{"id":"https://openalex.org/W3212049797","doi":"https://doi.org/10.1038/s42256-021-00412-0","title":"A deep learning method for recovering missing signals in transcriptome-wide RNA structure profiles from probing experiments","display_name":"A deep learning method for recovering missing signals in transcriptome-wide RNA structure profiles from probing experiments","publication_year":2021,"publication_date":"2021-11-16","ids":{"openalex":"https://openalex.org/W3212049797","doi":"https://doi.org/10.1038/s42256-021-00412-0","mag":"3212049797"},"language":"en","primary_location":{"id":"doi:10.1038/s42256-021-00412-0","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s42256-021-00412-0","pdf_url":null,"source":{"id":"https://openalex.org/S2912241403","display_name":"Nature Machine Intelligence","issn_l":"2522-5839","issn":["2522-5839"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Machine Intelligence","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"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/A5101468464","display_name":"Jing Gong","orcid":"https://orcid.org/0000-0001-9907-7910"},"institutions":[{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jing Gong","raw_affiliation_strings":["Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China","MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China","Tsinghua-Peking Center for Life Sciences, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Tsinghua-Peking Center for Life Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210160507"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056328626","display_name":"Kui Xu","orcid":"https://orcid.org/0000-0001-7226-5479"},"institutions":[{"id":"https://openalex.org/I4210122302","display_name":"ShangHai JiAi Genetics & IVF Institute","ror":"https://ror.org/02rgbry52","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210122302"]},{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kui Xu","raw_affiliation_strings":["Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China","MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China","Shanghai Qi Zhi Institute, Shanghai, China","Tsinghua-Peking Center for Life Sciences, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0001-7226-5479","affiliations":[{"raw_affiliation_string":"Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Shanghai Qi Zhi Institute, Shanghai, China","institution_ids":["https://openalex.org/I4210122302"]},{"raw_affiliation_string":"Tsinghua-Peking Center for Life Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210160507"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005425377","display_name":"Zi-yuan Ma","orcid":"https://orcid.org/0000-0001-9461-7121"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ziyuan Ma","raw_affiliation_strings":["MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034615334","display_name":"Zhi L\u00fc","orcid":"https://orcid.org/0000-0003-3739-8756"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhi John Lu","raw_affiliation_strings":["MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5034479728","display_name":"Qiangfeng Cliff Zhang","orcid":"https://orcid.org/0000-0002-4913-0338"},"institutions":[{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Qiangfeng Cliff Zhang","raw_affiliation_strings":["Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China","MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China","Tsinghua-Peking Center for Life Sciences, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0002-4913-0338","affiliations":[{"raw_affiliation_string":"Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Tsinghua-Peking Center for Life Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210160507"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5034479728"],"corresponding_institution_ids":["https://openalex.org/I4210160507","https://openalex.org/I99065089"],"apc_list":{"value":9750,"currency":"EUR","value_usd":11690},"apc_paid":null,"fwci":0.6344,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.66737251,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"3","issue":"11","first_page":"995","last_page":"1006"},"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/T11482","display_name":"RNA modifications and cancer","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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991999864578247,"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":0.7508631348609924},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.6083291172981262},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5748155117034912},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.5527598857879639},{"id":"https://openalex.org/keywords/imputation","display_name":"Imputation (statistics)","score":0.536243200302124},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5187061429023743},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5176935195922852},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4905945360660553},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.45109862089157104},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4365784227848053},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.4208647906780243},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.3947780132293701},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.28260958194732666},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2370627224445343},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2040005624294281},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.17821359634399414},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15688404440879822}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.7508631348609924},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.6083291172981262},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5748155117034912},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.5527598857879639},{"id":"https://openalex.org/C58041806","wikidata":"https://www.wikidata.org/wiki/Q1660484","display_name":"Imputation (statistics)","level":3,"score":0.536243200302124},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5187061429023743},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5176935195922852},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4905945360660553},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.45109862089157104},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4365784227848053},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.4208647906780243},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.3947780132293701},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.28260958194732666},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2370627224445343},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2040005624294281},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.17821359634399414},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15688404440879822}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1038/s42256-021-00412-0","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s42256-021-00412-0","pdf_url":null,"source":{"id":"https://openalex.org/S2912241403","display_name":"Nature Machine Intelligence","issn_l":"2522-5839","issn":["2522-5839"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Machine Intelligence","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3603759127","display_name":null,"funder_award_id":"2018YFA0107603","funder_id":"https://openalex.org/F4320321540","funder_display_name":"Ministry of Science and Technology of the People's Republic of China"},{"id":"https://openalex.org/G4049383134","display_name":null,"funder_award_id":"91740204","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"},{"id":"https://openalex.org/F4320321540","display_name":"Ministry of Science and Technology of the People's Republic of China","ror":"https://ror.org/027s68j25"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":61,"referenced_works":["https://openalex.org/W166206240","https://openalex.org/W1502958771","https://openalex.org/W1974454061","https://openalex.org/W1985278607","https://openalex.org/W1986884782","https://openalex.org/W2003993220","https://openalex.org/W2034199961","https://openalex.org/W2039746015","https://openalex.org/W2039816251","https://openalex.org/W2064675550","https://openalex.org/W2071717527","https://openalex.org/W2076091642","https://openalex.org/W2076563297","https://openalex.org/W2081586346","https://openalex.org/W2112911320","https://openalex.org/W2120974004","https://openalex.org/W2125952821","https://openalex.org/W2140952049","https://openalex.org/W2162224067","https://openalex.org/W2194775991","https://openalex.org/W2233915997","https://openalex.org/W2295107390","https://openalex.org/W2342878844","https://openalex.org/W2388201280","https://openalex.org/W2460957862","https://openalex.org/W2538880572","https://openalex.org/W2585466487","https://openalex.org/W2762224301","https://openalex.org/W2762279748","https://openalex.org/W2766848373","https://openalex.org/W2784296343","https://openalex.org/W2785329615","https://openalex.org/W2792693509","https://openalex.org/W2799346732","https://openalex.org/W2805619986","https://openalex.org/W2883782161","https://openalex.org/W2903235092","https://openalex.org/W2907783748","https://openalex.org/W2919115771","https://openalex.org/W2922454987","https://openalex.org/W2924070408","https://openalex.org/W2949249029","https://openalex.org/W2951217100","https://openalex.org/W2952534796","https://openalex.org/W2958013639","https://openalex.org/W2962858109","https://openalex.org/W2963269831","https://openalex.org/W2963867516","https://openalex.org/W2972933339","https://openalex.org/W2979464975","https://openalex.org/W2979742573","https://openalex.org/W2980495984","https://openalex.org/W2986701260","https://openalex.org/W2990528340","https://openalex.org/W3003239522","https://openalex.org/W3028504898","https://openalex.org/W3106930452","https://openalex.org/W3110653837","https://openalex.org/W4253060000","https://openalex.org/W4394295633","https://openalex.org/W6893838382"],"related_works":["https://openalex.org/W2181530120","https://openalex.org/W4211215373","https://openalex.org/W2024529227","https://openalex.org/W2055961818","https://openalex.org/W2903115227","https://openalex.org/W1574575415","https://openalex.org/W3144172081","https://openalex.org/W3179858851","https://openalex.org/W2081476516","https://openalex.org/W2581984549"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-06-17T06:14:20.161405","created_date":"2025-10-10T00:00:00"}