{"id":"https://openalex.org/W4303859523","doi":"https://doi.org/10.1093/bib/bbac447","title":"DeepLncPro: an interpretable convolutional neural network model for identifying long non-coding RNA promoters","display_name":"DeepLncPro: an interpretable convolutional neural network model for identifying long non-coding RNA promoters","publication_year":2022,"publication_date":"2022-10-08","ids":{"openalex":"https://openalex.org/W4303859523","doi":"https://doi.org/10.1093/bib/bbac447","pmid":"https://pubmed.ncbi.nlm.nih.gov/36209437"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac447","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac447","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/A5100667597","display_name":"Tianyang Zhang","orcid":"https://orcid.org/0000-0001-9542-6685"},"institutions":[{"id":"https://openalex.org/I137506752","display_name":"North China University of Science and Technology","ror":"https://ror.org/04z4wmb81","country_code":"CN","type":"education","lineage":["https://openalex.org/I137506752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tianyang Zhang","raw_affiliation_strings":["School of Life Sciences, North China University of Science and Technology"],"affiliations":[{"raw_affiliation_string":"School of Life Sciences, North China University of Science and Technology","institution_ids":["https://openalex.org/I137506752"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026462731","display_name":"Qiang Tang","orcid":"https://orcid.org/0000-0001-5489-3690"},"institutions":[{"id":"https://openalex.org/I53411278","display_name":"Chengdu University of Traditional Chinese Medicine","ror":"https://ror.org/00pcrz470","country_code":"CN","type":"education","lineage":["https://openalex.org/I53411278"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qiang Tang","raw_affiliation_strings":["School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine"],"affiliations":[{"raw_affiliation_string":"School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine","institution_ids":["https://openalex.org/I53411278"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069460960","display_name":"Fulei Nie","orcid":null},"institutions":[{"id":"https://openalex.org/I137506752","display_name":"North China University of Science and Technology","ror":"https://ror.org/04z4wmb81","country_code":"CN","type":"education","lineage":["https://openalex.org/I137506752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fulei Nie","raw_affiliation_strings":["School of Life Sciences, North China University of Science and Technology"],"affiliations":[{"raw_affiliation_string":"School of Life Sciences, North China University of Science and Technology","institution_ids":["https://openalex.org/I137506752"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052565646","display_name":"Qi Zhao","orcid":"https://orcid.org/0000-0001-9713-1864"},"institutions":[{"id":"https://openalex.org/I114117164","display_name":"University of Science and Technology Liaoning","ror":"https://ror.org/03grx7119","country_code":"CN","type":"education","lineage":["https://openalex.org/I114117164"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Qi Zhao","raw_affiliation_strings":["School of Computer Science and Software Engineering, University of Science and Technology Liaoning"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Software Engineering, University of Science and Technology Liaoning","institution_ids":["https://openalex.org/I114117164"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100344463","display_name":"Wei Chen","orcid":"https://orcid.org/0000-0002-6857-7696"},"institutions":[{"id":"https://openalex.org/I53411278","display_name":"Chengdu University of Traditional Chinese Medicine","ror":"https://ror.org/00pcrz470","country_code":"CN","type":"education","lineage":["https://openalex.org/I53411278"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Wei Chen","raw_affiliation_strings":["Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine"],"affiliations":[{"raw_affiliation_string":"Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine","institution_ids":["https://openalex.org/I53411278"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5052565646","https://openalex.org/A5100344463"],"corresponding_institution_ids":["https://openalex.org/I114117164","https://openalex.org/I53411278"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.5954,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.84357662,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"23","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11482","display_name":"RNA modifications and cancer","score":0.9787999987602234,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9779999852180481,"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/promoter","display_name":"Promoter","score":0.8820480108261108},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.624546229839325},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.6193732619285583},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5974984765052795},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4846401810646057},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.46961838006973267},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.44360584020614624},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.4133601188659668},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.356735497713089},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.349236398935318},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.33221709728240967},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.21275898814201355},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20743975043296814},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.12028887867927551},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1028452217578888}],"concepts":[{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.8820480108261108},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.624546229839325},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