{"id":"https://openalex.org/W4380080316","doi":"https://doi.org/10.1021/acs.jcim.3c00366","title":"ABLNCPP: Attention Mechanism-Based Bidirectional Long Short-Term Memory for Noncoding RNA Coding Potential Prediction","display_name":"ABLNCPP: Attention Mechanism-Based Bidirectional Long Short-Term Memory for Noncoding RNA Coding Potential Prediction","publication_year":2023,"publication_date":"2023-06-09","ids":{"openalex":"https://openalex.org/W4380080316","doi":"https://doi.org/10.1021/acs.jcim.3c00366","pmid":"https://pubmed.ncbi.nlm.nih.gov/37294848"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c00366","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00366","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","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/A5085608332","display_name":"Lei Deng","orcid":"https://orcid.org/0000-0003-2869-1619"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lei Deng","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, Changsha 410018, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha 410018, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103161316","display_name":"Jiang Ying","orcid":"https://orcid.org/0000-0002-9576-9538"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ying Jiang","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, Changsha 410018, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha 410018, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101610203","display_name":"Xiaowen Hu","orcid":"https://orcid.org/0000-0002-7339-3007"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaowen Hu","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, Changsha 410018, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha 410018, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102763406","display_name":"Rongtao Zheng","orcid":"https://orcid.org/0000-0002-1241-7108"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rongtao Zheng","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, Changsha 410018, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha 410018, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015986813","display_name":"Zhijian Huang","orcid":"https://orcid.org/0000-0003-1601-3802"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhijian Huang","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, Changsha 410018, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha 410018, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012966716","display_name":"Jingpu Zhang","orcid":"https://orcid.org/0000-0002-8006-747X"},"institutions":[{"id":"https://openalex.org/I4210113703","display_name":"Henan University of Urban Construction","ror":"https://ror.org/01x1skr92","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210113703"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jingpu Zhang","raw_affiliation_strings":["School of Computer and Data Science, Henan University of Urban Construction, Pingdingshan 467000, China"],"affiliations":[{"raw_affiliation_string":"School of Computer and Data Science, Henan University of Urban Construction, Pingdingshan 467000, China","institution_ids":["https://openalex.org/I4210113703"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5012966716"],"corresponding_institution_ids":["https://openalex.org/I4210113703"],"apc_list":null,"apc_paid":null,"fwci":3.1283,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.91706364,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"63","issue":"12","first_page":"3955","last_page":"3966"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9998999834060669,"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":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9980000257492065,"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":0.996399998664856,"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/non-coding-rna","display_name":"Non-coding RNA","score":0.7405321598052979},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5420016646385193},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5334779024124146},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.5283917784690857},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.49362242221832275},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.46574151515960693},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.41153091192245483},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.39928290247917175},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1794053018093109},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16485267877578735}],"concepts":[{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.7405321598052979},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5420016646385193},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5334779024124146},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.5283917784690857},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.49362242221832275},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.46574151515960693},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.41153091192245483},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.39928290247917175},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1794053018093109},