{"id":"https://openalex.org/W4282945580","doi":"https://doi.org/10.1093/bib/bbac205","title":"Secondary structure prediction of long noncoding RNA: review and experimental comparison of existing approaches","display_name":"Secondary structure prediction of long noncoding RNA: review and experimental comparison of existing approaches","publication_year":2022,"publication_date":"2022-05-04","ids":{"openalex":"https://openalex.org/W4282945580","doi":"https://doi.org/10.1093/bib/bbac205","pmid":"https://pubmed.ncbi.nlm.nih.gov/35692094"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac205","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac205","pdf_url":"https://academic.oup.com/bib/article-pdf/23/4/bbac205/45017094/bbac205.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":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/23/4/bbac205/45017094/bbac205.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053316160","display_name":"Leandro A. Bugnon","orcid":"https://orcid.org/0000-0001-5702-946X"},"institutions":[{"id":"https://openalex.org/I151201029","display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","ror":"https://ror.org/03cqe8w59","country_code":"AR","type":"government","lineage":["https://openalex.org/I151201029","https://openalex.org/I4210123736","https://openalex.org/I4387155568"]}],"countries":["AR"],"is_corresponding":true,"raw_author_name":"L A Bugnon","raw_affiliation_strings":["Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria , Santa Fe , Argentina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria , Santa Fe , Argentina","institution_ids":["https://openalex.org/I151201029"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031950827","display_name":"Alejando A Edera","orcid":null},"institutions":[{"id":"https://openalex.org/I151201029","display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","ror":"https://ror.org/03cqe8w59","country_code":"AR","type":"government","lineage":["https://openalex.org/I151201029","https://openalex.org/I4210123736","https://openalex.org/I4387155568"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"A A Edera","raw_affiliation_strings":["Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria , Santa Fe , Argentina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria , Santa Fe , Argentina","institution_ids":["https://openalex.org/I151201029"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030418384","display_name":"Santiago Prochetto","orcid":"https://orcid.org/0000-0002-8591-149X"},"institutions":[{"id":"https://openalex.org/I151201029","display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","ror":"https://ror.org/03cqe8w59","country_code":"AR","type":"government","lineage":["https://openalex.org/I151201029","https://openalex.org/I4210123736","https://openalex.org/I4387155568"]},{"id":"https://openalex.org/I4210149924","display_name":"Instituto de Agrobiotecnolog\u00eda del Litoral","ror":"https://ror.org/057915t59","country_code":"AR","type":"facility","lineage":["https://openalex.org/I151201029","https://openalex.org/I3121987637","https://openalex.org/I4210087694","https://openalex.org/I4210123736","https://openalex.org/I4210149924","https://openalex.org/I4387155568"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"S Prochetto","raw_affiliation_strings":["IAL, CONICET, Ciudad Universitaria UNL , (3000) Santa Fe , Argentina","Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria , Santa Fe , Argentina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IAL, CONICET, Ciudad Universitaria UNL , (3000) Santa Fe , Argentina","institution_ids":["https://openalex.org/I4210149924"]},{"raw_affiliation_string":"Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria , Santa Fe , Argentina","institution_ids":["https://openalex.org/I151201029"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048439836","display_name":"M. G\u00e9rard","orcid":"https://orcid.org/0000-0001-5145-5943"},"institutions":[{"id":"https://openalex.org/I151201029","display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","ror":"https://ror.org/03cqe8w59","country_code":"AR","type":"government","lineage":["https://openalex.org/I151201029","https://openalex.org/I4210123736","https://openalex.org/I4387155568"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"M Gerard","raw_affiliation_strings":["Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria , Santa Fe , Argentina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria , Santa Fe , Argentina","institution_ids":["https://openalex.org/I151201029"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009906466","display_name":"Jonathan Raad","orcid":"https://orcid.org/0000-0002-9585-1531"},"institutions":[{"id":"https://openalex.org/I151201029","display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","ror":"https://ror.org/03cqe8w59","country_code":"AR","type":"government","lineage":["https://openalex.org/I151201029","https://openalex.org/I4210123736","https://openalex.org/I4387155568"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"J