{"id":"https://openalex.org/W2899360977","doi":"https://doi.org/10.1186/s12859-019-2646-3","title":"A new class of constitutively active super-enhancers is associated with fast recovery of 3D chromatin loops","display_name":"A new class of constitutively active super-enhancers is associated with fast recovery of 3D chromatin loops","publication_year":2019,"publication_date":"2019-03-01","ids":{"openalex":"https://openalex.org/W2899360977","doi":"https://doi.org/10.1186/s12859-019-2646-3","mag":"2899360977","pmid":"https://pubmed.ncbi.nlm.nih.gov/30925856"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-2646-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2646-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2646-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2646-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076560493","display_name":"Jayoung Ryu","orcid":"https://orcid.org/0000-0001-8710-8898"},"institutions":[{"id":"https://openalex.org/I157485424","display_name":"Korea Advanced Institute of Science and Technology","ror":"https://ror.org/05apxxy63","country_code":"KR","type":"education","lineage":["https://openalex.org/I157485424"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Jayoung Ryu","raw_affiliation_strings":["Department of Biological Sciences, KAIST, Daejeon, 34141, South Korea","Department of Biological Sciences, KAIST, Daejeon, South Korea"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, KAIST, Daejeon, 34141, South Korea","institution_ids":["https://openalex.org/I157485424"]},{"raw_affiliation_string":"Department of Biological Sciences, KAIST, Daejeon, South Korea","institution_ids":["https://openalex.org/I157485424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101703911","display_name":"Hyun-Woong Kim","orcid":"https://orcid.org/0000-0003-0220-0084"},"institutions":[{"id":"https://openalex.org/I157485424","display_name":"Korea Advanced Institute of Science and Technology","ror":"https://ror.org/05apxxy63","country_code":"KR","type":"education","lineage":["https://openalex.org/I157485424"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Hyunwoong Kim","raw_affiliation_strings":["Department of Biological Sciences, KAIST, Daejeon, 34141, South Korea","Department of Biological Sciences, KAIST, Daejeon, South Korea"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, KAIST, Daejeon, 34141, South Korea","institution_ids":["https://openalex.org/I157485424"]},{"raw_affiliation_string":"Department of Biological Sciences, KAIST, Daejeon, South Korea","institution_ids":["https://openalex.org/I157485424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017634865","display_name":"Dongchan Yang","orcid":"https://orcid.org/0000-0003-2311-5794"},"institutions":[{"id":"https://openalex.org/I157485424","display_name":"Korea Advanced Institute of Science and Technology","ror":"https://ror.org/05apxxy63","country_code":"KR","type":"education","lineage":["https://openalex.org/I157485424"]},{"id":"https://openalex.org/I4210101891","display_name":"Korea Institute of Brain Science","ror":"https://ror.org/017stnw60","country_code":"KR","type":"facility","lineage":["https://openalex.org/I4210101891"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Dongchan Yang","raw_affiliation_strings":["Department of Bio and Brain Engineering, KAIST, Daejeon, 34141, South Korea","Department of Bio and Brain Engineering, KAIST, Daejeon, South Korea"],"affiliations":[{"raw_affiliation_string":"Department of Bio and Brain Engineering, KAIST, Daejeon, 34141, South Korea","institution_ids":["https://openalex.org/I157485424"]},{"raw_affiliation_string":"Department of Bio and Brain Engineering, KAIST, Daejeon, South Korea","institution_ids":["https://openalex.org/I4210101891","https://openalex.org/I157485424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100450493","display_name":"Andrew Lee","orcid":"https://orcid.org/0000-0001-9917-8834"},"institutions":[{"id":"https://openalex.org/I157485424","display_name":"Korea Advanced Institute of Science and Technology","ror":"https://ror.org/05apxxy63","country_code":"KR","type":"education","lineage":["https://openalex.org/I157485424"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Andrew J. Lee","raw_affiliation_strings":["Department of Biological Sciences, KAIST, Daejeon, 34141, South Korea","Department of Biological Sciences, KAIST, Daejeon, South Korea"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, KAIST, Daejeon, 34141, South Korea","institution_ids":["https://openalex.org/I157485424"]},{"raw_affiliation_string":"Department of Biological Sciences, KAIST, Daejeon, South Korea","institution_ids":["https://openalex.org/I157485424"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080272556","display_name":"Inkyung Jung","orcid":"https://orcid.org/0000-0002-5885-2754"},"institutions":[{"id":"https://openalex.org/I157485424","display_name":"Korea Advanced Institute of Science and Technology","ror":"https://ror.org/05apxxy63","country_code":"KR","type":"education","lineage":["https://openalex.org/I157485424"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Inkyung Jung","raw_affiliation_strings":["Department of Biological Sciences, KAIST, Daejeon, 34141, South Korea. ijung@kaist.ac.kr","Department of Biological Sciences, KAIST, Daejeon, South Korea"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, KAIST, Daejeon, 34141, South Korea. ijung@kaist.ac.kr","institution_ids":[]},{"raw_affiliation_string":"Department of Biological Sciences, KAIST, Daejeon, South