{"id":"https://openalex.org/W4376131959","doi":"https://doi.org/10.1093/nar/gkad404","title":"RNAincoder: a deep learning-based encoder for RNA and RNA-associated interaction","display_name":"RNAincoder: a deep learning-based encoder for RNA and RNA-associated interaction","publication_year":2023,"publication_date":"2023-05-11","ids":{"openalex":"https://openalex.org/W4376131959","doi":"https://doi.org/10.1093/nar/gkad404","pmid":"https://pubmed.ncbi.nlm.nih.gov/37166951"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkad404","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkad404","pdf_url":"https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad404/50279488/gkad404.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad404/50279488/gkad404.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100658319","display_name":"Yunxia Wang","orcid":"https://orcid.org/0000-0003-1951-942X"},"institutions":[{"id":"https://openalex.org/I4210158318","display_name":"Second Affiliated Hospital of Zhejiang University","ror":"https://ror.org/059cjpv64","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210158318"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yunxia Wang","raw_affiliation_strings":["College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China","institution_ids":["https://openalex.org/I4210158318"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055707588","display_name":"Zhen Chen","orcid":"https://orcid.org/0000-0002-6766-9046"},"institutions":[{"id":"https://openalex.org/I4210158318","display_name":"Second Affiliated Hospital of Zhejiang University","ror":"https://ror.org/059cjpv64","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210158318"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhen Chen","raw_affiliation_strings":["College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China","institution_ids":["https://openalex.org/I4210158318"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101441641","display_name":"Ziqi Pan","orcid":"https://orcid.org/0000-0002-3883-4161"},"institutions":[{"id":"https://openalex.org/I4210158318","display_name":"Second Affiliated Hospital of Zhejiang University","ror":"https://ror.org/059cjpv64","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210158318"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ziqi Pan","raw_affiliation_strings":["College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China","institution_ids":["https://openalex.org/I4210158318"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101655408","display_name":"Shijie Huang","orcid":"https://orcid.org/0000-0001-6755-4735"},"institutions":[{"id":"https://openalex.org/I4210158318","display_name":"Second Affiliated Hospital of Zhejiang University","ror":"https://ror.org/059cjpv64","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210158318"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shijie Huang","raw_affiliation_strings":["College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China","institution_ids":["https://openalex.org/I4210158318"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113189595","display_name":"Jin Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I4210158318","display_name":"Second Affiliated Hospital of Zhejiang University","ror":"https://ror.org/059cjpv64","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210158318"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jin Liu","raw_affiliation_strings":["College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China","institution_ids":["https://openalex.org/I4210158318"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067308783","display_name":"Weiqi Xia","orcid":"https://orcid.org/0000-0001-8213-5272"},"institutions":[{"id":"https://openalex.org/I4210158318","display_name":"Second Affiliated Hospital of Zhejiang University","ror":"https://ror.org/059cjpv64","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210158318"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weiqi Xia","raw_affiliation_strings":["College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China","institution_ids":["https://openalex.org/I4210158318"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038164630","display_name":"Hongning Zhang","orcid":"https://orcid.org/0000-0002-7818-7915"},"institutions":[{"id":"https://openalex.org/I4210158318","display_name":"Second Affiliated Hospital of Zhejiang University","ror":"https://ror.org/059cjpv64","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210158318"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongning Zhang","raw_affiliation_strings":["College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China"],"raw_orcid":"https://orcid.org/0000-0002-7818-7915","affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China","institution_ids":["https://openalex.org/I4210158318"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075749706","display_name":"Mingyue Zheng","orcid":"https://orcid.org/0000-0002-3323-3092"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mingyue Zheng","raw_affiliation_strings":["Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai \u00a0201203, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai \u00a0201203, China","institution_ids":["https://openalex.org/I4210112820","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100688144","display_name":"Honglin Li","orcid":"https://orcid.org/0000-0003-2270-1900"},"institutions":[{"id":"https://openalex.org/I143593769","display_name":"East China University of Science and Technology","ror":"https://ror.org/01vyrm377","country_code":"CN","type":"education","lineage":["https://openalex.org/I143593769"]},{"id":"https://openalex.org/I4210158318","display_name":"Second Affiliated Hospital of Zhejiang University","ror":"https://ror.org/059cjpv64","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210158318"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Honglin Li","raw_affiliation_strings":["College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China","School of Pharmacy, East China University of Science and Technology , Shanghai \u00a0200237, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China","institution_ids":["https://openalex.org/I4210158318"]},{"raw_affiliation_string":"School of Pharmacy, East China University of Science and Technology , Shanghai \u00a0200237, China","institution_ids":["https://openalex.org/I143593769"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028525523","display_name":"Tingjun