{"id":"https://openalex.org/W3011049612","doi":"https://doi.org/10.1109/tcbb.2020.2981335","title":"Improved Predicting of The Sequence Specificities of RNA Binding Proteins by Deep Learning","display_name":"Improved Predicting of The Sequence Specificities of RNA Binding Proteins by Deep Learning","publication_year":2020,"publication_date":"2020-03-18","ids":{"openalex":"https://openalex.org/W3011049612","doi":"https://doi.org/10.1109/tcbb.2020.2981335","mag":"3011049612","pmid":"https://pubmed.ncbi.nlm.nih.gov/32191896"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2020.2981335","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbb.2020.2981335","pdf_url":"https://ieeexplore.ieee.org/ielx7/8857/9642421/09040403.pdf","source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://ieeexplore.ieee.org/ielx7/8857/9642421/09040403.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008953921","display_name":"Hilal Tayara","orcid":"https://orcid.org/0000-0001-5678-3479"},"institutions":[{"id":"https://openalex.org/I80611190","display_name":"Jeonbuk National University","ror":"https://ror.org/05q92br09","country_code":"KR","type":"education","lineage":["https://openalex.org/I80611190"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Hilal Tayara","raw_affiliation_strings":["Department of Electronics and Information Engineering, Chonbuk National University, Jeonju, South Korea"],"affiliations":[{"raw_affiliation_string":"Department of Electronics and Information Engineering, Chonbuk National University, Jeonju, South Korea","institution_ids":["https://openalex.org/I80611190"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031342322","display_name":"Kil To Chong","orcid":"https://orcid.org/0000-0002-1952-0001"},"institutions":[{"id":"https://openalex.org/I80611190","display_name":"Jeonbuk National University","ror":"https://ror.org/05q92br09","country_code":"KR","type":"education","lineage":["https://openalex.org/I80611190"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Kil To Chong","raw_affiliation_strings":["Advanced Electronics and Information Research Center, Chonbuk National University, Jeonju, South Korea"],"affiliations":[{"raw_affiliation_string":"Advanced Electronics and Information Research Center, Chonbuk National University, Jeonju, South Korea","institution_ids":["https://openalex.org/I80611190"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5008953921"],"corresponding_institution_ids":["https://openalex.org/I80611190"],"apc_list":null,"apc_paid":null,"fwci":1.3372,"has_fulltext":true,"cited_by_count":21,"citation_normalized_percentile":{"value":0.79848082,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"18","issue":"6","first_page":"2526","last_page":"2534"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","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/T10521","display_name":"RNA and protein synthesis mechanisms","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/T10604","display_name":"RNA Research and Splicing","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/T11482","display_name":"RNA modifications and cancer","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"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5815616250038147},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4947780966758728},{"id":"https://openalex.org/keywords/rna-binding-protein","display_name":"RNA-binding protein","score":0.4237039089202881},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4139712452888489},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.37249428033828735},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3582914471626282},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.32045114040374756},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.30267947912216187},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1745941936969757}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5815616250038147},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4947780966758728},{"id":"https://openalex.org/C41282012","wikidata":"https://www.wikidata.org/wiki/Q3928341","display_name":"RNA-binding protein","level":4,"score":0.4237039089202881},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4139712452888489},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37249428033828735},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3582914471626282},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32045114040374756},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.30267947912216187},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1745941936969757}],"mesh":[{"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":"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":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2020.2981335","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbb.2020.2981335","pdf_url":"https://ieeexplore.ieee.org/ielx7/8857/9642421/09040403.pdf","source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32191896","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32191896","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":{"id":"doi:10.1109/tcbb.2020.2981335","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbb.2020.2981335","pdf_url":"https://ieeexplore.ieee.org/ielx7/8857/9642421/09040403.pdf","source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.6299999952316284,"id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G2134140259","display_name":null,"funder_award_id":"NRF-2017M3C7A1044815","funder_id":"https://openalex.org/F4320320671","funder_display_name":"National Research Foundation"},{"id":"https://openalex.org/G2833317907","display_name":null,"funder_award_id":"NRF-2017M3C7A1044815","funder_id":"https://openalex.org/F4320328359","funder_display_name":"Ministry of Science and ICT, South Korea"}],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320328359","display_name":"Ministry of Science and ICT, South