{"id":"https://openalex.org/W2347162849","doi":"https://doi.org/10.1093/nar/gkw362","title":"RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data","display_name":"RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data","publication_year":2016,"publication_date":"2016-05-02","ids":{"openalex":"https://openalex.org/W2347162849","doi":"https://doi.org/10.1093/nar/gkw362","mag":"2347162849","pmid":"https://pubmed.ncbi.nlm.nih.gov/27137891"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkw362","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkw362","pdf_url":"https://academic.oup.com/nar/article-pdf/44/W1/W294/18787816/gkw362.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/article-pdf/44/W1/W294/18787816/gkw362.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059651530","display_name":"Yang Wu","orcid":"https://orcid.org/0000-0001-6547-9524"},"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":"Yang Wu","raw_affiliation_strings":["MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China","institution_ids":["https://openalex.org/I4210160507","https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007150854","display_name":"Rihao Qu","orcid":"https://orcid.org/0000-0002-8258-8287"},"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":"Rihao Qu","raw_affiliation_strings":["MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China","institution_ids":["https://openalex.org/I4210160507","https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009289945","display_name":"Yiming Huang","orcid":"https://orcid.org/0000-0003-1932-2803"},"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":"Yiming Huang","raw_affiliation_strings":["MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China","institution_ids":["https://openalex.org/I4210160507","https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091191988","display_name":"Binbin Shi","orcid":"https://orcid.org/0000-0001-6257-5289"},"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":"Binbin Shi","raw_affiliation_strings":["MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China","institution_ids":["https://openalex.org/I4210160507","https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043632264","display_name":"Mengrong Liu","orcid":null},"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":"Mengrong Liu","raw_affiliation_strings":["MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China","institution_ids":["https://openalex.org/I4210160507","https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100421418","display_name":"Yang Li","orcid":"https://orcid.org/0000-0002-0736-251X"},"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":"Yang Li","raw_affiliation_strings":["MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China","institution_ids":["https://openalex.org/I4210160507","https://openalex.org/I99065089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031246881","display_name":"Zhi John Lu","orcid":"https://orcid.org/0000-0003-4751-9400"},"institutions":[{"id":"https://openalex.org/I2802444338","display_name":"King Center","ror":"https://ror.org/03nxex423","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802444338"]},{"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"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Zhi John Lu","raw_affiliation_strings":["MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China zhilu@tsinghua.edu.cn"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China zhilu@tsinghua.edu.cn","institution_ids":["https://openalex.org/I2802444338","https://openalex.org/I4210160507"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"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":0.6414,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.71720782,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"44","issue":"W1","first_page":"W294","last_page":"W301"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"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":1.0,"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":1.0,"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":0.9994999766349792,"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":0.7444107532501221},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7391327619552612},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.7075607776641846},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.7044796943664551},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.6581147909164429},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6416635513305664},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.5329027771949768},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.5059162974357605},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.5027022361755371},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.37127619981765747},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.304934561252594},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.26707109808921814},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.15814262628555298},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.15759718418121338}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.7444107532501221},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7391327619552612},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.7075607776641846},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.7044796943664551},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.6581147909164429},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6416635513305664},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.5329027771949768},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5059162974357605},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.5027022361755371},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.37127619981765747},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.304934561252594},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.26707109808921814},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.15814262628555298},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.15759718418121338},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017393","descriptor_name":"RNA