.6193732619285583},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5974984765052795},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4846401810646057},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.46961838006973267},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.44360584020614624},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.4133601188659668},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.356735497713089},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.349236398935318},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.33221709728240967},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.21275898814201355},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20743975043296814},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.12028887867927551},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1028452217578888},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D000818","descriptor_name":"Animals","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac447","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac447","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36209437","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36209437","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.4300000071525574}],"awards":[{"id":"https://openalex.org/G1843573243","display_name":null,"funder_award_id":"2022NSFSC1770","funder_id":"https://openalex.org/F4320309612","funder_display_name":"Natural Science Foundation of Shanghai"},{"id":"https://openalex.org/G3040512177","display_name":null,"funder_award_id":"31771471","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3635234882","display_name":null,"funder_award_id":"LJKZ0280","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320309612","display_name":"Natural Science Foundation of Shanghai","ror":null},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W1499959019","https://openalex.org/W1964125655","https://openalex.org/W1964733653","https://openalex.org/W1978811100","https://openalex.org/W2003553455","https://openalex.org/W2014317080","https://openalex.org/W2027010998","https://openalex.org/W2027585195","https://openalex.org/W2030658020","https://openalex.org/W2057094700","https://openalex.org/W2058970225","https://openalex.org/W2066807386","https://openalex.org/W2067272680","https://openalex.org/W2087528029","https://openalex.org/W2103777723","https://openalex.org/W2105389823","https://openalex.org/W2106800367","https://openalex.org/W2107878631","https://openalex.org/W2111400482","https://openalex.org/W2124266758","https://openalex.org/W2129578444","https://openalex.org/W2132247880","https://openalex.org/W2139166279","https://openalex.org/W2293880235","https://openalex.org/W2737592062","https://openalex.org/W2784570320","https://openalex.org/W2808191239","https://openalex.org/W2897570487","https://openalex.org/W2902652978","https://openalex.org/W2903162518","https://openalex.org/W2918598256","https://openalex.org/W2919719345","https://openalex.org/W2932524182","https://openalex.org/W2988641336","https://openalex.org/W2991346114","https://openalex.org/W3006191517","https://openalex.org/W3036354173","https://openalex.org/W3046351677","https://openalex.org/W3080500495","https://openalex.org/W3084492347","https://openalex.org/W3089123840","https://openalex.org/W3095189661","https://openalex.org/W3115618828","https://openalex.org/W3133473745","https://openalex.org/W3137208070","https://openalex.org/W3144893534","https://openalex.org/W4200409924","https://openalex.org/W4213140257","https://openalex.org/W4213420903","https://openalex.org/W6770792585","https://openalex.org/W6771031645"],"related_works":["https://openalex.org/W1969771092","https://openalex.org/W2795723184","https://openalex.org/W2025529750","https://openalex.org/W2891858816","https://openalex.org/W184057646","https://openalex.org/W2042874675","https://openalex.org/W129398428","https://openalex.org/W3212414177","https://openalex.org/W2007418658","https://openalex.org/W1967718992"],"abstract_inverted_index":{"Long":[0],"non-coding":[1],"RNA":[2],"(lncRNA)":[3],"plays":[4],"important":[5],"roles":[6],"in":[7,93],"a":[8,79,148],"series":[9],"of":[10,15,25],"biological":[11],"processes.":[12],"The":[13],"transcription":[14,126],"lncRNA":[16,26,63,91,115,153],"is":[17],"regulated":[18],"by":[19],"its":[20,33],"promoter.":[21],"Hence,":[22],"accurate":[23],"identification":[24],"promoter":[27,44,64],"will":[28],"be":[29,73],"helpful":[30],"to":[31,49,72,89,104,122],"understand":[32],"regulatory":[34],"mechanisms.":[35],"Since":[36],"experimental":[37],"techniques":[38],"remain":[39],"time":[40],"consuming":[41],"for":[42,62,113,151,158],"gnome-wide":[43],"identification,":[45],"developing":[46],"computational":[47,57],"tools":[48],"identify":[50,90],"promoters":[51,92],"are":[52],"necessary.":[53],"However,":[54],"only":[55],"few":[56],"methods":[58,109],"have":[59,70],"been":[60],"proposed":[61,88],"prediction":[65],"and":[66,95,110,124],"their":[67],"performances":[68],"still":[69],"room":[71],"improved.":[74],"In":[75],"the":[76,120,143],"present":[77],"work,":[78],"convolutional":[80],"neural":[81],"network":[82],"based":[83],"model,":[84],"called":[85],"DeepLncPro,":[86],"was":[87,102,160],"human":[94],"mouse.":[96],"Comparative":[97],"results":[98,140],"demonstrated":[99],"that":[100,142],"DeepLncPro":[101,118,144,159],"superior":[103],"both":[105],"state-of-the-art":[106],"machine":[107],"learning":[108],"existing":[111],"models":[112],"identifying":[114,152],"promoters.":[116,154],"Furthermore,":[117],"has":[119],"ability":[121],"extract":[123],"analyze":[125],"factor":[127],"binding":[128],"motifs":[129],"from":[130],"lncRNAs,":[131],"which":[132],"made":[133],"it":[134],"become":[135],"an":[136],"interpretable":[137],"model.":[138],"These":[139],"indicate":[141],"can":[145],"server":[146],"as":[147],"powerful":[149],"tool":[150,157],"An":[155],"open-source":[156],"provided":[161],"at":[162],"https://github.com/zhangtian-yang/DeepLncPro.":[163]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