Hou","orcid":"https://orcid.org/0000-0001-7227-2580"},"institutions":[{"id":"https://openalex.org/I4210158318","display_name":"Second Affiliated Hospital of Zhejiang University","ror":"https://ror.org/059cjpv64","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210158318"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tingjun Hou","raw_affiliation_strings":["College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China","institution_ids":["https://openalex.org/I4210158318"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100755257","display_name":"Feng Zhu","orcid":"https://orcid.org/0000-0001-8069-0053"},"institutions":[{"id":"https://openalex.org/I3133055985","display_name":"Westlake University","ror":"https://ror.org/05hfa4n20","country_code":"CN","type":"education","lineage":["https://openalex.org/I3133055985"]},{"id":"https://openalex.org/I4210158318","display_name":"Second Affiliated Hospital of Zhejiang University","ror":"https://ror.org/059cjpv64","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210158318"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Feng Zhu","raw_affiliation_strings":["College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China","Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare , Hangzhou \u00a0330110, China","Westlake Laboratory of Life Sciences and Biomedicine , Hangzhou , Zhejiang , China"],"raw_orcid":"https://orcid.org/0000-0001-8069-0053","affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou \u00a0310058, China","institution_ids":["https://openalex.org/I4210158318"]},{"raw_affiliation_string":"Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare , Hangzhou \u00a0330110, China","institution_ids":["https://openalex.org/I76130692"]},{"raw_affiliation_string":"Westlake Laboratory of Life Sciences and Biomedicine , Hangzhou , Zhejiang , China","institution_ids":["https://openalex.org/I3133055985"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":4.6236,"has_fulltext":true,"cited_by_count":49,"citation_normalized_percentile":{"value":0.96252454,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"51","issue":"W1","first_page":"W509","last_page":"W519"},"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9983000159263611,"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":0.9980000257492065,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.778504490852356},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.7005330324172974},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.626388430595398},{"id":"https://openalex.org/keywords/encoding","display_name":"Encoding (memory)","score":0.6258352398872375},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5720428228378296},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.5477400422096252},{"id":"https://openalex.org/keywords/complement","display_name":"Complement (music)","score":0.5149469971656799},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5144617557525635},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4909956753253937},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46795570850372314},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4617498219013214},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4441906213760376},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.43776270747184753},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26806968450546265},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1680150032043457},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.06714224815368652}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.778504490852356},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.7005330324172974},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.626388430595398},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.6258352398872375},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5720428228378296},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.5477400422096252},{"id":"https://openalex.org/C112313634","wikidata":"https://www.wikidata.org/wiki/Q7886648","display_name":"Complement (music)","level":5,"score":0.5149469971656799},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5144617557525635},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4909956753253937},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46795570850372314},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4617498219013214},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4441906213760376},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.43776270747184753},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26806968450546265},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1680150032043457},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.06714224815368652},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C188082640","wikidata":"https://www.wikidata.org/wiki/Q1780899","display_name":"Complementation","level":4,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"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/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkad404","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkad404","pdf_url":"https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad404/50279488/gkad404.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:37166951","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37166951","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10320175","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10320175","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10320175/pdf/gkad404.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkad404","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkad404","pdf_url":"https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad404/50279488/gkad404.