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16485267877578735},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D008570","descriptor_name":"Memory, Short-Term","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008570","descriptor_name":"Memory, Short-Term","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.3c00366","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00366","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:37294848","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37294848","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.6200000047683716}],"awards":[{"id":"https://openalex.org/G2008773563","display_name":null,"funder_award_id":"62272490","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3509375425","display_name":null,"funder_award_id":"62172140","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"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W1970569349","https://openalex.org/W1998422171","https://openalex.org/W2048194168","https://openalex.org/W2052503008","https://openalex.org/W2059237622","https://openalex.org/W2070777085","https://openalex.org/W2075320162","https://openalex.org/W2131987814","https://openalex.org/W2139658526","https://openalex.org/W2154053567","https://openalex.org/W2156125289","https://openalex.org/W2160333540","https://openalex.org/W2165423269","https://openalex.org/W2517194566","https://openalex.org/W2559953833","https://openalex.org/W2567665210","https://openalex.org/W2571489439","https://openalex.org/W2593488635","https://openalex.org/W2615786037","https://openalex.org/W2752880228","https://openalex.org/W2761249484","https://openalex.org/W2783029521","https://openalex.org/W2789926271","https://openalex.org/W2886900083","https://openalex.org/W2897137698","https://openalex.org/W2899028887","https://openalex.org/W2899798803","https://openalex.org/W2912721696","https://openalex.org/W2914698725","https://openalex.org/W2914767245","https://openalex.org/W2944031662","https://openalex.org/W2945697904","https://openalex.org/W2951413354","https://openalex.org/W2971055195","https://openalex.org/W2999606367","https://openalex.org/W2999743161","https://openalex.org/W3011176158","https://openalex.org/W3013495013","https://openalex.org/W3015100957","https://openalex.org/W3083074502","https://openalex.org/W3092514200","https://openalex.org/W3198604700","https://openalex.org/W3202397671","https://openalex.org/W3214286775","https://openalex.org/W4294608026","https://openalex.org/W4295242737","https://openalex.org/W4308834336"],"related_works":["https://openalex.org/W1657880117","https://openalex.org/W2595172197","https://openalex.org/W2127970246","https://openalex.org/W2084856301","https://openalex.org/W1001352512","https://openalex.org/W2058984380","https://openalex.org/W1988125422","https://openalex.org/W2900182103","https://openalex.org/W4365136234","https://openalex.org/W3183769948"],"abstract_inverted_index":{"With":[0],"the":[1,100,107,145,165],"continuous":[2],"development":[3],"of":[4,23,103,147],"ribosome":[5],"profiling,":[6],"sequencing":[7],"technology,":[8],"and":[9,29,38,43,68,70,152,162,170],"proteomics,":[10],"evidence":[11],"is":[12,54,153],"mounting":[13],"that":[14,135],"noncoding":[15],"RNA":[16],"(ncRNA)":[17],"may":[18],"be":[19],"a":[20,116],"novel":[21,117],"source":[22,168],"peptides":[24,28],"or":[25],"proteins.":[26],"These":[27],"proteins":[30],"play":[31],"crucial":[32],"roles":[33],"in":[34,65,111,164],"inhibiting":[35],"tumor":[36],"progression":[37],"interfering":[39],"with":[40,51],"cancer":[41,160],"metabolism":[42],"other":[44,138],"essential":[45],"physiological":[46],"processes.":[47],"Therefore,":[48],"identifying":[49],"ncRNAs":[50,67,124],"coding":[52,83,101,149],"potential":[53,150],"vital":[55],"to":[56,77,98,125,155,159],"ncRNA":[57,80,104,148],"functional":[58],"research.":[59],"However,":[60],"existing":[61],"studies":[62],"perform":[63],"well":[64],"classifying":[66],"mRNAs,":[69],"no":[71],"research":[72],"has":[73],"been":[74],"explicitly":[75],"raised":[76],"distinguish":[78],"whether":[79],"transcripts":[81],"have":[82],"potential.":[84],"For":[85],"this":[86],"reason,":[87],"we":[88,114],"propose":[89],"an":[90],"attention":[91],"mechanism-based":[92],"bidirectional":[93],"LSTM":[94],"network":[95],"called":[96],"ABLNCPP":[97,136,143],"assess":[99],"possibility":[102],"sequences.":[105],"Considering":[106],"sequential":[108,129],"information":[109],"loss":[110],"previous":[112],"methods,":[113],"introduce":[115],"nonoverlapping":[118],"trinucleotide":[119],"embedding":[120],"(NOLTE)":[121],"method":[122],"for":[123],"obtain":[126],"embeddings":[127],"containing":[128],"features.":[130],"The":[131,167],"extensive":[132],"evaluations":[133],"show":[134],"outperforms":[137],"state-of-the-art":[139],"models.":[140],"In":[141],"general,":[142],"overcomes":[144],"bottleneck":[146],"prediction":[151],"expected":[154],"provide":[156],"valuable":[157],"contributions":[158],"discovery":[161],"treatment":[163],"future.":[166],"code":[169],"data":[171],"sets":[172],"are":[173],"freely":[174],"available":[175],"at":[176],"https://github.com/YinggggJ/ABLNCPP.":[177]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1}],"updated_date":"2026-03-24T08:02:53.985720","created_date":"2025-10-10T00:00:00"}