Raad","raw_affiliation_strings":["Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria , Santa Fe , Argentina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria , Santa Fe , Argentina","institution_ids":["https://openalex.org/I151201029"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026537582","display_name":"Emilio Fenoy","orcid":"https://orcid.org/0000-0001-9121-7149"},"institutions":[{"id":"https://openalex.org/I151201029","display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","ror":"https://ror.org/03cqe8w59","country_code":"AR","type":"government","lineage":["https://openalex.org/I151201029","https://openalex.org/I4210123736","https://openalex.org/I4387155568"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"E Fenoy","raw_affiliation_strings":["Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria , Santa Fe , Argentina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria , Santa Fe , Argentina","institution_ids":["https://openalex.org/I151201029"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013986713","display_name":"Mar\u00eda Florencia Rubiolo","orcid":"https://orcid.org/0000-0002-5669-7332"},"institutions":[{"id":"https://openalex.org/I151201029","display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","ror":"https://ror.org/03cqe8w59","country_code":"AR","type":"government","lineage":["https://openalex.org/I151201029","https://openalex.org/I4210123736","https://openalex.org/I4387155568"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"M Rubiolo","raw_affiliation_strings":["Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria , Santa Fe , Argentina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria , Santa Fe , Argentina","institution_ids":["https://openalex.org/I151201029"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048708321","display_name":"Uciel Chorostecki","orcid":"https://orcid.org/0000-0003-2229-6853"},"institutions":[{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"U Chorostecki","raw_affiliation_strings":["Barcelona Supercomputing Center (BSC-CNS), Institute of Research in Biomedicine (IRB) , Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center (BSC-CNS), Institute of Research in Biomedicine (IRB) , Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003394700","display_name":"Toni Gabald\u00f3n","orcid":"https://orcid.org/0000-0003-0019-1735"},"institutions":[{"id":"https://openalex.org/I11932220","display_name":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats","ror":"https://ror.org/0371hy230","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I11932220"]},{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I4210115082","display_name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red","ror":"https://ror.org/02g87qh62","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2801357902","https://openalex.org/I4210115082","https://openalex.org/I4387152914"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"T Gabald\u00f3n","raw_affiliation_strings":["Barcelona Supercomputing Center (BSC-CNS), Institute of Research in Biomedicine (IRB) , Spain","Catalan Institution for Research and Advanced Studies (ICREA) , Barcelona , Spain","Centro de Investigaci\u00f3n Biom\u00e9dica En Red de Enfermedades Infecciosas (CIBERINFEC) , Barcelona , Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center (BSC-CNS), Institute of Research in Biomedicine (IRB) , Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]},{"raw_affiliation_string":"Catalan Institution for Research and Advanced Studies (ICREA) , Barcelona , Spain","institution_ids":["https://openalex.org/I11932220"]},{"raw_affiliation_string":"Centro de Investigaci\u00f3n Biom\u00e9dica En Red de Enfermedades Infecciosas (CIBERINFEC) , Barcelona , Spain","institution_ids":["https://openalex.org/I4210115082"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076773729","display_name":"Federico Ariel","orcid":"https://orcid.org/0000-0001-8478-8808"},"institutions":[{"id":"https://openalex.org/I4210149924","display_name":"Instituto de Agrobiotecnolog\u00eda del Litoral","ror":"https://ror.org/057915t59","country_code":"AR","type":"facility","lineage":["https://openalex.org/I151201029","https://openalex.org/I3121987637","https://openalex.org/I4210087694","https://openalex.org/I4210123736","https://openalex.org/I4210149924","https://openalex.org/I4387155568"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"F Ariel","raw_affiliation_strings":["IAL, CONICET, Ciudad Universitaria UNL , (3000) Santa Fe , Argentina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IAL, CONICET, Ciudad Universitaria UNL , (3000) Santa Fe , Argentina","institution_ids":["https://openalex.org/I4210149924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030230762","display_name":"Leandro E. Di