Korea","ror":"https://ror.org/01wpjm123"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3011049612.pdf","grobid_xml":"https://content.openalex.org/works/W3011049612.grobid-xml"},"referenced_works_count":90,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1522301498","https://openalex.org/W1665214252","https://openalex.org/W1965173359","https://openalex.org/W1969156759","https://openalex.org/W1983658501","https://openalex.org/W2001012564","https://openalex.org/W2019522436","https://openalex.org/W2021282293","https://openalex.org/W2021862696","https://openalex.org/W2022268135","https://openalex.org/W2024694407","https://openalex.org/W2038438413","https://openalex.org/W2040356728","https://openalex.org/W2044117548","https://openalex.org/W2052034930","https://openalex.org/W2053003053","https://openalex.org/W2053758959","https://openalex.org/W2062402656","https://openalex.org/W2064675550","https://openalex.org/W2074141093","https://openalex.org/W2080505162","https://openalex.org/W2082102894","https://openalex.org/W2087025873","https://openalex.org/W2087892194","https://openalex.org/W2090123586","https://openalex.org/W2095705004","https://openalex.org/W2103375140","https://openalex.org/W2103777723","https://openalex.org/W2104305103","https://openalex.org/W2105694586","https://openalex.org/W2106309105","https://openalex.org/W2112796928","https://openalex.org/W2114532236","https://openalex.org/W2116251070","https://openalex.org/W2117092553","https://openalex.org/W2122538520","https://openalex.org/W2127616922","https://openalex.org/W2136949432","https://openalex.org/W2147339185","https://openalex.org/W2150248355","https://openalex.org/W2153234291","https://openalex.org/W2153561273","https://openalex.org/W2157331557","https://openalex.org/W2158482911","https://openalex.org/W2163489349","https://openalex.org/W2164552612","https://openalex.org/W2170226759","https://openalex.org/W2198606573","https://openalex.org/W2245239316","https://openalex.org/W2285139619","https://openalex.org/W2307041907","https://openalex.org/W2336509392","https://openalex.org/W2412782625","https://openalex.org/W2596494923","https://openalex.org/W2602034649","https://openalex.org/W2740048744","https://openalex.org/W2771079624","https://openalex.org/W2771169143","https://openalex.org/W2789652838","https://openalex.org/W2799487719","https://openalex.org/W2885815722","https://openalex.org/W2893045341","https://openalex.org/W2896699990","https://openalex.org/W2897898606","https://openalex.org/W2904497009","https://openalex.org/W2906046752","https://openalex.org/W2925252074","https://openalex.org/W2932524182","https://openalex.org/W2941152881","https://openalex.org/W2942090527","https://openalex.org/W2950463913","https://openalex.org/W2951748044","https://openalex.org/W2952935243","https://openalex.org/W2958675005","https://openalex.org/W2965952014","https://openalex.org/W2969891778","https://openalex.org/W2973586775","https://openalex.org/W2976217562","https://openalex.org/W2980975636","https://openalex.org/W2986421215","https://openalex.org/W2991019646","https://openalex.org/W2995912276","https://openalex.org/W3003684254","https://openalex.org/W4294238563","https://openalex.org/W6631190155","https://openalex.org/W6637242042","https://openalex.org/W6674330103","https://openalex.org/W6734429903","https://openalex.org/W6764680637"],"related_works":["https://openalex.org/W2147993839","https://openalex.org/W1840103016","https://openalex.org/W54859794","https://openalex.org/W2064941026","https://openalex.org/W2057323302","https://openalex.org/W2359508303","https://openalex.org/W4379233576","https://openalex.org/W2753172052","https://openalex.org/W1935063092","https://openalex.org/W3080365360"],"abstract_inverted_index":{"RNA-binding":[0],"proteins":[1],"(RBPs)":[2],"have":[3,36],"a":[4],"significant":[5],"role":[6],"in":[7],"various":[8],"regulatory":[9],"tasks.":[10],"However,":[11],"the":[12,18,41,83,86,101,107,111,116,120,129,142,148,152,162],"mechanism":[13],"by":[14,158,168],"which":[15],"RBPs":[16],"identify":[17],"subsequence":[19],"target":[20],"RNAs":[21],"is":[22],"still":[23],"not":[24],"clear.":[25],"In":[26,67,114],"recent":[27],"years,":[28],"several":[29],"machine":[30],"and":[31,60,74,90,161,173],"deep":[32],"learning-based":[33],"computational":[34],"models":[35],"been":[37],"proposed":[38,112],"for":[39,100],"understanding":[40,127],"binding":[42,121,130],"preferences":[43],"of":[44,85,110,119,128,132],"RBPs.":[45,133],"These":[46],"methods":[47],"required":[48],"integrating":[49],"multiple":[50],"features":[51],"with":[52],"raw":[53,87],"RNA":[54,88,102],"sequences":[55,103],"such":[56],"as":[57],"secondary":[58],"structure":[59],"their":[61],"performances":[62],"can":[63,104,124,175],"be":[64,176],"further":[65],"improved.":[66],"this":[68],"paper,":[69],"we":[70],"propose":[71],"an":[72],"efficient":[73],"simple":[75],"convolution":[76],"neural":[77],"network,":[78],"RBPCNN,":[79],"that":[80,95,138],"relies":[81],"on":[82],"combination":[84],"sequence":[89,122],"evolutionary":[91],"information.":[92],"We":[93],"show":[94,137],"conservation":[96],"scores":[97],"(evolutionary":[98],"information)":[99],"significantly":[105,141],"improve":[106],"overall":[108],"performance":[109],"predictor.":[113],"addition,":[115],"automatic":[117],"extraction":[118],"motifs":[123],"enhance":[125],"our":[126],"specificities":[131],"The":[134,171],"experimental":[135],"results":[136,174],"RBPCNN":[139],"outperforms":[140],"current":[143],"state-of-the-art":[144],"methods.":[145],"More":[146],"specifically,":[147],"average":[149,164],"area":[150],"under":[151],"receiver":[153],"operator":[154],"curve":[155],"was":[156,166],"improved":[157,167],"2.67":[159],"percent":[160],"mean":[163],"precision":[165],"8.03":[169],"percent.":[170],"datasets":[172],"downloaded":[177],"from":[178],"https://home.jbnu.ac.kr/NSCL/RBPCNN.htm.":[179]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":4}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
