{"id":"https://openalex.org/W4292722723","doi":"https://doi.org/10.1093/bioinformatics/btac575","title":"CLNN-loop: a deep learning model to predict CTCF-mediated chromatin loops in the different cell lines and CTCF-binding sites (CBS) pair types","display_name":"CLNN-loop: a deep learning model to predict CTCF-mediated chromatin loops in the different cell lines and CTCF-binding sites (CBS) pair types","publication_year":2022,"publication_date":"2022-08-23","ids":{"openalex":"https://openalex.org/W4292722723","doi":"https://doi.org/10.1093/bioinformatics/btac575","pmid":"https://pubmed.ncbi.nlm.nih.gov/35997565"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac575","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac575","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100653968","display_name":"Pengyu Zhang","orcid":"https://orcid.org/0000-0001-8696-4983"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]},{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pengyu Zhang","raw_affiliation_strings":["College of Information Engineering, Northwest A&F University , Yangling, Shaanxi 712100, China","School of Software, Shandong University , Jinan, Shandong 250101, China"],"raw_orcid":"https://orcid.org/0000-0001-8696-4983","affiliations":[{"raw_affiliation_string":"College of Information Engineering, Northwest A&F University , Yangling, Shaanxi 712100, China","institution_ids":["https://openalex.org/I89652312"]},{"raw_affiliation_string":"School of Software, Shandong University , Jinan, Shandong 250101, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011266301","display_name":"Yingfu Wu","orcid":"https://orcid.org/0000-0002-8142-6999"},"institutions":[{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yingfu Wu","raw_affiliation_strings":["College of Information Engineering, Northwest A&F University , Yangling, Shaanxi 712100, China"],"raw_orcid":"https://orcid.org/0000-0002-8142-6999","affiliations":[{"raw_affiliation_string":"College of Information Engineering, Northwest A&F University , Yangling, Shaanxi 712100, China","institution_ids":["https://openalex.org/I89652312"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034490149","display_name":"Haoru Zhou","orcid":"https://orcid.org/0000-0003-1524-0093"},"institutions":[{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haoru Zhou","raw_affiliation_strings":["College of Information Engineering, Northwest A&F University , Yangling, Shaanxi 712100, China"],"raw_orcid":"https://orcid.org/0000-0003-1524-0093","affiliations":[{"raw_affiliation_string":"College of Information Engineering, Northwest A&F University , Yangling, Shaanxi 712100, China","institution_ids":["https://openalex.org/I89652312"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048890418","display_name":"Bing Zhou","orcid":"https://orcid.org/0000-0002-5872-8358"},"institutions":[{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bing Zhou","raw_affiliation_strings":["College of Information Engineering, Northwest A&F University , Yangling, Shaanxi 712100, China"],"raw_orcid":"https://orcid.org/0000-0002-5872-8358","affiliations":[{"raw_affiliation_string":"College of Information Engineering, Northwest A&F University , Yangling, Shaanxi 712100, China","institution_ids":["https://openalex.org/I89652312"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100445041","display_name":"Hongming Zhang","orcid":"https://orcid.org/0000-0003-4605-8577"},"institutions":[{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongming Zhang","raw_affiliation_strings":["College of Information Engineering, Northwest A&F University , Yangling, Shaanxi 712100, China"],"raw_orcid":"https://orcid.org/0000-0003-4605-8577","affiliations":[{"raw_affiliation_string":"College of Information Engineering, Northwest A&F University , Yangling, Shaanxi 712100, China","institution_ids":["https://openalex.org/I89652312"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036176693","display_name":"Hao Wu","orcid":"https://orcid.org/0000-0003-2340-9258"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Hao Wu","raw_affiliation_strings":["School of Software, Shandong University , Jinan, Shandong 250101, China"],"raw_orcid":"https://orcid.org/0000-0003-2340-9258","affiliations":[{"raw_affiliation_string":"School of Software, Shandong University , Jinan, Shandong 