Persia","orcid":"https://orcid.org/0000-0002-0331-6989"},"institutions":[{"id":"https://openalex.org/I151201029","display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","ror":"https://ror.org/03cqe8w59","country_code":"AR","type":"government","lineage":["https://openalex.org/I151201029","https://openalex.org/I4210123736","https://openalex.org/I4387155568"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"L E Di Persia","raw_affiliation_strings":["Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria , Santa Fe , Argentina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria , Santa Fe , Argentina","institution_ids":["https://openalex.org/I151201029"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077266711","display_name":"Diego H. Milone","orcid":"https://orcid.org/0000-0003-2182-4351"},"institutions":[{"id":"https://openalex.org/I151201029","display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","ror":"https://ror.org/03cqe8w59","country_code":"AR","type":"government","lineage":["https://openalex.org/I151201029","https://openalex.org/I4210123736","https://openalex.org/I4387155568"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"D H Milone","raw_affiliation_strings":["Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria , Santa Fe , Argentina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria , Santa Fe , Argentina","institution_ids":["https://openalex.org/I151201029"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091024901","display_name":"Georgina Stegmayer","orcid":"https://orcid.org/0000-0003-4459-4560"},"institutions":[{"id":"https://openalex.org/I151201029","display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","ror":"https://ror.org/03cqe8w59","country_code":"AR","type":"government","lineage":["https://openalex.org/I151201029","https://openalex.org/I4210123736","https://openalex.org/I4387155568"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"G Stegmayer","raw_affiliation_strings":["Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria , Santa Fe , Argentina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria , Santa Fe , Argentina","institution_ids":["https://openalex.org/I151201029"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":13,"corresponding_author_ids":["https://openalex.org/A5053316160"],"corresponding_institution_ids":["https://openalex.org/I151201029"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":3.8115,"has_fulltext":false,"cited_by_count":51,"citation_normalized_percentile":{"value":0.94764806,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"23","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.6531000137329102,"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":0.6531000137329102,"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":0.15410000085830688,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.1145000010728836,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6727297306060791},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5970640182495117},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5907623767852783},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.5452646613121033},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5190784931182861},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5025365352630615},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4934183657169342},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4762018918991089},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.47167453169822693},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.460464209318161},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.4395278990268707},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40565910935401917},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32353514432907104},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19970977306365967},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08949011564254761}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6727297306060791},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5970640182495117},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5907623767852783},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.5452646613121033},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5190784931182861},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5025365352630615},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4934183657169342},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4762018918991089},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.47167453169822693},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.460464209318161},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.4395278990268707},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40565910935401917},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32353514432907104},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19970977306365967},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08949011564254761},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","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/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbac205","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac205","pdf_url":"https://academic.oup.com/bib/article-pdf/23/4/bbac205/45017094/bbac205.