata.org/wiki/Q188619","display_name":"Hierarchy","level":2,"score":0.6129191517829895},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6043044924736023},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.6039186120033264},{"id":"https://openalex.org/C2778760011","wikidata":"https://www.wikidata.org/wiki/Q21163346","display_name":"CTCF","level":5,"score":0.5354922413825989},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5173339247703552},{"id":"https://openalex.org/C93946551","wikidata":"https://www.wikidata.org/wiki/Q5113914","display_name":"Chromosome conformation capture","level":5,"score":0.5043231248855591},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4478267431259155},{"id":"https://openalex.org/C88006597","wikidata":"https://www.wikidata.org/wiki/Q690117","display_name":"Disk formatting","level":2,"score":0.4166390299797058},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3564136326313019},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3237009346485138},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2887915372848511},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24656417965888977},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.21478083729743958},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1702350378036499},{"id":"https://openalex.org/C34447519","wikidata":"https://www.wikidata.org/wiki/Q179522","display_name":"Market economy","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btv485","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv485","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/11/1601/22643996/btv485.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26315910","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26315910","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:4299507","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC4892410","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:4892410","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4892410","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/11/1601","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/11/1601","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv485","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv485","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/11/1601/22643996/btv485.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2089771574","display_name":null,"funder_award_id":"R01HG005690","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G361500113","display_name":"CAREER:  Algorithms for Next-Generation Genomics","funder_award_id":"1053753","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4632009408","display_name":"Computational Approaches for Structural Variation Studies in Genomes","funder_award_id":"5r01hg005690-05","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6671297155","display_name":null,"funder_award_id":"CAREER","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306133","display_name":"Burroughs Wellcome Fund","ror":"https://ror.org/01d35cw23"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2310342073.pdf","grobid_xml":"https://content.openalex.org/works/W2310342073.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W658181765","https://openalex.org/W1945579058","https://openalex.org/W1965863160","https://openalex.org/W1973062929","https://openalex.org/W2001576815","https://openalex.org/W2002399114","https://openalex.org/W2018658338","https://openalex.org/W2032464841","https://openalex.org/W2036663020","https://openalex.org/W2040329023","https://openalex.org/W2042930277","https://openalex.org/W2043024569","https://openalex.org/W2056482755","https://openalex.org/W2070021921","https://openalex.org/W2090037139","https://openalex.org/W2099034339","https://openalex.org/W2107866789","https://openalex.org/W2109949710","https://openalex.org/W2114083195","https://openalex.org/W2129070834","https://openalex.org/W2157576490","https://openalex.org/W2161212572","https://openalex.org/W2163605769","https://openalex.org/W2340006107","https://openalex.org/W2412795750","https://openalex.org/W3100350271","https://openalex.org/W4285719527","https://openalex.org/W6785789649"],"related_works":["https://openalex.org/W4220758050","https://openalex.org/W2898514070","https://openalex.org/W3195254751","https://openalex.org/W3116849561","https://openalex.org/W2001502812","https://openalex.org/W2136004413","https://openalex.org/W1968273299","https://openalex.org/W3180808842","https://openalex.org/W2521860411","https://openalex.org/W2111997778"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1],"three-dimensional":[2],"structure":[3,64],"of":[4,11,35,81,87,97,112,156,171,186],"the":[5,123,133,138,150],"genome":[6],"is":[7,92,130,188],"an":[8],"important":[9],"regulator":[10],"many":[12,44],"cellular":[13],"processes":[14],"including":[15],"differentiation":[16],"and":[17,68],"gene":[18],"regulation.":[19],"Recently,":[20],"technologies":[21],"such":[22,174],"as":[23,175],"Hi-C":[24,52],"that":[25,55,104,116,122],"combine":[26],"proximity":[27],"ligation":[28],"with":[29,128,162,167],"high-throughput":[30],"sequencing":[31],"have":[32,108],"revealed":[33],"domains":[34,41],"self-interacting":[36],"chromatin,":[37],"called":[38],"topologically":[39],"associating":[40],"(TADs),":[42],"in":[43,65,125,141],"organisms.":[45],"Current":[46],"methods":[47],"for":[48,61,79,132,137,153],"identifying":[49],"TADs":[50,56,67,166],"using":[51],"data":[53,197],"assume":[54],"are":[57,105,117,198],"non-overlapping,":[58],"despite":[59],"evidence":[60],"a":[62,71,77,85,109,142,168],"nested":[63,88,157],"which":[66],"sub-TADs":[69],"form":[70],"complex":[72],"hierarchy.":[73],"RESULTS:":[74],"We":[75,120],"introduce":[76],"model":[78,91],"decomposition":[80],"contact":[82,98,126],"frequencies":[83,99],"into":[84],"hierarchy":[86],"TADs.":[89,158],"This":[90],"based":[93],"on":[94],"empirical":[95],"distributions":[96],"within":[100],"TADs,":[101],"where":[102],"positions":[103,115],"far":[106],"apart":[107],"greater":[110,169],"enrichment":[111,127,170],"contacts":[113],"than":[114,136],"close":[118],"together.":[119],"find":[121],"increase":[124],"distance":[129],"stronger":[131],"inner":[134],"TAD":[135,140],"outer":[139],"TAD/sub-TAD":[143],"pair.":[144],"Using":[145],"this":[146],"model,":[147],"we":[148],"develop":[149],"TADtree":[151,159,187],"algorithm":[152],"detecting":[154],"hierarchies":[155],"compares":[160],"favorably":[161],"previous":[163],"methods,":[164],"finding":[165],"chromatin":[172],"marks":[173],"CTCF":[176],"at":[177,190,200],"their":[178],"boundaries.":[179],"AVAILABILITY":[180],"AND":[181],"IMPLEMENTATION:":[182],"A":[183],"python":[184],"implementation":[185],"available":[189,199],"http://compbio.cs.brown.edu/software/":[191],"CONTACT:":[192],"braphael@cs.brown.edu":[193],"SUPPLEMENTARY":[194],"INFORMATION:":[195],"Supplementary":[196],"Bioinformatics":[201],"online.":[202]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":15},{"year":2021,"cited_by_count":35},{"year":2020,"cited_by_count":18},{"year":2019,"cited_by_count":24},{"year":2018,"cited_by_count":30},{"year":2017,"cited_by_count":16},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":1}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
