{"id":"https://openalex.org/W3204096889","doi":"https://doi.org/10.1093/bib/bbab395","title":"Prediction of RNA secondary structure including pseudoknots for long sequences","display_name":"Prediction of RNA secondary structure including pseudoknots for long sequences","publication_year":2021,"publication_date":"2021-09-08","ids":{"openalex":"https://openalex.org/W3204096889","doi":"https://doi.org/10.1093/bib/bbab395","mag":"3204096889","pmid":"https://pubmed.ncbi.nlm.nih.gov/34601552"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbab395","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbab395","pdf_url":"https://academic.oup.com/bib/article-pdf/23/1/bbab395/42230695/bbab395.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/23/1/bbab395/42230695/bbab395.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076175043","display_name":"Kengo Sato","orcid":"https://orcid.org/0000-0001-6744-7390"},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Kengo Sato","raw_affiliation_strings":["Department of Biosciences and Informatics, Keio University, 3\u201314\u20131 Hiyoshi, Kohoku-ku, Yokohama 223\u20138522, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosciences and Informatics, Keio University, 3\u201314\u20131 Hiyoshi, Kohoku-ku, Yokohama 223\u20138522, Japan","institution_ids":["https://openalex.org/I203951103"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085946915","display_name":"Yuki Kato","orcid":"https://orcid.org/0000-0002-1526-2754"},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yuki Kato","raw_affiliation_strings":["Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565\u20130871, Japan","Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565\u20130871, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka 565\u20130871, Japan","institution_ids":["https://openalex.org/I98285908"]},{"raw_affiliation_string":"Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565\u20130871, Japan","institution_ids":["https://openalex.org/I98285908"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5076175043"],"corresponding_institution_ids":["https://openalex.org/I203951103"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":4.7218,"has_fulltext":true,"cited_by_count":76,"citation_normalized_percentile":{"value":0.96330117,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"23","issue":"1","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":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":0.9939000010490417,"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":0.9923999905586243,"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/computational-biology","display_name":"Computational biology","score":0.5596545934677124},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5573670268058777},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5259459614753723},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30796438455581665},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21716400980949402},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1029115617275238}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5596545934677124},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5573670268058777},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5259459614753723},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30796438455581665},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21716400980949402},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1029115617275238}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":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":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbab395","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbab395","pdf_url":"https://academic.oup.com/bib/article-pdf/23/1/bbab395/42230695/bbab395.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34601552","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34601552","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:pubmedcentral.nih.gov:8769711","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8769711","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbab395","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbab395","pdf_url":"https://academic.oup.com/bib/article-pdf/23/1/bbab395/42230695/bbab395.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/G2585757194","display_name":null,"funder_award_id":"18K11526","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G3433819449","display_name":null,"funder_award_id":"19H04210","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G3602104047","display_name":null,"funder_award_id":"19K22897","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G7494324072","display_name":null,"funder_award_id":"21K12109","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320314183","display_name":"Research Organization of Information and Systems","ror":"https://ror.org/04p4e8t29"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320338065","display_name":"Institute of Genetics","ror":"https://ror.org/03gwhmn95"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3204096889.pdf","grobid_xml":"https://content.openalex.org/works/W3204096889.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1965243792","https://openalex.org/W1979245300","https://openalex.org/W1984675364","https://openalex.org/W2031352989","https://openalex.org/W2052158622","https://openalex.org/W2056742043","https://openalex.org/W2074882547","https://openalex.org/W2076756368","https://openalex.org/W2086561953","https://openalex.org/W2098571862","https://openalex.org/W2101497682","https://openalex.org/W2101535367","https://openalex.org/W2102017611","https://openalex.org/W2102046276","https://openalex.org/W2106293441","https://openalex.org/W2108230379","https://openalex.org/W2109297587","https://openalex.org/W2123241418","https://openalex.org/W2134489577","https://openalex.org/W2141157874","https://openalex.org/W2141351700","https://openalex.org/W2142056356","https://openalex.org/W2148599336","https://openalex.org/W2158267024","https://openalex.org/W2160378127","https://openalex.org/W2162224067","https://openalex.org/W2163557777","https://openalex.org/W2170747616","https://openalex.org/W2807635396","https://openalex.org/W2951298881","https://openalex.org/W2989622064","https://openalex.org/W2990528340","https://openalex.org/W3036482641","https://openalex.org/W3043664941","https://openalex.org/W3100348855","https://openalex.org/W3126773939","https://openalex.org/W6772161278"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189"],"abstract_inverted_index":{"RNA":[0,63],"structural":[1],"elements":[2],"called":[3],"pseudoknots":[4,33],"are":[5,34],"involved":[6],"in":[7,98,131],"various":[8],"biological":[9],"phenomena":[10],"including":[11,26],"ribosomal":[12],"frameshifts.":[13],"Because":[14],"it":[15,50,56,68],"is":[16],"infeasible":[17],"to":[18,45,54,57,75,84],"construct":[19],"an":[20,91],"efficiently":[21],"computable":[22],"secondary":[23,28],"structure":[24,29],"model":[25,105],"pseudoknots,":[27],"prediction":[30,123],"methods":[31],"considering":[32],"not":[35,135],"yet":[36],"widely":[37],"available.":[38],"We":[39],"developed":[40],"IPknot,":[41],"which":[42],"uses":[43],"heuristics":[44],"speed":[46],"up":[47],"computations,":[48],"but":[49,140],"has":[51,79],"remained":[52],"difficult":[53],"apply":[55],"long":[58],"sequences,":[59],"such":[60],"as":[61],"messenger":[62],"and":[64,78,106],"viral":[65],"RNA,":[66],"because":[67],"requires":[69],"cubic":[70],"computational":[71],"time":[72,100],"with":[73],"respect":[74],"sequence":[76],"length":[77],"threshold":[80,111],"parameters":[81,112],"that":[82,95],"need":[83],"be":[85],"manually":[86],"adjusted.":[87],"Here,":[88],"we":[89],"propose":[90],"improvement":[92],"of":[93,129],"IPknot":[94,120],"enables":[96],"calculation":[97],"linear":[99],"by":[101],"employing":[102],"the":[103,109,115],"LinearPartition":[104],"automatically":[107],"selects":[108],"optimal":[110],"based":[113],"on":[114],"pseudo-expected":[116],"accuracy.":[117],"In":[118],"addition,":[119],"showed":[121],"favorable":[122],"accuracy":[124],"across":[125],"a":[126],"wide":[127],"range":[128],"conditions":[130],"our":[132],"exhaustive":[133],"benchmarking,":[134],"only":[136],"for":[137,142],"single":[138],"sequences":[139],"also":[141],"multiple":[143],"alignments.":[144]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":14},{"year":2024,"cited_by_count":27},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":18}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