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:35692094","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35692094","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:upcommons.upc.edu:2117/371630","is_oa":true,"landing_page_url":"http://hdl.handle.net/2117/371630","pdf_url":null,"source":{"id":"https://openalex.org/S4377196262","display_name":"UPCommons institutional repository (Universitat Polit\u00e8cnica de Catalunya)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9617848","host_organization_name":"Universitat Polit\u00e8cnica de Catalunya","host_organization_lineage":["https://openalex.org/I9617848"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbac205","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac205","pdf_url":"https://academic.oup.com/bib/article-pdf/23/4/bbac205/45017094/bbac205.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/G3034095715","display_name":null,"funder_award_id":"AC-00010-18","funder_id":"https://openalex.org/F4320329199","funder_display_name":"Agencia Santafesina de Ciencia, Tecnolog\u00eda e Innovaci\u00f3n"},{"id":"https://openalex.org/G4272053702","display_name":null,"funder_award_id":"PICT 2018 3384","funder_id":"https://openalex.org/F4320334832","funder_display_name":"Agencia Nacional de Promoci\u00f3n Cient\u00edfica y Tecnol\u00f3gica"},{"id":"https://openalex.org/G5089161312","display_name":null,"funder_award_id":"PICT 2018 2905","funder_id":"https://openalex.org/F4320334832","funder_display_name":"Agencia Nacional de Promoci\u00f3n Cient\u00edfica y Tecnol\u00f3gica"},{"id":"https://openalex.org/G7678787324","display_name":null,"funder_award_id":"PICT 2019 3420","funder_id":"https://openalex.org/F4320334832","funder_display_name":"Agencia Nacional de Promoci\u00f3n Cient\u00edfica y Tecnol\u00f3gica"},{"id":"https://openalex.org/G8732257632","display_name":null,"funder_award_id":"117/14","funder_id":"https://openalex.org/F4320329199","funder_display_name":"Agencia Santafesina de Ciencia, Tecnolog\u00eda e Innovaci\u00f3n"}],"funders":[{"id":"https://openalex.org/F4320329199","display_name":"Agencia Santafesina de Ciencia, Tecnolog\u00eda e Innovaci\u00f3n","ror":null},{"id":"https://openalex.org/F4320334832","display_name":"Agencia Nacional de Promoci\u00f3n Cient\u00edfica y Tecnol\u00f3gica","ror":"https://ror.org/03stxzb56"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4282945580.pdf"},"referenced_works_count":99,"referenced_works":["https://openalex.org/W1565746575","https://openalex.org/W1577392641","https://openalex.org/W1932179720","https://openalex.org/W1975390562","https://openalex.org/W1976459963","https://openalex.org/W1989949418","https://openalex.org/W1992138704","https://openalex.org/W1999955287","https://openalex.org/W2009818318","https://openalex.org/W2012206989","https://openalex.org/W2025763720","https://openalex.org/W2031352989","https://openalex.org/W2032183472","https://openalex.org/W2032741347","https://openalex.org/W2033088902","https://openalex.org/W2036402097","https://openalex.org/W2038598202","https://openalex.org/W2041882488","https://openalex.org/W2045777307","https://openalex.org/W2053695683","https://openalex.org/W2058615001","https://openalex.org/W2064675550","https://openalex.org/W2071883352","https://openalex.org/W2075479129","https://openalex.org/W2076091642","https://openalex.org/W2086561953","https://openalex.org/W2086708241","https://openalex.org/W2098571862","https://openalex.org/W2099145028","https://openalex.org/W2102017611","https://openalex.org/W2104846587","https://openalex.org/W2108895594","https://openalex.org/W2112001233","https://openalex.org/W2117552736","https://openalex.org/W2131462431","https://openalex.org/W2134489577","https://openalex.org/W2141351700","https://openalex.org/W2141601045","https://openalex.org/W2142038007","https://openalex.org/W2143900153","https://openalex.org/W2153268494","https://openalex.org/W2159117141","https://openalex.org/W2162224067","https://openalex.org/W2259938310","https://openalex.org/W2462461504","https://openalex.org/W2464391643","https://openalex.org/W2509925948","https://openalex.org/W2568142275","https://openalex.org/W2604714425","https://openalex.org/W2612690371","https://openalex.org/W2615786037","https://openalex.org/W2617487728","https://openalex.org/W2725568163","https://openalex.org/W2768096340","https://openalex.org/W2786696891","https://openalex.org/W2792104241","https://openalex.org/W2888226663","https://openalex.org/W2919479895","https://openalex.org/W2933083636","https://openalex.org/W2945901478","https://openalex.org/W2951298881","https://openalex.org/W2952731402","https://openalex.org/W2954102902","https://openalex.org/W2969823493","https