Editing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017393","descriptor_name":"RNA Editing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017393","descriptor_name":"RNA Editing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","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},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057166","descriptor_name":"High-Throughput Screening Assays","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057166","descriptor_name":"High-Throughput Screening Assays","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057166","descriptor_name":"High-Throughput Screening Assays","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gkw362","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkw362","pdf_url":"https://academic.oup.com/nar/article-pdf/44/W1/W294/18787816/gkw362.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:27137891","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27137891","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:europepmc.org:3952893","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4987914","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"},{"id":"pmh:oai:open-archive.highwire.org:nar:44/W1/W294","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/44/W1/W294","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/nar/gkw362","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkw362","pdf_url":"https://academic.oup.com/nar/article-pdf/44/W1/W294/18787816/gkw362.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":[{"display_name":"Affordable and clean energy","score":0.8199999928474426,"id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W1217705870","https://openalex.org/W1947267113","https://openalex.org/W1954585750","https://openalex.org/W1974454061","https://openalex.org/W1994958179","https://openalex.org/W2003993220","https://openalex.org/W2009818318","https://openalex.org/W2020077467","https://openalex.org/W2038598202","https://openalex.org/W2039746015","https://openalex.org/W2046335009","https://openalex.org/W2054584406","https://openalex.org/W2069177506","https://openalex.org/W2071717527","https://openalex.org/W2071883352","https://openalex.org/W2076091642","https://openalex.org/W2086561953","https://openalex.org/W2096465161","https://openalex.org/W2098553089","https://openalex.org/W2102017611","https://openalex.org/W2102221598","https://openalex.org/W2105950741","https://openalex.org/W2107424892","https://openalex.org/W2110436930","https://openalex.org/W2113816707","https://openalex.org/W2122732537","https://openalex.org/W2129275368","https://openalex.org/W2134943543","https://openalex.org/W2135230723","https://openalex.org/W2137640371","https://openalex.org/W2137786443","https://openalex.org/W2141157874","https://openalex.org/W2142217851","https://openalex.org/W2148419405","https://openalex.org/W2153140501","https://openalex.org/W2163186478","https://openalex.org/W2167155938","https://openalex.org/W2217108432","https://openalex.org/W2270602636"],"related_works":["https://openalex.org/W1975806245","https://openalex.org/W2558432341","https://openalex.org/W3047450301","https://openalex.org/W1971402940","https://openalex.org/W2345156963","https://openalex.org/W2144151678","https://openalex.org/W2159621058","https://openalex.org/W1998495298","https://openalex.org/W2039746015","https://openalex.org/W2412575231"],"abstract_inverted_index":{"Several":[0],"high-throughput":[1],"technologies":[2],"have":[3],"been":[4,132],"developed":[5,50],"to":[6,21,35,72,150,161],"probe":[7],"RNA":[8,25,52,80,94,96,170],"base":[9],"pairs":[10],"and":[11,30,41,78,87,98,115,168,176],"loops":[12],"at":[13,184],"the":[14,23,38,93,102,122,142,147,151],"transcriptome":[15],"level":[16],"in":[17,85,88,172],"multiple":[18],"species.":[19,156],"However,":[20],"obtain":[22],"final":[24],"secondary":[26,53,81,163],"structure,":[27],"extensive":[28],"effort":[29],"considerable":[31],"expertise":[32],"is":[33,58,65,182],"required":[34],"statistically":[36],"process":[37],"probing":[39,148],"data":[40,62,77,145],"combine":[42],"them":[43],"with":[44],"free":[45],"energy":[46],"models.":[47],"Therefore,":[48],"we":[49],"an":[51],"structure":[54],"prediction":[55],"server":[56,181],"that":[57,69,117],"enhanced":[59,83],"by":[60,84,121,134],"experimental":[61],"(RNAex).":[63],"RNAex":[64,91,157,179],"a":[66],"web":[67,180],"interface":[68],"enables":[70,159],"non-specialists":[71],"easily":[73],"access":[74],"cutting-edge":[75],"structure-probing":[76],"predict":[79,162],"structures":[82,164],"vivo":[86],"vitro":[89],"data.":[90],"annotates":[92],"editing,":[95],"modification":[97],"SNP":[99],"sites":[100],"on":[101,137],"predicted":[103],"structures.":[104,139],"It":[105],"provides":[106],"four":[107,128],"structure-folding":[108],"methods,":[109],"restrained":[110],"MaxExpect,":[111],"SeqFold,":[112],"RNAstructure":[113],"(Fold)":[114],"RNAfold":[116],"can":[118],"be":[119],"selected":[120],"user.":[123],"The":[124,178],"performance":[125],"of":[126,146],"these":[127],"folding":[129],"methods":[130],"has":[131],"verified":[133],"previous":[135],"publications":[136],"known":[138,167],"We":[140],"re-mapped":[141],"raw":[143],"sequencing":[144],"experiments":[149],"whole":[152],"genome":[153],"for":[154,165],"each":[155],"thus":[158],"users":[160],"both":[166],"novel":[169],"transcripts":[171],"human,":[173],"mouse,":[174],"yeast":[175],"Arabidopsis":[177],"available":[183],"http://RNAex.ncrnalab.org/.":[185]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2020,"cited_by_count":3},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}