250101, China","institution_ids":["https://openalex.org/I154099455"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5036176693"],"corresponding_institution_ids":["https://openalex.org/I154099455"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":5.4561,"has_fulltext":false,"cited_by_count":69,"citation_normalized_percentile":{"value":0.97193855,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"38","issue":"19","first_page":"4497","last_page":"4504"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9965000152587891,"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":0.9965000152587891,"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":0.0012000000569969416,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.0003000000142492354,"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":0.9366676807403564},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.9211111068725586},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6737910509109497},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6127671003341675},{"id":"https://openalex.org/keywords/loop","display_name":"Loop (graph theory)","score":0.48727262020111084},{"id":"https://openalex.org/keywords/generalization","display_name":"Generalization","score":0.4821907579898834},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.47915738821029663},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.395643949508667},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3023239076137543},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.24663841724395752},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.19675523042678833},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09688001871109009}],"concepts":[{"id":"https://openalex.org/C2778760011","wikidata":"https://www.wikidata.org/wiki/Q21163346","display_name":"CTCF","level":5,"score":0.9366676807403564},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.9211111068725586},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6737910509109497},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6127671003341675},{"id":"https://openalex.org/C184670325","wikidata":"https://www.wikidata.org/wiki/Q512604","display_name":"Loop (graph theory)","level":2,"score":0.48727262020111084},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.4821907579898834},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.47915738821029663},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.395643949508667},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3023239076137543},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.24663841724395752},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.19675523042678833},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09688001871109009},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000076246","descriptor_name":"CCCTC-Binding Factor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000076246","descriptor_name":"CCCTC-Binding Factor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000076246","descriptor_name":"CCCTC-Binding Factor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"D002460","descriptor_name":"Cell Line","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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btac575","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac575","pdf_url":null,"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:35997565","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35997565","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":null,"sustainable_development_goals":[{"display_name":"Life in Land","score":0.4000000059604645,"id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G2698802062","display_name":null,"funder_award_id":"2021YFF0704103","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G2885452329","display_name":null,"funder_award_id":"2021JM110","funder_id":"https://openalex.org/F4320324173","funder_display_name":"Natural Science Foundation of Shaanxi Province"},{"id":"https://openalex.org/G715904284","display_name":"\u4e09\u7ef4\u57fa\u56e0\u7ec4\u8c03\u63a7\u5c42\u9762\u7684\u764c\u75c7\u81f4\u75c5\u901a\u8def\u6316\u6398\u65b9\u6cd5\u7814\u7a76","funder_award_id":"61972322","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320324173","display_name":"Natural Science Foundation of Shaanxi