://openalex.org/W2981537718","https://openalex.org/W2990528340","https://openalex.org/W2995183626","https://openalex.org/W2998238598","https://openalex.org/W3005909538","https://openalex.org/W3007927309","https://openalex.org/W3014154699","https://openalex.org/W3014847050","https://openalex.org/W3031237064","https://openalex.org/W3036354173","https://openalex.org/W3043664941","https://openalex.org/W3049756659","https://openalex.org/W3082088158","https://openalex.org/W3087202564","https://openalex.org/W3095111022","https://openalex.org/W3098223552","https://openalex.org/W3101505571","https://openalex.org/W3115880421","https://openalex.org/W3126773939","https://openalex.org/W3135161193","https://openalex.org/W3151619623","https://openalex.org/W3171007138","https://openalex.org/W3177828909","https://openalex.org/W3185104144","https://openalex.org/W3192568146","https://openalex.org/W3198840069","https://openalex.org/W3204096889","https://openalex.org/W3212533323","https://openalex.org/W4205118596","https://openalex.org/W4390843259","https://openalex.org/W6633774736","https://openalex.org/W6634621888","https://openalex.org/W6760368948","https://openalex.org/W6762648206","https://openalex.org/W6771520483"],"related_works":["https://openalex.org/W2558432341","https://openalex.org/W1975806245","https://openalex.org/W3047450301","https://openalex.org/W2345156963","https://openalex.org/W1971402940","https://openalex.org/W2919479895","https://openalex.org/W4318218930","https://openalex.org/W2159621058","https://openalex.org/W2412575231","https://openalex.org/W2001187219"],"abstract_inverted_index":{"MOTIVATION:":[0],"In":[1,62,127],"contrast":[2],"to":[3,42,189,238],"messenger":[4],"RNAs,":[5],"the":[6,9,30,35,63,101,114,132,135,141,162,191,199,241],"function":[7],"of":[8,12,34,38,70,86,116,134,150,176,194,228,245],"wide":[10],"range":[11],"existing":[13,229],"long":[14],"noncoding":[15],"RNAs":[16],"(lncRNAs)":[17],"largely":[18],"depends":[19],"on":[20,56,198],"their":[21,44],"structure,":[22],"which":[23],"determines":[24],"interactions":[25],"with":[26],"partner":[27],"molecules.":[28],"Thus,":[29],"determination":[31],"or":[32],"prediction":[33,85,103,149],"secondary":[36,51,147],"structure":[37,52,84,148],"lncRNAs":[39],"is":[40],"critical":[41],"uncover":[43],"function.":[45],"Classical":[46],"approaches":[47,145],"for":[48,104,146,167,205],"predicting":[49],"RNA":[50,151,170,207],"have":[53,79,92],"been":[54,121],"based":[55,197],"dynamic":[57],"programming":[58],"and":[59,91,123,156,172,231,234,243,252],"thermodynamic":[60],"calculations.":[61],"last":[64],"4":[65],"years,":[66],"a":[67,154,173,186,224,232],"growing":[68],"number":[69],"machine":[71],"learning":[72,77],"(ML)-based":[73],"models,":[74],"including":[75],"deep":[76],"(DL),":[78],"achieved":[80],"breakthrough":[81],"performance":[82,133,193],"in":[83,96,240],"biomolecules":[87],"such":[88],"as":[89,138,140],"proteins":[90],"outperformed":[93],"classical":[94,136],"methods":[95,137],"short":[97],"transcripts":[98],"folding.":[99],"Nevertheless,":[100],"accurate":[102],"lncRNA":[105,178],"still":[106],"remains":[107],"far":[108],"from":[109,180],"being":[110],"effectively":[111],"solved.":[112],"Notably,":[113],"myriad":[115],"new":[117],"proposals":[118],"has":[119],"not":[120],"systematically":[122],"experimentally":[124],"evaluated.":[125],"RESULTS:":[126],"this":[128],"work,":[129],"we":[130,184],"compare":[131],"well":[139],"most":[142],"recently":[143],"proposed":[144],"sequences":[152],"using":[153,218],"unified":[155],"consistent":[157],"experimental":[158],"setup.":[159],"We":[160],"use":[161],"publicly":[163],"available":[164,256],"structural":[165],"profiles":[166],"3023":[168],"yeast":[169],"sequences,":[171],"novel":[174,187,233],"benchmark":[175,236,253],"well-characterized":[177],"structures":[179],"different":[181],"species.":[182],"Moreover,":[183],"propose":[185],"metric":[188],"assess":[190],"predictive":[192],"methods,":[195],"exclusively":[196],"chemical":[200],"probing":[201],"data":[202],"commonly":[203],"used":[204],"profiling":[206],"structures,":[208],"avoiding":[209],"any":[210],"potential":[211],"bias":[212],"incorporated":[213],"by":[214],"computational":[215],"predictions":[216],"when":[217],"dot-bracket":[219],"references.":[220],"Our":[221],"results":[222],"provide":[223],"comprehensive":[225],"comparative":[226],"assessment":[227],"methodologies,":[230],"public":[235],"resource":[237],"aid":[239],"development":[242],"comparison":[244],"future":[246],"approaches.":[247],"AVAILABILITY:":[248],"Full":[249],"source":[250],"code":[251],"datasets":[254],"are":[255],"at:":[257],"https://github.com/sinc-lab/lncRNA-folding.":[258],"CONTACT:":[259],"lbugnon@sinc.unl.edu.ar.":[260]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":16},{"year":2024,"cited_by_count":18},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":1}],"updated_date":"2026-06-05T09:01:59.212387","created_date":"2025-10-10T00:00:00"}
