{"id":"https://openalex.org/W4206494592","doi":"https://doi.org/10.1109/bibm52615.2021.9669531","title":"Deep learning predicts boundaries of topologically associated domains in human cell lines using CTCF, RAD21, and 12 epigenetic signals","display_name":"Deep learning predicts boundaries of topologically associated domains in human cell lines using CTCF, RAD21, and 12 epigenetic signals","publication_year":2021,"publication_date":"2021-12-09","ids":{"openalex":"https://openalex.org/W4206494592","doi":"https://doi.org/10.1109/bibm52615.2021.9669531"},"language":"en","primary_location":{"id":"doi:10.1109/bibm52615.2021.9669531","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm52615.2021.9669531","pdf_url":null,"source":{"id":"https://openalex.org/S4363607735","display_name":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001072414","display_name":"Benjamin Soibam","orcid":"https://orcid.org/0000-0002-1532-9955"},"institutions":[{"id":"https://openalex.org/I16277215","display_name":"University of Houston - Downtown","ror":"https://ror.org/05mj6fy81","country_code":"US","type":"education","lineage":["https://openalex.org/I16277215"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Benjamin Soibam","raw_affiliation_strings":["Computer Science and Engineering Technology, University of Houston-Downtown, Houston, USA"],"affiliations":[{"raw_affiliation_string":"Computer Science and Engineering Technology, University of Houston-Downtown, Houston, USA","institution_ids":["https://openalex.org/I16277215"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5001072414"],"corresponding_institution_ids":["https://openalex.org/I16277215"],"apc_list":null,"apc_paid":null,"fwci":0.5188,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.57992565,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"145","last_page":"150"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998999834060669,"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":0.9998999834060669,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9991000294685364,"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":0.9983999729156494,"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":0.9842668771743774},{"id":"https://openalex.org/keywords/cohesin","display_name":"Cohesin","score":0.8294651508331299},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.7095557451248169},{"id":"https://openalex.org/keywords/epigenetics","display_name":"Epigenetics","score":0.6757675409317017},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5845625400543213},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4683235287666321},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.45848509669303894},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.44980916380882263},{"id":"https://openalex.org/keywords/convolution","display_name":"Convolution (computer science)","score":0.4427284896373749},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3527938723564148},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33654117584228516},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.32590678334236145},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2242770493030548},{"id":"https://openalex.org/keywords/enhancer","display_name":"Enhancer","score":0.08611881732940674},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.08016592264175415}],"concepts":[{"id":"https://openalex.org/C2778760011","wikidata":"https://www.wikidata.org/wiki/Q21163346","display_name":"CTCF","level":5,"score":0.9842668771743774},{"id":"https://openalex.org/C115821613","wikidata":"https://www.wikidata.org/wiki/Q21103063","display_name":"Cohesin","level":4,"score":0.8294651508331299},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.7095557451248169},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.6757675409317017},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5845625400543213},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4683235287666321},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.45848509669303894},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.44980916380882263},{"id":"https://openalex.org/C45347329","wikidata":"https://www.wikidata.org/wiki/Q5166604","display_name":"Convolution (computer science)","level":3,"score":0.4427284896373749},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3527938723564148},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33654117584228516},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.32590678334236145},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2242770493030548},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.08611881732940674},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.08016592264175415}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm52615.2021.9669531","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm52615.2021.9669531","pdf_url":null,"source":{"id":"https://openalex.org/S4363607735","display_name":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1915238740","https://openalex.org/W1978902427","https://openalex.org/W2070021921","https://openalex.org/W2090037139","https://openalex.org/W2102619694","https://openalex.org/W2109949710","https://openalex.org/W2114083195","https://openalex.org/W2156509269","https://openalex.org/W2161535481","https://openalex.org/W2310342073","https://openalex.org/W2324629078","https://openalex.org/W2345512687","https://openalex.org/W2433743436","https://openalex.org/W2605409611","https://openalex.org/W2798115135","https://openalex.org/W2943761358","https://openalex.org/W2960370523","https://openalex.org/W2963468488","https://openalex.org/W2998689926","https://openalex.org/W3094755456","https://openalex.org/W4253990352"],"related_works":["https://openalex.org/W2999147745","https://openalex.org/W3018341089","https://openalex.org/W4221005434","https://openalex.org/W3038795558","https://openalex.org/W2998399076","https://openalex.org/W2567008309","https://openalex.org/W4226081743","https://openalex.org/W1975403665","https://openalex.org/W3201074590","https://openalex.org/W1999512975"],"abstract_inverted_index":{"Genomes":[0],"are":[1,16,72,91],"organized":[2],"into":[3],"self-interacting":[4],"units":[5],"called":[6],"Topologically":[7],"Associated":[8],"Domains":[9],"or":[10],"TADs.":[11],"The":[12,82],"boundaries":[13,33,49,90,119],"of":[14,32,47,108,128,151,175,187,197],"TADs":[15],"characterized":[17],"by":[18,85,156,171],"enriched":[19,201],"CTCF":[20],"binding":[21],"sites":[22],"and":[23,26,43,68,112,142,170,194],"active":[24],"gene":[25,44],"chromatin":[27],"activity.":[28],"Deciphering":[29],"the":[30,38,69,161,188,198],"locations":[31],"is":[34,50],"key":[35],"to":[36,116],"understanding":[37],"relationship":[39],"between":[40],"genome":[41],"organization":[42],"expression.":[45],"Detection":[46],"these":[48,86],"mainly":[51],"based":[52],"on":[53,104],"interaction":[54],"frequency":[55],"matrices":[56],"from":[57],"costly":[58],"Hi-C":[59],"experiments.":[60],"Recent":[61],"studies":[62],"suggest":[63],"that":[64,78,102,133,147,183],"epigenetic":[65,114],"features,":[66],"CTCF,":[67,109,193],"Cohesin":[70,110,199],"complex":[71],"more":[73],"important":[74],"than":[75],"sequence":[76],"features":[77,87,106,115,190],"characterize":[79],"TAD":[80,89,118,165,176,203],"boundaries.":[81,166,204],"patterns":[83,186],"exhibited":[84],"in":[88,120,163,202],"also":[92],"unknown.":[93],"In":[94],"this":[95,168],"paper,":[96],"we":[97,145,178],"propose":[98],"deep":[99,130],"learning":[100,131],"models":[101,132],"rely":[103],"14":[105,189],"comprising":[107],"complex,":[111],"12":[113],"predict":[117],"human":[121],"cell":[122],"lines.":[123],"By":[124],"exploring":[125],"different":[126],"architectures":[127],"popular":[129],"incorporate":[134],"dense":[135,158],"layer,":[136,138,141],"convolution":[137,153],"long":[139],"short-term":[140],"residual":[143],"blocks,":[144],"find":[146],"a":[148,157],"model":[149,169],"consisting":[150],"four":[152,180],"layers":[154],"followed":[155],"layer":[159],"performs":[160],"best":[162],"predicting":[164],"Using":[167],"computing":[172],"saliency":[173],"maps":[174],"boundaries,":[177],"uncover":[179],"main":[181],"motifs":[182],"capture":[184],"recurring":[185],"(12":[191],"epigenetic,":[192],"RAD21":[195],"(subunit":[196],"Complex))":[200]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}