{"id":"https://openalex.org/W2980150645","doi":"https://doi.org/10.1093/bioinformatics/btz775","title":"Studying 3D genome evolution using genomic sequence","display_name":"Studying 3D genome evolution using genomic sequence","publication_year":2019,"publication_date":"2019-10-08","ids":{"openalex":"https://openalex.org/W2980150645","doi":"https://doi.org/10.1093/bioinformatics/btz775","mag":"2980150645","pmid":"https://pubmed.ncbi.nlm.nih.gov/31605131"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz775","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz775","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/5/1367/32794136/btz775.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/36/5/1367/32794136/btz775.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069731113","display_name":"Rapha\u00ebl Mourad","orcid":"https://orcid.org/0000-0001-6700-5728"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I134560555","display_name":"Universit\u00e9 Toulouse III - Paul Sabatier","ror":"https://ror.org/02v6kpv12","country_code":"FR","type":"education","lineage":["https://openalex.org/I134560555"]},{"id":"https://openalex.org/I17866349","display_name":"Universit\u00e9 F\u00e9d\u00e9rale de Toulouse Midi-Pyr\u00e9n\u00e9es","ror":"https://ror.org/004raaa70","country_code":"FR","type":"education","lineage":["https://openalex.org/I17866349"]},{"id":"https://openalex.org/I4210116516","display_name":"Laboratoire de Biologie Cellulaire et Mol\u00e9culaire du Contr\u00f4le de la Prolif\u00e9ration","ror":"https://ror.org/02aqr8687","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I134560555","https://openalex.org/I4210096427","https://openalex.org/I4210116516"]},{"id":"https://openalex.org/I4405266242","display_name":"Centre de Biologie Int\u00e9grative de Toulouse","ror":"https://ror.org/01f4pb571","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I4405258862","https://openalex.org/I4405266242"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Rapha\u00ebl Mourad","raw_affiliation_strings":["LBCMCP, Centre de Biologie Int\u00e9grative (CBI), Universit\u00e9 de Toulouse , CNRS, UPS, 31062 Toulouse, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LBCMCP, Centre de Biologie Int\u00e9grative (CBI), Universit\u00e9 de Toulouse , CNRS, UPS, 31062 Toulouse, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I134560555","https://openalex.org/I17866349","https://openalex.org/I4210116516","https://openalex.org/I4405266242"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5069731113"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I134560555","https://openalex.org/I17866349","https://openalex.org/I4210116516","https://openalex.org/I4405266242"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.3792,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.58127131,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":97},"biblio":{"volume":"36","issue":"5","first_page":"1367","last_page":"1373"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9621000289916992,"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":0.9621000289916992,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.00800000037997961,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.006200000178068876,"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/ctcf","display_name":"CTCF","score":0.8838397264480591},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.7548494935035706},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.6416181921958923},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6375032067298889},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6270046830177307},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.491525262594223},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4646816551685333},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.41492176055908203},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3536180555820465},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08013775944709778}],"concepts":[{"id":"https://openalex.org/C2778760011","wikidata":"https://www.wikidata.org/wiki/Q21163346","display_name":"CTCF","level":5,"score":0.8838397264480591},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7548494935035706},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.6416181921958923},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6375032067298889},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6270046830177307},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.491525262594223},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4646816551685333},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.41492176055908203},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3536180555820465},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08013775944709778},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btz775","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz775","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/5/1367/32794136/btz775.