Province","ror":null},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W1558882143","https://openalex.org/W1605145036","https://openalex.org/W1831401007","https://openalex.org/W1915238740","https://openalex.org/W1922881706","https://openalex.org/W1964184081","https://openalex.org/W1973062929","https://openalex.org/W1985258161","https://openalex.org/W1985621639","https://openalex.org/W2064675550","https://openalex.org/W2068315875","https://openalex.org/W2090037139","https://openalex.org/W2099665470","https://openalex.org/W2112796928","https://openalex.org/W2131186458","https://openalex.org/W2153635508","https://openalex.org/W2156509269","https://openalex.org/W2187089797","https://openalex.org/W2333286569","https://openalex.org/W2401568148","https://openalex.org/W2781657900","https://openalex.org/W2782190517","https://openalex.org/W2792734199","https://openalex.org/W2795091386","https://openalex.org/W2799200068","https://openalex.org/W2802659202","https://openalex.org/W2883534252","https://openalex.org/W2921983621","https://openalex.org/W2943761358","https://openalex.org/W2951218167","https://openalex.org/W2962862931","https://openalex.org/W2967960129","https://openalex.org/W3013230828","https://openalex.org/W3041895828","https://openalex.org/W3091921516","https://openalex.org/W3096505797","https://openalex.org/W3132963234","https://openalex.org/W3134384141","https://openalex.org/W3138043598","https://openalex.org/W3178078266","https://openalex.org/W3202112943","https://openalex.org/W4200473661","https://openalex.org/W4210880116","https://openalex.org/W4230397979","https://openalex.org/W6737947904"],"related_works":["https://openalex.org/W3083199549","https://openalex.org/W2010297690","https://openalex.org/W4362507076","https://openalex.org/W4292590360","https://openalex.org/W2341637133","https://openalex.org/W3004934868","https://openalex.org/W2755337536","https://openalex.org/W2582488421","https://openalex.org/W4394834518","https://openalex.org/W4220758050"],"abstract_inverted_index":{"MOTIVATION:":[0],"Three-dimensional":[1],"(3D)":[2],"genome":[3,63],"organization":[4,64],"is":[5,136,192,202],"of":[6,30,61,116,119,144,159,173,190,200],"vital":[7],"importance":[8],"in":[9,80,99,125,142,176],"gene":[10],"regulation":[11],"and":[12,50,65,76,103,135,162,167,180,197],"disease":[13],"mechanisms.":[14],"Previous":[15],"studies":[16],"have":[17,36,44,73],"shown":[18],"that":[19,130,164],"CTCF-mediated":[20],"chromatin":[21,41,68,82,97,146,174],"loops":[22,98,175],"are":[23,170,211],"crucial":[24],"to":[25,39,47,95,138,155],"studying":[26],"the":[27,123,126,139,152,157,198],"3D":[28,62],"structure":[29],"cells.":[31],"Although":[32],"various":[33,53],"experimental":[34],"techniques":[35],"been":[37,45],"developed":[38],"detect":[40],"loops,":[42],"they":[43],"found":[46],"be":[48],"time-consuming":[49],"costly.":[51],"Nowadays,":[52],"sequence-based":[54,112],"computational":[55],"methods":[56,72,141],"can":[57],"capture":[58],"significant":[59],"features":[60],"help":[66],"predict":[67,96],"loops.":[69,83,147],"However,":[70],"these":[71],"low":[74],"performance":[75,134],"poor":[77],"generalization":[78],"ability":[79],"predicting":[81,145],"RESULTS:":[84],"Here,":[85],"we":[86,150],"propose":[87],"a":[88,117],"novel":[89],"deep":[90],"learning":[91],"model,":[92],"called":[93],"CLNN-loop,":[94],"different":[100,160,177],"cell":[101,178],"lines":[102,179],"CTCF-binding":[104],"sites":[105],"(CBS)":[106],"pair":[107,182],"types":[108],"by":[109],"fusing":[110],"multiple":[111],"features.":[113],"The":[114,187],"analysis":[115],"series":[118],"examinations":[120],"based":[121],"on":[122],"datasets":[124],"previous":[127],"study":[128],"shows":[129],"CLNN-loop":[131,191,201],"has":[132],"satisfactory":[133],"superior":[137],"existing":[140],"terms":[143],"In":[148],"addition,":[149],"apply":[151],"SHAP":[153],"framework":[154],"interpret":[156],"predictions":[158],"models,":[161],"find":[163],"CTCF":[165],"motif":[166],"sequence":[168],"conservation":[169],"important":[171],"signs":[172],"CBS":[181],"types.":[183],"AVAILABILITY":[184],"AND":[185],"IMPLEMENTATION:":[186],"source":[188],"code":[189],"freely":[193,203],"available":[194,204,212],"at":[195,205,213],"https://github.com/HaoWuLab-Bioinformatics/CLNN-loop":[196],"webserver":[199],"http://hwclnn.sdu.edu.cn.":[206],"SUPPLEMENTARY":[207],"INFORMATION:":[208],"Supplementary":[209],"data":[210],"Bioinformatics":[214],"online.":[215]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":21},{"year":2024,"cited_by_count":23},{"year":2023,"cited_by_count":20},{"year":2022,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
