{"id":"https://openalex.org/W2052158622","doi":"https://doi.org/10.1186/1471-2105-11-586","title":"Prediction of RNA secondary structure by maximizing pseudo-expected accuracy","display_name":"Prediction of RNA secondary structure by maximizing pseudo-expected accuracy","publication_year":2010,"publication_date":"2010-11-30","ids":{"openalex":"https://openalex.org/W2052158622","doi":"https://doi.org/10.1186/1471-2105-11-586","mag":"2052158622","pmid":"https://pubmed.ncbi.nlm.nih.gov/21118522"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-586","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-586","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-586","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-586","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025857432","display_name":"Michiaki Hamada","orcid":"https://orcid.org/0000-0001-9466-1034"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]},{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Michiaki Hamada","raw_affiliation_strings":["Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, Japan. hamada-michiaki@aist.go.jp","the University of Tokyo","National Institute of Advanced Industrial Science and Technology (AIST)"],"affiliations":[{"raw_affiliation_string":"Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, Japan. hamada-michiaki@aist.go.jp","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"the University of Tokyo","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"National Institute of Advanced Industrial Science and Technology (AIST)","institution_ids":["https://openalex.org/I73613424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076175043","display_name":"Kengo Sato","orcid":"https://orcid.org/0000-0001-6744-7390"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kengo Sato","raw_affiliation_strings":["Graduate School of Frontier Sciences, The University of Tokyo,5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan","The University of Tokyo"],"affiliations":[{"raw_affiliation_string":"Graduate School of Frontier Sciences, The University of Tokyo,5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"The University of Tokyo","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082068847","display_name":"Kiyoshi Asai","orcid":"https://orcid.org/0000-0003-0909-4982"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]},{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kiyoshi Asai","raw_affiliation_strings":["Graduate School of Frontier Sciences, The University of Tokyo,5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan","National Institute of Advanced Industrial Science and Technology (AIST)","the University of Tokyo"],"affiliations":[{"raw_affiliation_string":"Graduate School of Frontier Sciences, The University of Tokyo,5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"National Institute of Advanced Industrial Science and Technology (AIST)","institution_ids":["https://openalex.org/I73613424"]},{"raw_affiliation_string":"the University of Tokyo","institution_ids":["https://openalex.org/I74801974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5025857432"],"corresponding_institution_ids":["https://openalex.org/I73613424","https://openalex.org/I74801974"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.6265,"has_fulltext":true,"cited_by_count":27,"citation_normalized_percentile":{"value":0.82638552,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"11","issue":"1","first_page":"586","last_page":"586"},"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":0.9933000206947327,"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":0.9864000082015991,"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/estimator","display_name":"Estimator","score":0.718652606010437},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.6943826079368591},{"id":"https://openalex.org/keywords/expected-value","display_name":"Expected value","score":0.5008423328399658},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.48164358735084534},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4749103784561157},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.464724600315094},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.44778168201446533},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.40484678745269775},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.39302051067352295},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.2285231649875641},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08835789561271667}],"concepts":[{"id":"https://openalex.org/C185429906","wikidata":"https://www.wikidata.org/wiki/Q1130160","display_name":"Estimator","level":2,"score":0.718652606010437},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.6943826079368591},{"id":"https://openalex.org/C141042865","wikidata":"https://www.wikidata.org/wiki/Q200125","display_name":"Expected value","level":2,"score":0.5008423328399658},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48164358735084534},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4749103784561157},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.464724600315094},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.44778168201446533},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.40484678745269775},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.39302051067352295},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.2285231649875641},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08835789561271667},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","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/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","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},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","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":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","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":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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-11-586","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-586","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-586","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21118522","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21118522","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:95a8d77a1cff457990c95c1d12f59956","is_oa":true,"landing_page_url":"https://doaj.org/article/95a8d77a1cff457990c95c1d12f59956","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 11, Iss 1, p 586 (2010)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3003279","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3003279","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:t2r2.star.titech.ac.jp:50744908","is_oa":false,"landing_page_url":"http://t2r2.star.titech.ac.jp/cgi-bin/publicationinfo.cgi?q_publication_content_number=CTT100937986","pdf_url":null,"source":{"id":"https://openalex.org/S4377196385","display_name":"Tokyo Tech Research Repository (Tokyo Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I114531698","host_organization_name":"Tokyo Institute of Technology","host_organization_lineage":["https://openalex.org/I114531698"],"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":"Journal Article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-11-586","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-586","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-586","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4300000071525574,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2052158622.pdf","grobid_xml":"https://content.openalex.org/works/W2052158622.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1506654643","https://openalex.org/W1543796220","https://openalex.org/W1976021976","https://openalex.org/W1981576666","https://openalex.org/W1984675364","https://openalex.org/W1988409793","https://openalex.org/W1990529500","https://openalex.org/W1994958179","https://openalex.org/W2004945910","https://openalex.org/W2007135806","https://openalex.org/W2009736453","https://openalex.org/W2011289056","https://openalex.org/W2025763720","https://openalex.org/W2042881722","https://openalex.org/W2049283139","https://openalex.org/W2101497682","https://openalex.org/W2101535367","https://openalex.org/W2102017611","https://openalex.org/W2107432340","https://openalex.org/W2111272410","https://openalex.org/W2113816707","https://openalex.org/W2118829610","https://openalex.org/W2131054067","https://openalex.org/W2133876293","https://openalex.org/W2137640371","https://openalex.org/W2139449083","https://openalex.org/W2141157874","https://openalex.org/W2141411594","https://openalex.org/W2142038007","https://openalex.org/W2145158851","https://openalex.org/W2153140501","https://openalex.org/W2156976607","https://openalex.org/W2158267024","https://openalex.org/W2158623906","https://openalex.org/W2162224067","https://openalex.org/W2610493105","https://openalex.org/W3214380909","https://openalex.org/W4245668478"],"related_works":["https://openalex.org/W4287880334","https://openalex.org/W4366700029","https://openalex.org/W4285230481","https://openalex.org/W4385769873","https://openalex.org/W2015759683","https://openalex.org/W4281634296","https://openalex.org/W4319161863","https://openalex.org/W2371687270","https://openalex.org/W2898674639","https://openalex.org/W4311888330"],"abstract_inverted_index":{"This":[0],"study":[1],"gives":[2],"not":[3],"only":[4],"a":[5,20],"method":[6,22],"for":[7,23],"predicting":[8],"the":[9,26],"secondary":[10],"structure":[11],"that":[12],"balances":[13],"between":[14],"sensitivity":[15],"and":[16,37],"PPV,":[17],"but":[18],"also":[19],"general":[21],"approximately":[24],"maximizing":[25],"(pseudo-)expected":[27],"accuracy":[28],"with":[29],"respect":[30],"to":[31],"various":[32],"evaluation":[33],"measures":[34],"including":[35],"MCC":[36],"F-score.":[38]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":4},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":3}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}