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:31605131","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31605131","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz775","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz775","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/5/1367/32794136/btz775.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":[{"score":0.4300000071525574,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1637500350","https://openalex.org/W1831401007","https://openalex.org/W1859117663","https://openalex.org/W1973062929","https://openalex.org/W1975297840","https://openalex.org/W2016696510","https://openalex.org/W2018658338","https://openalex.org/W2021200545","https://openalex.org/W2032140335","https://openalex.org/W2056482755","https://openalex.org/W2064537118","https://openalex.org/W2065006553","https://openalex.org/W2067686625","https://openalex.org/W2070021921","https://openalex.org/W2090037139","https://openalex.org/W2117977423","https://openalex.org/W2139818536","https://openalex.org/W2163605769","https://openalex.org/W2169509504","https://openalex.org/W2172561760","https://openalex.org/W2243544746","https://openalex.org/W2259938310","https://openalex.org/W2481029670","https://openalex.org/W2774733631","https://openalex.org/W2810823898","https://openalex.org/W2951956418","https://openalex.org/W2952220073","https://openalex.org/W3105701304","https://openalex.org/W6685333394"],"related_works":["https://openalex.org/W2010297690","https://openalex.org/W3083199549","https://openalex.org/W4362507076","https://openalex.org/W4384070931","https://openalex.org/W4292590360","https://openalex.org/W2341637133","https://openalex.org/W2755337536","https://openalex.org/W3004934868","https://openalex.org/W2582488421","https://openalex.org/W4220758050"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,102,200],"three":[2],"dimensions":[3],"(3D)":[4],"genome":[5,86,145],"is":[6,27,104,133,203],"essential":[7],"to":[8,82,137,191],"numerous":[9],"key":[10],"processes":[11],"such":[12],"as":[13],"the":[14,20,84,91,97,110,124,143,158],"regulation":[15],"of":[16,73],"gene":[17],"expression":[18],"and":[19,32,59,106,114,155,174,182],"replication-timing":[21],"program.":[22],"In":[23],"vertebrates,":[24],"chromatin":[25,49],"looping":[26,50,140,173],"often":[28],"mediated":[29],"by":[30,34,118],"CTCF,":[31],"marked":[33],"CTCF":[35,116,139,172],"motif":[36],"pairs":[37],"in":[38,88,142,153,194],"convergent":[39,113],"orientation.":[40],"Comparative":[41],"high-throughput":[42],"sequencing":[43],"technique":[44],"(Hi-C)":[45],"recently":[46],"revealed":[47],"that":[48,131,168,184],"evolves":[51,179],"across":[52],"species.":[53,74],"However,":[54],"Hi-C":[55,100],"experiments":[56],"are":[57,211],"complex":[58],"costly,":[60],"which":[61,170],"currently":[62],"limits":[63],"their":[64],"use":[65],"for":[66,99],"evolutionary":[67,150],"studies":[68],"over":[69,180],"a":[70,79,120,134],"large":[71],"number":[72],"RESULTS:":[75],"Here,":[76],"we":[77,122],"propose":[78],"novel":[80],"approach":[81,103],"study":[83],"3D":[85,125,159],"evolution":[87],"vertebrates":[89],"using":[90],"genomic":[92],"sequence":[93],"only,":[94],"e.g.":[95],"without":[96],"need":[98],"data.":[101],"simple":[105],"relies":[107],"on":[108],"comparing":[109,162],"distances":[111],"between":[112],"divergent":[115],"motifs":[117],"computing":[119],"ratio":[121,126],"named":[123],"or":[127],"'3DR'.":[128],"We":[129],"show":[130],"3DR":[132,169,193],"powerful":[135],"statistic":[136],"detect":[138],"encoded":[141,152],"human":[144],"sequence,":[146],"thus":[147],"reflecting":[148],"strong":[149],"constraints":[151],"DNA":[154],"associated":[156],"with":[157],"genome.":[160],"When":[161],"vertebrate":[163],"genomes,":[164],"our":[165],"results":[166],"reveal":[167],"underlies":[171],"topologically":[175],"associating":[176],"domain":[177],"organization":[178],"time":[181],"suggest":[183],"ancestral":[185,195],"character":[186],"reconstruction":[187],"can":[188],"be":[189],"used":[190],"infer":[192],"genomes.":[196],"AVAILABILITY":[197],"AND":[198],"IMPLEMENTATION:":[199],"R":[201],"code":[202],"available":[204,212],"at":[205,213],"https://github.com/morphos30/PhyloCTCFLooping.":[206],"SUPPLEMENTARY":[207],"INFORMATION:":[208],"Supplementary":[209],"data":[210],"Bioinformatics":[214],"online.":[215]},"counts_by_year":[{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":2}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}