{"id":"https://openalex.org/W3096581305","doi":"https://doi.org/10.1109/tcbb.2020.3034313","title":"Identification of Functional piRNAs Using a Convolutional Neural Network","display_name":"Identification of Functional piRNAs Using a Convolutional Neural Network","publication_year":2020,"publication_date":"2020-10-29","ids":{"openalex":"https://openalex.org/W3096581305","doi":"https://doi.org/10.1109/tcbb.2020.3034313","mag":"3096581305","pmid":"https://pubmed.ncbi.nlm.nih.gov/33119510"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2020.3034313","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2020.3034313","pdf_url":null,"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":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":"journal-article"},"type":"article","indexed_in":["crossref","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/A5076289546","display_name":"Syed Danish Ali","orcid":"https://orcid.org/0000-0001-5204-5073"},"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":"Syed Danish Ali","raw_affiliation_strings":["Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju, South Korea","[Jeonbuk National University, 26714 Jeonju, Jeollabukdo Korea (the Republic of) 54896 (e-mail: mashdi.danish@gmail.com)]"],"affiliations":[{"raw_affiliation_string":"Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju, South Korea","institution_ids":["https://openalex.org/I80611190"]},{"raw_affiliation_string":"[Jeonbuk National University, 26714 Jeonju, Jeollabukdo Korea (the Republic of) 54896 (e-mail: mashdi.danish@gmail.com)]","institution_ids":["https://openalex.org/I80611190"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087172301","display_name":"Waleed Alam","orcid":"https://orcid.org/0000-0001-8622-4985"},"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":"Waleed Alam","raw_affiliation_strings":["Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju, South Korea","[Chonbuk National University, 26714 Jeonju, Jeonllbukdo Korea (the Republic of) (e-mail: waleedtkr@gmail.com)]"],"affiliations":[{"raw_affiliation_string":"Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju, South Korea","institution_ids":["https://openalex.org/I80611190"]},{"raw_affiliation_string":"[Chonbuk National University, 26714 Jeonju, Jeonllbukdo Korea (the Republic of) (e-mail: waleedtkr@gmail.com)]","institution_ids":["https://openalex.org/I80611190"]}]},{"author_position":"middle","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":false,"raw_author_name":"Hilal Tayara","raw_affiliation_strings":["School of International Engineering and Science, Jeonbuk National University, Jeonju, South Korea","[School of International Engineering and Science, Chonbuk National University, 26714 Jeonju, Jeollabuk-do Korea (the Republic of) (e-mail: hilaltayara@jbnu.ac.kr)]"],"affiliations":[{"raw_affiliation_string":"School of International Engineering and Science, Jeonbuk National University, Jeonju, South Korea","institution_ids":["https://openalex.org/I80611190"]},{"raw_affiliation_string":"[School of International Engineering and Science, Chonbuk National University, 26714 Jeonju, Jeollabuk-do Korea (the Republic of) (e-mail: hilaltayara@jbnu.ac.kr)]","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, Jeonbuk National University, Jeonju, South Korea","[Chonbuk National University, 26714 Jeonju, Jeonllbukdo Korea (the Republic of) 54896 (e-mail: kitchong@jbnu.ac.kr)]"],"affiliations":[{"raw_affiliation_string":"Advanced Electronics and Information Research Center, Jeonbuk National University, Jeonju, South Korea","institution_ids":["https://openalex.org/I80611190"]},{"raw_affiliation_string":"[Chonbuk National University, 26714 Jeonju, Jeonllbukdo Korea (the Republic of) 54896 (e-mail: kitchong@jbnu.ac.kr)]","institution_ids":["https://openalex.org/I80611190"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5076289546"],"corresponding_institution_ids":["https://openalex.org/I80611190"],"apc_list":null,"apc_paid":null,"fwci":2.0713,"has_fulltext":false,"cited_by_count":32,"citation_normalized_percentile":{"value":0.87837331,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"19","issue":"3","first_page":"1661","last_page":"1669"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9977999925613403,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9973999857902527,"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/identification","display_name":"Identification (biology)","score":0.7379506826400757},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.6283742189407349},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6019256114959717},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.41376858949661255},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.41267046332359314},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.211713969707489},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.06716057658195496}],"concepts":[{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.7379506826400757},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.6283742189407349},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6019256114959717},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41376858949661255},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.41267046332359314},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.211713969707489},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.06716057658195496}],"mesh":[{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2020.3034313","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2020.3034313","pdf_url":null,"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":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":"journal-article"},{"id":"pmid:33119510","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33119510","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":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4069871152","display_name":null,"funder_award_id":"2020R1A2C2005612","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"},{"id":"https://openalex.org/G8509831517","display_name":null,"funder_award_id":"NRF-2017M3C7A1044816","funder_id":"https://openalex.org/F4320320671","funder_display_name":"National Research Foundation"}],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320322120","display_name":"National Research Foundation of Korea","ror":"https://ror.org/013aysd81"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W1666984270","https://openalex.org/W1823358129","https://openalex.org/W1976342457","https://openalex.org/W1977733607","https://openalex.org/W1977927254","https://openalex.org/W2035930185","https://openalex.org/W2048218599","https://openalex.org/W2075196167","https://openalex.org/W2103012554","https://openalex.org/W2106141559","https://openalex.org/W2108051165","https://openalex.org/W2120026469","https://openalex.org/W2120081922","https://openalex.org/W2132083787","https://openalex.org/W2132102978","https://openalex.org/W2234938965","https://openalex.org/W2313411748","https://openalex.org/W2339812959","https://openalex.org/W2508414719","https://openalex.org/W2605763657","https://openalex.org/W2767070506","https://openalex.org/W2771079624","https://openalex.org/W2772515592","https://openalex.org/W2787719063","https://openalex.org/W2794864022","https://openalex.org/W2886966121","https://openalex.org/W2895734781","https://openalex.org/W2901455448","https://openalex.org/W2904497009","https://openalex.org/W2906046752","https://openalex.org/W2919115771","https://openalex.org/W2925252074","https://openalex.org/W2932524182","https://openalex.org/W2937997287","https://openalex.org/W2940473304","https://openalex.org/W2961926658","https://openalex.org/W2964046515","https://openalex.org/W2964874436","https://openalex.org/W2965952014","https://openalex.org/W2969662046","https://openalex.org/W2976262693","https://openalex.org/W2979999916","https://openalex.org/W2994619710","https://openalex.org/W2995912276","https://openalex.org/W2996489182","https://openalex.org/W3011049612","https://openalex.org/W3013230828","https://openalex.org/W3036278095","https://openalex.org/W4239315130","https://openalex.org/W4250482878","https://openalex.org/W6771982476"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Piwi-interacting":[0],"RNAs":[1,10],"(piRNAs)":[2],"are":[3,12,32],"a":[4,69,74,82,113,138],"distinct":[5],"sub-class":[6],"of":[7,28,41,127],"small":[8],"non-coding":[9],"that":[11],"mainly":[13],"responsible":[14],"for":[15,98],"germline":[16],"stem":[17],"cell":[18],"maintenance,":[19],"gene":[20],"stability,":[21],"and":[22,36,46,76,129,140],"maintaining":[23],"genome":[24],"integrity":[25],"by":[26],"repression":[27],"transposable":[29],"elements.":[30],"piRNAs":[31,45,128],"also":[33],"expressed":[34],"aberrantly":[35],"associated":[37],"with":[38],"various":[39],"kinds":[40],"cancers.":[42],"To":[43,64],"identify":[44],"their":[47,130],"role":[48,131],"in":[49,62,124,132],"guiding":[50],"target":[51,133],"mRNA":[52,134],"deadenylation,":[53],"the":[54,96,125],"currently":[55],"available":[56,145],"computational":[57,122],"methods":[58,123],"require":[59],"urgent":[60],"improvements":[61],"performance.":[63],"facilitate":[65],"this,":[66],"we":[67],"propose":[68],"robust":[70],"predictor":[71],"based":[72],"on":[73,112],"lightweight":[75],"simplified":[77],"deep":[78],"learning":[79],"architecture":[80],"using":[81,109],"convolutional":[83],"neural":[84],"network":[85],"(CNN)":[86],"to":[87],"extract":[88],"significant":[89],"features":[90],"from":[91],"raw":[92],"RNA":[93],"sequences":[94],"without":[95],"need":[97],"more":[99],"customized":[100],"features.":[101],"The":[102,116],"proposed":[103,117],"model's":[104],"performance":[105],"is":[106,144],"comprehensively":[107],"evaluated":[108],"k-fold":[110],"cross-validation":[111],"benchmark":[114],"dataset.":[115],"model":[118],"significantly":[119],"outperforms":[120],"existing":[121],"prediction":[126],"deadenylation.":[135],"In":[136],"addition,":[137],"user-friendly":[139],"publicly-accessible":[141],"web":[142],"server":[143],"at":[146],"http://nsclbio.jbnu.ac.kr/tools/2S-piRCNN/.":[147]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}