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4099999964237213,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G1171080475","display_name":null,"funder_award_id":"2020C03010","funder_id":"https://openalex.org/F8142712028","funder_display_name":"Key Research and Development Program of Zhejiang Province"},{"id":"https://openalex.org/G2446395889","display_name":null,"funder_award_id":"81872798","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4938249675","display_name":null,"funder_award_id":"2020C03010","funder_id":"https://openalex.org/F4320322927","funder_display_name":"Zhejiang University"},{"id":"https://openalex.org/G7903508730","display_name":null,"funder_award_id":"22220102001","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8196091623","display_name":null,"funder_award_id":"U1909208","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8951279597","display_name":null,"funder_award_id":"LR21H300001","funder_id":"https://openalex.org/F4320338464","funder_display_name":"Natural Science Foundation of Zhejiang Province"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322927","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884"},{"id":"https://openalex.org/F4320338464","display_name":"Natural Science Foundation of Zhejiang Province","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F8142712028","display_name":"Key Research and Development Program of Zhejiang Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4376131959.pdf"},"referenced_works_count":88,"referenced_works":["https://openalex.org/W7721663","https://openalex.org/W1019830208","https://openalex.org/W1635391495","https://openalex.org/W1990909403","https://openalex.org/W1997113958","https://openalex.org/W2009113274","https://openalex.org/W2010712786","https://openalex.org/W2028707203","https://openalex.org/W2031198583","https://openalex.org/W2052503008","https://openalex.org/W2052611179","https://openalex.org/W2075692164","https://openalex.org/W2076358430","https://openalex.org/W2081530255","https://openalex.org/W2087439897","https://openalex.org/W2094836090","https://openalex.org/W2097694646","https://openalex.org/W2114024619","https://openalex.org/W2130291362","https://openalex.org/W2130479394","https://openalex.org/W2136769496","https://openalex.org/W2145957695","https://openalex.org/W2152678443","https://openalex.org/W2152800101","https://openalex.org/W2159887157","https://openalex.org/W2163639779","https://openalex.org/W2167884443","https://openalex.org/W2175060414","https://openalex.org/W2203559469","https://openalex.org/W2341424800","https://openalex.org/W2507804718","https://openalex.org/W2512299449","https://openalex.org/W2513786151","https://openalex.org/W2513880868","https://openalex.org/W2571489439","https://openalex.org/W2599859080","https://openalex.org/W2615786037","https://openalex.org/W2791355014","https://openalex.org/W2793344725","https://openalex.org/W2799487719","https://openalex.org/W2807607992","https://openalex.org/W2810756255","https://openalex.org/W2886900083","https://openalex.org/W2890017579","https://openalex.org/W2894749196","https://openalex.org/W2914698725","https://openalex.org/W2917724292","https://openalex.org/W2920083709","https://openalex.org/W2924197217","https://openalex.org/W2927893014","https://openalex.org/W2946035471","https://openalex.org/W2951413354","https://openalex.org/W2951748044","https://openalex.org/W2956076207","https://openalex.org/W2964443466","https://openalex.org/W2967960129","https://openalex.org/W2972083913","https://openalex.org/W2972528761","https://openalex.org/W2995517528","https://openalex.org/W2999743161","https://openalex.org/W3008496114","https://openalex.org/W3009479537","https://openalex.org/W3020855961","https://openalex.org/W3022604539","https://openalex.org/W3032843171","https://openalex.org/W3036509318","https://openalex.org/W3041118201","https://openalex.org/W3089123840","https://openalex.org/W3093432916","https://openalex.org/W3094159415","https://openalex.org/W3134163647","https://openalex.org/W3134490799","https://openalex.org/W3158366868","https://openalex.org/W3164382315","https://openalex.org/W3194560548","https://openalex.org/W3195820203","https://openalex.org/W3197697158","https://openalex.org/W3212618755","https://openalex.org/W4210483366","https://openalex.org/W4226079848","https://openalex.org/W4242086441","https://openalex.org/W4248167110","https://openalex.org/W4283770085","https://openalex.org/W4313311738","https://openalex.org/W6600307240","https://openalex.org/W6685204640","https://openalex.org/W6725628906","https://openalex.org/W6731700065"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W4321353415","https://openalex.org/W2745001401","https://openalex.org/W2130974462","https://openalex.org/W2028665553","https://openalex.org/W2086519370","https://openalex.org/W4246352526","https://openalex.org/W2121910908","https://openalex.org/W2129146436","https://openalex.org/W2032507829"],"abstract_inverted_index":{"Ribonucleic":[0],"acids":[1],"(RNAs)":[2],"involve":[3],"in":[4,134,152,160],"various":[5],"physiological/pathological":[6],"processes":[7],"by":[8,145],"interacting":[9,45,69],"with":[10],"proteins,":[11],"compounds,":[12],"and":[13,117],"other":[14,52,176],"RNAs.":[15],"A":[16],"variety":[17],"of":[18,43,97,105,122,131,140,166],"powerful":[19,61],"computational":[20],"methods":[21,33],"have":[22,59],"been":[23],"developed":[24],"to":[25,58,91,127,175],"predict":[26],"such":[27],"valuable":[28],"interactions.":[29],"However,":[30],"all":[31,123],"these":[32],"rely":[34],"heavily":[35],"on":[36,110,148],"the":[37,103,129],"'digitalization'":[38],"(also":[39],"known":[40],"as":[41],"'encoding')":[42],"RNA-associated":[44,86,107,135,167],"pairs":[46],"into":[47,76],"a":[48,60,77,94,111,162],"computer-recognizable":[49,78],"descriptor.":[50],"In":[51],"words,":[53],"it":[54,171],"is":[55,155],"urgently":[56],"needed":[57],"tool":[62],"that":[63],"can":[64,180],"not":[65],"only":[66],"represent":[67],"each":[68],"partner":[70],"but":[71],"also":[72],"integrate":[73],"both":[74],"partners":[75],"interaction.":[79],"Herein,":[80],"RNAincoder":[81,141,154,179],"(deep":[82],"learning-based":[83,114],"encoder":[84],"for":[85,157],"interactions)":[87],"was":[88,142],"therefore":[89],"proposed":[90],"(a)":[92],"provide":[93],"comprehensive":[95],"collection":[96],"RNA":[98],"encoding":[99],"features,":[100],"(b)":[101],"realize":[102],"representation":[104,165],"any":[106],"interaction":[108,136],"based":[109],"well-established":[112],"deep":[113],"embedding":[115],"strategy":[116],"(c)":[118],"enable":[119],"large-scale":[120],"scanning":[121],"possible":[124],"feature":[125],"combinations":[126],"identify":[128],"one":[130],"optimal":[132],"performance":[133],"prediction.":[137],"The":[138],"effectiveness":[139],"extensively":[143],"validated":[144],"case":[146],"studies":[147],"benchmark":[149],"datasets.":[150],"All":[151],"all,":[153],"distinguished":[156],"its":[158],"capability":[159],"providing":[161],"more":[163],"accurate":[164],"interactions,":[168],"which":[169],"makes":[170],"an":[172],"indispensable":[173],"complement":[174],"available":[177],"tools.":[178],"be":[181],"accessed":[182],"at":[183],"https://idrblab.org/rnaincoder/.":[184]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":21},{"year":2024,"cited_by_count":14},{"year":2023,"cited_by_count":7}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