Korea","institution_ids":["https://openalex.org/I157485424"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5080272556"],"corresponding_institution_ids":["https://openalex.org/I157485424"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.569,"has_fulltext":true,"cited_by_count":35,"citation_normalized_percentile":{"value":0.9027404,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"20","issue":"S3","first_page":"127","last_page":"127"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998000264167786,"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":0.9998000264167786,"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/T12534","display_name":"Protein Degradation and Inhibitors","score":0.9987000226974487,"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/T11041","display_name":"Ubiquitin and proteasome pathways","score":0.9898999929428101,"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/chromatin","display_name":"Chromatin","score":0.8447615504264832},{"id":"https://openalex.org/keywords/enhancer","display_name":"Enhancer","score":0.8159344792366028},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5540649890899658},{"id":"https://openalex.org/keywords/class","display_name":"Class (philosophy)","score":0.5238066911697388},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.47068125009536743},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.44680798053741455},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.4429304003715515},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.418714314699173},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.38339778780937195},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.26135706901550293},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19289615750312805},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.17771145701408386},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1302860677242279},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.08985799551010132}],"concepts":[{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.8447615504264832},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.8159344792366028},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5540649890899658},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.5238066911697388},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.47068125009536743},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.44680798053741455},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.4429304003715515},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.418714314699173},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.38339778780937195},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.26135706901550293},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19289615750312805},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.17771145701408386},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1302860677242279},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.08985799551010132}],"mesh":[{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","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":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","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":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","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":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-019-2646-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2646-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2646-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30925856","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30925856","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:3c59e37fe9b8444f9267340803478f7c","is_oa":true,"landing_page_url":"https://doaj.org/article/3c59e37fe9b8444f9267340803478f7c","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 20, Iss S3, Pp 25-36 (2019)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5441295","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6439976","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-2646-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2646-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2646-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2899360977.pdf","grobid_xml":"https://content.openalex.org/works/W2899360977.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1963740134","https://openalex.org/W1969161156","https://openalex.org/W1971578941","https://openalex.org/W1978329681","https://openalex.org/W2060484997","https://openalex.org/W2072153595","https://openalex.org/W2076154138","https://openalex.org/W2079407198","https://openalex.org/W2103441770","https://openalex.org/W2158217645","https://openalex.org/W2171808845","https://openalex.org/W2280788332","https://openalex.org/W2481029670","https://openalex.org/W2761461280","https://openalex.org/W2794373321"],"related_works":["https://openalex.org/W2113330652","https://openalex.org/W2061914098","https://openalex.org/W4309683845","https://openalex.org/W2152841149","https://openalex.org/W2586783543","https://openalex.org/W4387598842","https://openalex.org/W4225831698","https://openalex.org/W2973036402","https://openalex.org/W3198436517","https://openalex.org/W1607718650"],"abstract_inverted_index":{"In":[0],"this":[1],"study,":[2],"we":[3],"propose":[4],"that":[5],"a":[6],"new":[7],"class":[8],"of":[9,20],"super-enhancers":[10],"may":[11],"play":[12],"an":[13],"important":[14],"role":[15],"in":[16],"the":[17],"early":[18],"establishment":[19],"3D":[21],"chromatin":[22],"structure.":[23]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":16},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}