{"id":"https://openalex.org/W2962655813","doi":"https://doi.org/10.1093/bioinformatics/btz337","title":"Prediction of mRNA subcellular localization using deep recurrent neural networks","display_name":"Prediction of mRNA subcellular localization using deep recurrent neural networks","publication_year":2019,"publication_date":"2019-05-09","ids":{"openalex":"https://openalex.org/W2962655813","doi":"https://doi.org/10.1093/bioinformatics/btz337","mag":"2962655813","pmid":"https://pubmed.ncbi.nlm.nih.gov/31510698"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz337","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz337","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/14/i333/28913727/btz337.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/14/i333/28913727/btz337.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036927472","display_name":"Zichao Yan","orcid":"https://orcid.org/0000-0002-9420-739X"},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Zichao Yan","raw_affiliation_strings":["School of Computer Science, McGill University, Montreal, QC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, McGill University, Montreal, QC, Canada","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018570031","display_name":"\u00c9ric L\u00e9cuyer","orcid":"https://orcid.org/0000-0002-4383-342X"},"institutions":[{"id":"https://openalex.org/I4210158752","display_name":"Montreal Clinical Research Institute","ror":"https://ror.org/05m8pzq90","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210158752","https://openalex.org/I70931966"]},{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]},{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Eric L\u00e9cuyer","raw_affiliation_strings":["Department of Biochemistry, University of Montreal, Montreal, QC, Canada","Division of Experimental Medicine, McGill University, Montreal, QC, Canada","Institut de Recherches Clinique de Montr\u00e9al (IRCM), Montreal, QC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Montreal, Montreal, QC, Canada","institution_ids":["https://openalex.org/I70931966"]},{"raw_affiliation_string":"Division of Experimental Medicine, McGill University, Montreal, QC, Canada","institution_ids":["https://openalex.org/I5023651"]},{"raw_affiliation_string":"Institut de Recherches Clinique de Montr\u00e9al (IRCM), Montreal, QC, Canada","institution_ids":["https://openalex.org/I4210158752"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065720651","display_name":"Mathieu Blanchette","orcid":"https://orcid.org/0000-0002-9555-860X"},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Mathieu Blanchette","raw_affiliation_strings":["School of Computer Science, McGill University, Montreal, QC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, McGill University, Montreal, QC, Canada","institution_ids":["https://openalex.org/I5023651"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5065720651"],"corresponding_institution_ids":["https://openalex.org/I5023651"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.0759,"has_fulltext":false,"cited_by_count":86,"citation_normalized_percentile":{"value":0.92536671,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"35","issue":"14","first_page":"i333","last_page":"i342"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9114999771118164,"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":0.9114999771118164,"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":0.048700001090765,"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":0.010099999606609344,"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":0.6102221012115479},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6052598357200623},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5456822514533997},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5115236043930054},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5046995878219604},{"id":"https://openalex.org/keywords/subcellular-localization","display_name":"Subcellular localization","score":0.4930054843425751},{"id":"https://openalex.org/keywords/variety","display_name":"Variety (cybernetics)","score":0.46504369378089905},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.4637477993965149},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.45733505487442017},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.45395344495773315},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.44692346453666687},{"id":"https://openalex.org/keywords/rna-binding-protein","display_name":"RNA-binding protein","score":0.43572166562080383},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.43282926082611084},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.40143871307373047},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3500674366950989},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2210170328617096}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6102221012115479},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6052598357200623},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5456822514533997},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5115236043930054},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5046995878219604},{"id":"https://openalex.org/C2776879804","wikidata":"https://www.wikidata.org/wiki/Q7630919","display_name":"Subcellular localization","level":3,"score":0.4930054843425751},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.46504369378089905},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.4637477993965149},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.45733505487442017},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.45395344495773315},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.44692346453666687},{"id":"https://openalex.org/C41282012","wikidata":"https://www.wikidata.org/wiki/Q3928341","display_name":"RNA-binding protein","level":4,"score":0.43572166562080383},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.43282926082611084},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.40143871307373047},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3500674366950989},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2210170328617096},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","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":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":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz337","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz337","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/14/i333/28913727/btz337.