{"id":"https://openalex.org/W3162028695","doi":"https://doi.org/10.1093/bioinformatics/btab349","title":"CrepHAN: cross-species prediction of enhancers by using hierarchical attention networks","display_name":"CrepHAN: cross-species prediction of enhancers by using hierarchical attention networks","publication_year":2021,"publication_date":"2021-05-06","ids":{"openalex":"https://openalex.org/W3162028695","doi":"https://doi.org/10.1093/bioinformatics/btab349","mag":"3162028695","pmid":"https://pubmed.ncbi.nlm.nih.gov/33978703"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab349","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab349","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/A5103678885","display_name":"Jianwei Hong","orcid":null},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianwei Hong","raw_affiliation_strings":["Department of Computer Science and Engineering, Shanghai Jiao Tong University , Shanghai 200240, China","School of Agriculture and Biology, Shanghai Jiao Tong University , Shanghai 200240, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Shanghai Jiao Tong University , Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"School of Agriculture and Biology, Shanghai Jiao Tong University , Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087567274","display_name":"Ruitian Gao","orcid":null},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ruitian Gao","raw_affiliation_strings":["Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University , Shanghai 200240, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University , Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100397381","display_name":"Yang Yang","orcid":"https://orcid.org/0000-0001-5720-773X"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I4210165726","display_name":"Shanghai Municipal Education Commission","ror":"https://ror.org/05tewj457","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210165456","https://openalex.org/I4210165726"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yang Yang","raw_affiliation_strings":["Department of Computer Science and Engineering, Shanghai Jiao Tong University , Shanghai 200240, China","Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering , Shanghai 200240, China"],"raw_orcid":"https://orcid.org/0000-0001-5720-773X","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Shanghai Jiao Tong University , Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering , Shanghai 200240, China","institution_ids":["https://openalex.org/I4210165726"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100397381"],"corresponding_institution_ids":["https://openalex.org/I183067930","https://openalex.org/I4210165726"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.2688,"has_fulltext":false,"cited_by_count":21,"citation_normalized_percentile":{"value":0.79197348,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"37","issue":"20","first_page":"3436","last_page":"3443"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.6963000297546387,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.6963000297546387,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.23520000278949738,"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":0.00860000029206276,"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/enhancer","display_name":"Enhancer","score":0.8516266345977783},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.7282325625419617},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.666090726852417},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6390730738639832},{"id":"https://openalex.org/keywords/human-genome","display_name":"Human genome","score":0.5923810601234436},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.582975447177887},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5306832790374756},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4908514618873596},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.42451170086860657},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3398370146751404},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.33870142698287964},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3364947736263275},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.25866052508354187}],"concepts":[{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.8516266345977783},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.7282325625419617},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.666090726852417},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6390730738639832},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.5923810601234436},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.582975447177887},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5306832790374756},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4908514618873596},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.42451170086860657},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3398370146751404},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.33870142698287964},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3364947736263275},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.25866052508354187},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btab349","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab349","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:33978703","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33978703","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":[],"awards":[{"id":"https://openalex.org/G1724776241","display_name":null,"funder_award_id":"2018YFC0910500","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G3365264765","display_name":null,"funder_award_id":"61972251","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/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":48,"referenced_works":["https://openalex.org/W1501531009","https://openalex.org/W1525488578","https://openalex.org/W1595688369","https://openalex.org/W1964733653","https://openalex.org/W1969770714","https://openalex.org/W1977855308","https://openalex.org/W2030545812","https://openalex.org/W2033201031","https://openalex.org/W2046842005","https://openalex.org/W2064675550","https://openalex.org/W2082103906","https://openalex.org/W2095903180","https://openalex.org/W2108811623","https://openalex.org/W2115272837","https://openalex.org/W2134854530","https://openalex.org/W2135284568","https://openalex.org/W2140240158","https://openalex.org/W2147166867","https://openalex.org/W2154855927","https://openalex.org/W2157009395","https://openalex.org/W2158670138","https://openalex.org/W2159164310","https://openalex.org/W2159664283","https://openalex.org/W2168602111","https://openalex.org/W2169056802","https://openalex.org/W2169819154","https://openalex.org/W2183523328","https://openalex.org/W2250539671","https://openalex.org/W2259938310","https://openalex.org/W2465336312","https://openalex.org/W2470673105","https://openalex.org/W2512558912","https://openalex.org/W2574349495","https://openalex.org/W2588342025","https://openalex.org/W2591130492","https://openalex.org/W2613358096","https://openalex.org/W2733564669","https://openalex.org/W2766812108","https://openalex.org/W2772741766","https://openalex.org/W2807186140","https://openalex.org/W2895408675","https://openalex.org/W2917268863","https://openalex.org/W2942788469","https://openalex.org/W2951472018","https://openalex.org/W2971769670","https://openalex.org/W6691431627","https://openalex.org/W6720133668","https://openalex.org/W6737870451"],"related_works":["https://openalex.org/W2247766769","https://openalex.org/W2187917240","https://openalex.org/W2295325708","https://openalex.org/W2395068850","https://openalex.org/W1989130879","https://openalex.org/W2366650996","https://openalex.org/W2784408333","https://openalex.org/W1544691147","https://openalex.org/W1966558370","https://openalex.org/W2372339860"],"abstract_inverted_index":{"MOTIVATION:":[0],"Enhancers":[1],"are":[2,118,254],"important":[3],"functional":[4],"elements":[5],"in":[6,66,127],"genome":[7,175],"sequences.":[8,165],"The":[9,193],"identification":[10,130],"of":[11,23,51,55,62,78,85,100,131,172,229],"enhancers":[12,37,63,88,102,132],"is":[13,151,232],"a":[14,82,142,154,211],"very":[15],"challenging":[16],"task":[17],"due":[18],"to":[19,71,124,176],"the":[20,27,34,49,52,60,72,76,93,114,128,168,173,178,207,218,221,237],"great":[21],"diversity":[22],"enhancer":[24,116],"sequences":[25],"and":[26,38,75,110,159,180,185,191,205,241],"flexible":[28],"localization":[29],"on":[30,92,183,202,236,243],"genomes.":[31,135],"Till":[32],"now,":[33],"interactions":[35],"between":[36],"genes":[39],"have":[40,64,89],"not":[41],"been":[42,90],"fully":[43],"understood":[44],"yet.":[45],"To":[46],"speed":[47],"up":[48],"studies":[50],"regulatory":[53],"roles":[54],"enhancers,":[56,147],"computational":[57,129],"tools":[58],"for":[59,108,120,133,146,163,215],"prediction":[61],"emerged":[65],"recent":[67],"years.":[68],"Especially,":[69,214],"thanks":[70],"ENCODE":[73],"project":[74],"advances":[77],"high-throughput":[79],"experimental":[80,194],"techniques,":[81],"large":[83,212],"amount":[84],"experimentally":[86,169],"verified":[87],"annotated":[91],"human":[94,109,174,184],"genome,":[95],"which":[96,150],"allows":[97],"large-scale":[98],"predictions":[99],"unknown":[101],"using":[103],"data-driven":[104],"methods.":[105],"However,":[106],"except":[107],"some":[111],"model":[112],"organisms,":[113],"validated":[115],"annotations":[117],"scarce":[119],"most":[121],"species,":[122],"leading":[123],"more":[125,200],"difficulties":[126],"their":[134],"RESULTS:":[136],"In":[137],"this":[138],"study,":[139],"we":[140],"propose":[141],"deep":[143],"learning-based":[144],"predictor":[145],"named":[148],"CrepHAN,":[149],"featured":[152],"by":[153,210,234],"hierarchical":[155],"attention":[156],"neural":[157],"network":[158],"word":[160],"embedding-based":[161],"representations":[162],"DNA":[164],"We":[166],"use":[167],"supported":[170],"data":[171,253],"train":[177],"model,":[179],"perform":[181],"experiments":[182],"other":[186],"mammals,":[187],"including":[188],"mouse,":[189],"cow":[190],"dog.":[192],"results":[195],"show":[196],"that":[197],"CrepHAN":[198],"has":[199],"advantages":[201],"cross-species":[203],"predictions,":[204],"outperforms":[206],"existing":[208],"models":[209],"margin.":[213],"human-mouse":[216],"cross-predictions,":[217],"area":[219],"under":[220],"receiver":[222],"operating":[223],"characteristic":[224],"(ROC)":[225],"curve":[226,231],"(AUC)":[227],"score":[228],"ROC":[230],"increased":[233],"0.033\u223c0.145":[235],"combined":[238],"tissue":[239],"dataset":[240],"0.032\u223c0.109":[242],"tissue-specific":[244],"datasets.":[245],"AVAILABILITY":[246],"AND":[247],"IMPLEMENTATION:":[248],"bcmi.sjtu.edu.cn/\u223cyangyang/CrepHAN.html.":[249],"SUPPLEMENTARY":[250],"INFORMATION:":[251],"Supplementary":[252],"available":[255],"at":[256],"Bioinformatics":[257],"online.":[258]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":7}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
