{"id":"https://openalex.org/W2807635396","doi":"https://doi.org/10.1093/bioinformatics/bty420","title":"Knotty: efficient and accurate prediction of complex RNA pseudoknot structures","display_name":"Knotty: efficient and accurate prediction of complex RNA pseudoknot structures","publication_year":2018,"publication_date":"2018-05-24","ids":{"openalex":"https://openalex.org/W2807635396","doi":"https://doi.org/10.1093/bioinformatics/bty420","mag":"2807635396","pmid":"https://pubmed.ncbi.nlm.nih.gov/29868872"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty420","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty420","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/22/3849/26441601/bty420.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/22/3849/26441601/bty420.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005818804","display_name":"Hosna Jabbari","orcid":"https://orcid.org/0000-0002-7155-2297"},"institutions":[{"id":"https://openalex.org/I111236770","display_name":"University of Vermont","ror":"https://ror.org/0155zta11","country_code":"US","type":"education","lineage":["https://openalex.org/I111236770"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hosna Jabbari","raw_affiliation_strings":["Department of Computer Science, University of Vermont, Burlington, VT, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Vermont, Burlington, VT, USA","institution_ids":["https://openalex.org/I111236770"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032922740","display_name":"Ian William Wark","orcid":null},"institutions":[{"id":"https://openalex.org/I154425047","display_name":"University of Alberta","ror":"https://ror.org/0160cpw27","country_code":"CA","type":"education","lineage":["https://openalex.org/I154425047"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Ian Wark","raw_affiliation_strings":["Ingenuity Lab, Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada"],"affiliations":[{"raw_affiliation_string":"Ingenuity Lab, Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada","institution_ids":["https://openalex.org/I154425047"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074592151","display_name":"Carlo Montemagno","orcid":"https://orcid.org/0000-0003-3169-2583"},"institutions":[{"id":"https://openalex.org/I110378019","display_name":"Southern Illinois University Carbondale","ror":"https://ror.org/049kefs16","country_code":"US","type":"education","lineage":["https://openalex.org/I110378019","https://openalex.org/I2801502357"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carlo Montemagno","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Southern Illinois University, Carbondale, IL, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Southern Illinois University, Carbondale, IL, USA","institution_ids":["https://openalex.org/I110378019"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103135268","display_name":"Sebastian Will","orcid":"https://orcid.org/0000-0002-2376-9205"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"Sebastian Will","raw_affiliation_strings":["Theoretical Biochemistry Group (TBI), Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria"],"affiliations":[{"raw_affiliation_string":"Theoretical Biochemistry Group (TBI), Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5005818804","https://openalex.org/A5103135268"],"corresponding_institution_ids":["https://openalex.org/I111236770","https://openalex.org/I129774422"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.306,"has_fulltext":false,"cited_by_count":61,"citation_normalized_percentile":{"value":0.80197063,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"34","issue":"22","first_page":"3849","last_page":"3856"},"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":0.9993000030517578,"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":0.9984999895095825,"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/pseudoknot","display_name":"Pseudoknot","score":0.9142106175422668},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.7815558910369873},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5961716771125793},{"id":"https://openalex.org/keywords/minification","display_name":"Minification","score":0.4613167941570282},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4254767894744873},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.4136171042919159},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.24160242080688477},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14523619413375854},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.06558564305305481}],"concepts":[{"id":"https://openalex.org/C105130999","wikidata":"https://www.wikidata.org/wiki/Q414976","display_name":"Pseudoknot","level":4,"score":0.9142106175422668},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7815558910369873},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5961716771125793},{"id":"https://openalex.org/C147764199","wikidata":"https://www.wikidata.org/wiki/Q6865248","display_name":"Minification","level":2,"score":0.4613167941570282},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4254767894744873},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.4136171042919159},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.24160242080688477},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14523619413375854},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.06558564305305481},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty420","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty420","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/22/3849/26441601/bty420.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29868872","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29868872","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:HAL:hal-02908990v1","is_oa":false,"landing_page_url":"https://inria.hal.science/hal-02908990","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2018, 34 (22), pp.3849-3856. &#x27E8;10.1093/bioinformatics/bty420&#x27E9;","raw_type":"Journal articles"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty420","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty420","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/22/3849/26441601/bty420.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.8999999761581421}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2807635396.pdf","grobid_xml":"https://content.openalex.org/works/W2807635396.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1975017903","https://openalex.org/W1978336838","https://openalex.org/W1981576666","https://openalex.org/W1999060916","https://openalex.org/W2000191287","https://openalex.org/W2042747303","https://openalex.org/W2043653977","https://openalex.org/W2044151171","https://openalex.org/W2048814860","https://openalex.org/W2054028885","https://openalex.org/W2064714768","https://openalex.org/W2065563872","https://openalex.org/W2083479074","https://openalex.org/W2086509077","https://openalex.org/W2087377443","https://openalex.org/W2090936113","https://openalex.org/W2104141342","https://openalex.org/W2106293441","https://openalex.org/W2109297587","https://openalex.org/W2115275409","https://openalex.org/W2123202877","https://openalex.org/W2123241418","https://openalex.org/W2128705009","https://openalex.org/W2134489577","https://openalex.org/W2140818786","https://openalex.org/W2141351700","https://openalex.org/W2162224067","https://openalex.org/W2167516501","https://openalex.org/W2339509753","https://openalex.org/W2791055994","https://openalex.org/W6662900732"],"related_works":["https://openalex.org/W2057901482","https://openalex.org/W2018280025","https://openalex.org/W1998399688","https://openalex.org/W2981287558","https://openalex.org/W2022565929","https://openalex.org/W2054306371","https://openalex.org/W2012192331","https://openalex.org/W2007550449","https://openalex.org/W2017993626","https://openalex.org/W1508042871"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":14},{"year":2023,"cited_by_count":12},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":2}],"updated_date":"2026-03-05T09:29:38.588285","created_date":"2025-10-10T00:00:00"}
