{"id":"https://openalex.org/W4310665480","doi":"https://doi.org/10.1093/bib/bbac509","title":"RNAlight: a machine learning model to identify nucleotide features determining RNA subcellular localization","display_name":"RNAlight: a machine learning model to identify nucleotide features determining RNA subcellular localization","publication_year":2022,"publication_date":"2022-10-26","ids":{"openalex":"https://openalex.org/W4310665480","doi":"https://doi.org/10.1093/bib/bbac509","pmid":"https://pubmed.ncbi.nlm.nih.gov/36464487"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac509","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac509","pdf_url":"https://academic.oup.com/bib/article-pdf/24/1/bbac509/48782054/bbac509.pdf","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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/24/1/bbac509/48782054/bbac509.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068977715","display_name":"Guo-Hua Yuan","orcid":"https://orcid.org/0000-0002-8459-3784"},"institutions":[{"id":"https://openalex.org/I4210096013","display_name":"Shanghai Institute of Nutrition and Health","ror":"https://ror.org/00rytkh49","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210096013"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guo-Hua Yuan","raw_affiliation_strings":["CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences , Chinese Academy of Sciences, Shanghai 200031 , China"],"raw_orcid":"https://orcid.org/0000-0002-8459-3784","affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences , Chinese Academy of Sciences, Shanghai 200031 , China","institution_ids":["https://openalex.org/I4210096013","https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035002240","display_name":"Ying Wang","orcid":"https://orcid.org/0000-0001-5230-4119"},"institutions":[{"id":"https://openalex.org/I4210096013","display_name":"Shanghai Institute of Nutrition and Health","ror":"https://ror.org/00rytkh49","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210096013"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ying Wang","raw_affiliation_strings":["CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences , Chinese Academy of Sciences, Shanghai 200031 , China"],"raw_orcid":"https://orcid.org/0000-0001-5230-4119","affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences , Chinese Academy of Sciences, Shanghai 200031 , China","institution_ids":["https://openalex.org/I4210096013","https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000963958","display_name":"Guang\u2010Zhong Wang","orcid":"https://orcid.org/0000-0001-6432-8310"},"institutions":[{"id":"https://openalex.org/I4210096013","display_name":"Shanghai Institute of Nutrition and Health","ror":"https://ror.org/00rytkh49","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210096013"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guang-Zhong Wang","raw_affiliation_strings":["CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences , Chinese Academy of Sciences, Shanghai 200031 , China"],"raw_orcid":"https://orcid.org/0000-0001-6432-8310","affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences , Chinese Academy of Sciences, Shanghai 200031 , China","institution_ids":["https://openalex.org/I4210096013","https://openalex.org/I4210165038"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112905610","display_name":"Li Yang","orcid":"https://orcid.org/0000-0001-8833-7473"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Li Yang","raw_affiliation_strings":["Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University , Shanghai 200032 , China"],"raw_orcid":"https://orcid.org/0000-0001-8833-7473","affiliations":[{"raw_affiliation_string":"Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University , Shanghai 200032 , China","institution_ids":["https://openalex.org/I24943067"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5112905610"],"corresponding_institution_ids":["https://openalex.org/I24943067"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":4.0823,"has_fulltext":true,"cited_by_count":45,"citation_normalized_percentile":{"value":0.95764374,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"24","issue":"1","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":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":0.9993000030517578,"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":0.9991000294685364,"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/subcellular-localization","display_name":"Subcellular localization","score":0.8877638578414917},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.6602576971054077},{"id":"https://openalex.org/keywords/small-nucleolar-rna","display_name":"Small nucleolar RNA","score":0.6505572199821472},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.595766544342041},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.585183322429657},{"id":"https://openalex.org/keywords/nucleotide","display_name":"Nucleotide","score":0.4307568669319153},{"id":"https://openalex.org/keywords/long-non-coding-rna","display_name":"Long non-coding RNA","score":0.4022788405418396},{"id":"https://openalex.org/keywords/cytoplasm","display_name":"Cytoplasm","score":0.3157440423965454},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2900601625442505},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.25980144739151}],"concepts":[{"id":"https://openalex.org/C2776879804","wikidata":"https://www.wikidata.org/wiki/Q7630919","display_name":"Subcellular localization","level":3,"score":0.8877638578414917},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6602576971054077},{"id":"https://openalex.org/C179255354","wikidata":"https://www.wikidata.org/wiki/Q284416","display_name":"Small nucleolar RNA","level":5,"score":0.6505572199821472},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.595766544342041},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.585183322429657},{"id":"https://openalex.org/C512185932","wikidata":"https://www.wikidata.org/wiki/Q28745","display_name":"Nucleotide","level":3,"score":0.4307568669319153},{"id":"https://openalex.org/C62203573","wikidata":"https://www.wikidata.org/wiki/Q15087973","display_name":"Long non-coding