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31510698","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31510698","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},{"id":"pmh:oai:europepmc.org:5588684","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6612824","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz337","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz337","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/14/i333/28913727/btz337.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320330273","display_name":"Institut de Valorisation des Donn\u00e9es","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W97743426","https://openalex.org/W1019830208","https://openalex.org/W1988581590","https://openalex.org/W1995224771","https://openalex.org/W1997535872","https://openalex.org/W2000951164","https://openalex.org/W2006617902","https://openalex.org/W2033159578","https://openalex.org/W2064675550","https://openalex.org/W2086561953","https://openalex.org/W2105694586","https://openalex.org/W2113525941","https://openalex.org/W2131774270","https://openalex.org/W2144015117","https://openalex.org/W2147800946","https://openalex.org/W2151994495","https://openalex.org/W2157009395","https://openalex.org/W2158266834","https://openalex.org/W2163482144","https://openalex.org/W2167852161","https://openalex.org/W2171584832","https://openalex.org/W2198606573","https://openalex.org/W2245239316","https://openalex.org/W2285139619","https://openalex.org/W2336509392","https://openalex.org/W2594622866","https://openalex.org/W2620688794","https://openalex.org/W2625599729","https://openalex.org/W2635766923","https://openalex.org/W2691563344","https://openalex.org/W2762250455","https://openalex.org/W2765281581","https://openalex.org/W2899322113","https://openalex.org/W2899616402","https://openalex.org/W2913683218","https://openalex.org/W2949671734","https://openalex.org/W2950463913","https://openalex.org/W2950856588","https://openalex.org/W4210659358"],"related_works":["https://openalex.org/W2359834996","https://openalex.org/W2384565783","https://openalex.org/W2070256704","https://openalex.org/W4375867731","https://openalex.org/W4282922129","https://openalex.org/W1964033480","https://openalex.org/W2099701744","https://openalex.org/W2375119535","https://openalex.org/W2012210483","https://openalex.org/W4322772305"],"abstract_inverted_index":{"MOTIVATION:":[0],"Messenger":[1],"RNA":[2],"subcellular":[3,41,84],"localization":[4],"mechanisms":[5,45],"play":[6],"a":[7,62,80,113,127],"crucial":[8],"role":[9],"in":[10],"post-transcriptional":[11],"gene":[12],"regulation.":[13],"This":[14],"trafficking":[15],"is":[16,123],"mediated":[17],"by":[18],"trans-acting":[19],"RNA-binding":[20],"proteins":[21],"interacting":[22],"with":[23],"cis-regulatory":[24],"elements":[25],"called":[26],"zipcodes.":[27],"While":[28],"new":[29],"sequencing-based":[30],"technologies":[31],"allow":[32],"the":[33,43,74,138],"high-throughput":[34],"identification":[35],"of":[36,76,83,103,115,129,137],"RNAs":[37],"localized":[38],"to":[39,68,126,143,150],"specific":[40,52],"compartments,":[42],"precise":[44],"at":[46,166,174],"play,":[47],"and":[48,96,99,106,149,161],"their":[49,71],"dependency":[50],"on":[51,112],"sequence":[53,72,105],"elements,":[54],"remain":[55],"poorly":[56],"understood.":[57],"RESULTS:":[58],"We":[59,110],"introduce":[60],"RNATracker,":[61],"novel":[63],"deep":[64,90],"neural":[65],"network":[66],"built":[67],"predict,":[69],"from":[70],"alone,":[73],"distributions":[75],"mRNA":[77],"transcripts":[78],"over":[79],"predefined":[81],"set":[82],"compartments.":[85],"RNATracker":[86],"integrates":[87],"several":[88,135],"state-of-the-art":[89],"learning":[91],"techniques":[92],"(e.g.":[93],"CNN,":[94],"LSTM":[95],"attention":[97],"layers)":[98],"can":[100,140,163],"make":[101],"use":[102],"both":[104],"secondary":[107],"structure":[108],"information.":[109],"report":[111],"variety":[114,128],"evaluations":[116],"showing":[117],"RNATracker's":[118],"strong":[119],"predictive":[120],"power,":[121],"which":[122],"significantly":[124],"superior":[125],"baseline":[130],"predictors.":[131],"Despite":[132],"its":[133],"complexity,":[134],"aspects":[136],"model":[139],"be":[141,164],"isolated":[142],"yield":[144],"valuable,":[145],"testable":[146],"mechanistic":[147],"hypotheses,":[148],"locate":[151],"candidate":[152],"zipcode":[153],"sequences":[154],"within":[155],"transcripts.":[156],"AVAILABILITY":[157],"AND":[158],"IMPLEMENTATION:":[159],"Code":[160],"data":[162,171],"accessed":[165],"https://www.github.com/HarveyYan/RNATracker.":[167],"SUPPLEMENTARY":[168],"INFORMATION:":[169],"Supplementary":[170],"are":[172],"available":[173],"Bioinformatics":[175],"online.":[176]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":22},{"year":2023,"cited_by_count":14},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}