RNA","level":4,"score":0.4022788405418396},{"id":"https://openalex.org/C190062978","wikidata":"https://www.wikidata.org/wiki/Q79899","display_name":"Cytoplasm","level":2,"score":0.3157440423965454},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2900601625442505},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.25980144739151}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009711","descriptor_name":"Nucleotides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009711","descriptor_name":"Nucleotides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009711","descriptor_name":"Nucleotides","qualifier_ui":null,"qualifier_name":null,"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":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbac509","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac509","pdf_url":"https://academic.oup.com/bib/article-pdf/24/1/bbac509/48782054/bbac509.pdf","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:36464487","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36464487","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},{"id":"pmh:oai:pubmedcentral.nih.gov:9851306","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9851306","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbac509","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac509","pdf_url":"https://academic.oup.com/bib/article-pdf/24/1/bbac509/48782054/bbac509.pdf","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"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2008766160","display_name":null,"funder_award_id":"2021TQ0342","funder_id":"https://openalex.org/F4320321543","funder_display_name":"China Postdoctoral Science Foundation"},{"id":"https://openalex.org/G7495289257","display_name":null,"funder_award_id":"31925011","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8517115763","display_name":null,"funder_award_id":"2021\u00a0M700159","funder_id":"https://openalex.org/F4320321543","funder_display_name":"China Postdoctoral Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321543","display_name":"China Postdoctoral Science Foundation","ror":"https://ror.org/0426zh255"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4310665480.pdf","grobid_xml":"https://content.openalex.org/works/W4310665480.grobid-xml"},"referenced_works_count":71,"referenced_works":["https://openalex.org/W1879996757","https://openalex.org/W1967791012","https://openalex.org/W1981988708","https://openalex.org/W2026141529","https://openalex.org/W2031408226","https://openalex.org/W2034305079","https://openalex.org/W2037363723","https://openalex.org/W2055493067","https://openalex.org/W2065466457","https://openalex.org/W2066379001","https://openalex.org/W2073987430","https://openalex.org/W2086561953","https://openalex.org/W2103777723","https://openalex.org/W2105694586","https://openalex.org/W2107920354","https://openalex.org/W2141172277","https://openalex.org/W2141831115","https://openalex.org/W2153661038","https://openalex.org/W2159591573","https://openalex.org/W2165781226","https://openalex.org/W2167491742","https://openalex.org/W2175136759","https://openalex.org/W2201924392","https://openalex.org/W2323385078","https://openalex.org/W2338433671","https://openalex.org/W2345512687","https://openalex.org/W2505384565","https://openalex.org/W2508362099","https://openalex.org/W2537505720","https://openalex.org/W2625910148","https://openalex.org/W2754070500","https://openalex.org/W2754846502","https://openalex.org/W2765281581","https://openalex.org/W2768348081","https://openalex.org/W2789926271","https://openalex.org/W2799487719","https://openalex.org/W2806725605","https://openalex.org/W2808919170","https://openalex.org/W2808950870","https://openalex.org/W2883062882","https://openalex.org/W2890017579","https://openalex.org/W2899322113","https://openalex.org/W2912768590","https://openalex.org/W2916252710","https://openalex.org/W2942134847","https://openalex.org/W2944735543","https://openalex.org/W2944901478","https://openalex.org/W2949674037","https://openalex.org/W2951298881","https://openalex.org/W2953177586","https://openalex.org/W2973637866","https://openalex.org/W2984059576","https://openalex.org/W2998081701","https://openalex.org/W2999615587","https://openalex.org/W3004263072","https://openalex.org/W3011709397","https://openalex.org/W3013900099","https://openalex.org/W3014773636","https://openalex.org/W3015761799","https://openalex.org/W3018733006","https://openalex.org/W3020855961","https://openalex.org/W3026307143","https://openalex.org/W3084175789","https://openalex.org/W3104088357","https://openalex.org/W3111456402","https://openalex.org/W3194704945","https://openalex.org/W3200488575","https://openalex.org/W4221024622","https://openalex.org/W4302362531","https://openalex.org/W6725105739","https://openalex.org/W6745609711"],"related_works":["https://openalex.org/W2802705617","https://openalex.org/W2357150105","https://openalex.org/W14849116","https://openalex.org/W4400937039","https://openalex.org/W25403435","https://openalex.org/W2763430914","https://openalex.org/W2136467378","https://openalex.org/W2547129954","https://openalex.org/W2056330045","https://openalex.org/W4391308270"],"abstract_inverted_index":{"Different":[0],"RNAs":[1],"have":[2,18],"distinct":[3,12,69,103],"subcellular":[4,42,71,104,114,137],"localizations.":[5,72,105],"However,":[6],"nucleotide":[7,37,55],"features":[8,56,78,90],"that":[9],"determine":[10],"these":[11],"distributions":[13],"of":[14,44,62,88,116,119,132],"lncRNAs":[15,99],"and":[16,46,79,91,100,124],"mRNAs":[17,45,101],"yet":[19],"to":[20,35,40,76,82,110],"be":[21],"fully":[22],"addressed.":[23],"Here,":[24],"we":[25,107],"develop":[26],"RNAlight,":[27],"a":[28],"machine":[29],"learning":[30],"model":[31],"based":[32],"on":[33],"LightGBM,":[34],"identify":[36],"k-mers":[38,75],"contributing":[39],"the":[41,49,65,113,130],"localizations":[43,115],"lncRNAs.":[47],"With":[48],"Tree":[50],"SHAP":[51],"algorithm,":[52],"RNAlight":[53,109,134],"extracts":[54],"for":[57,68,98,135],"cytoplasmic":[58],"or":[59],"nuclear":[60],"localization":[61,138],"RNAs,":[63,120],"indicating":[64],"sequence":[66,77,89],"basis":[67],"RNA":[70,127,136],"By":[73],"assembling":[74],"subsequently":[80],"mapping":[81],"known":[83],"RBP-associated":[84],"motifs,":[85],"different":[86,125],"types":[87,118],"their":[92],"associated":[93],"RBPs":[94],"were":[95],"additionally":[96],"uncovered":[97],"with":[102],"Finally,":[106],"extended":[108],"precisely":[111],"predict":[112],"other":[117],"including":[121],"snRNAs,":[122],"snoRNAs":[123],"circular":[126],"transcripts,":[128],"suggesting":[129],"generality":[131],"using":[133],"prediction.":[139]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":15},{"year":2024,"cited_by_count":22},{"year":2023,"cited_by_count":6}],"updated_date":"2025-11-23T05:10:03.516525","created_date":"2025-10-10T00:00:00"}
