{"id":"https://openalex.org/W1757958358","doi":"https://doi.org/10.1109/csb.2003.1227394","title":"An iterative loop matching approach to the prediction of RNA secondary structures with pseudoknots","display_name":"An iterative loop matching approach to the prediction of RNA secondary structures with pseudoknots","publication_year":2004,"publication_date":"2004-03-30","ids":{"openalex":"https://openalex.org/W1757958358","doi":"https://doi.org/10.1109/csb.2003.1227394","mag":"1757958358"},"language":"en","primary_location":{"id":"doi:10.1109/csb.2003.1227394","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2003.1227394","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.7936/k7h993k8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071995180","display_name":"Jianhua Ruan","orcid":"https://orcid.org/0000-0002-5622-3137"},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"J. Ruan","raw_affiliation_strings":["Department of Computer Science, Washington University of Saint Louis, Saint Louis, MO, USA","Department of Computer Science, Washington University, St. Louis, MO, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Washington University of Saint Louis, Saint Louis, MO, USA","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Department of Computer Science, Washington University, St. Louis, MO, USA","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040496643","display_name":"Gary D. Stormo","orcid":"https://orcid.org/0000-0001-6896-1850"},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"G.D. Stormo","raw_affiliation_strings":["Department of Genetics, Washington University of Saint Louis, Saint Louis, MO, USA","Washington University \u2013 St Louis"],"affiliations":[{"raw_affiliation_string":"Department of Genetics, Washington University of Saint Louis, Saint Louis, MO, USA","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Washington University \u2013 St Louis","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068659777","display_name":"Weixiong Zhang","orcid":"https://orcid.org/0000-0002-4998-9791"},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"W. Zhang","raw_affiliation_strings":["Washington University \u2013 St Louis"],"affiliations":[{"raw_affiliation_string":"Washington University \u2013 St Louis","institution_ids":["https://openalex.org/I204465549"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5071995180"],"corresponding_institution_ids":["https://openalex.org/I204465549"],"apc_list":null,"apc_paid":null,"fwci":0.1197,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.46362466,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"395","issue":null,"first_page":"519","last_page":"520"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","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/T11482","display_name":"RNA modifications and cancer","score":0.9927999973297119,"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/matching","display_name":"Matching (statistics)","score":0.6837767362594604},{"id":"https://openalex.org/keywords/loop","display_name":"Loop (graph theory)","score":0.6555591225624084},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5858239531517029},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.5758728981018066},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5672063231468201},{"id":"https://openalex.org/keywords/iterative-method","display_name":"Iterative method","score":0.4569246768951416},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4437929689884186},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2834223508834839},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.19532519578933716},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12134286761283875},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.1201162040233612},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10335800051689148},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08155938982963562}],"concepts":[{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.6837767362594604},{"id":"https://openalex.org/C184670325","wikidata":"https://www.wikidata.org/wiki/Q512604","display_name":"Loop (graph theory)","level":2,"score":0.6555591225624084},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5858239531517029},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.5758728981018066},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5672063231468201},{"id":"https://openalex.org/C159694833","wikidata":"https://www.wikidata.org/wiki/Q2321565","display_name":"Iterative method","level":2,"score":0.4569246768951416},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4437929689884186},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2834223508834839},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.19532519578933716},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12134286761283875},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.1201162040233612},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10335800051689148},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08155938982963562},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/csb.2003.1227394","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2003.1227394","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","raw_type":"proceedings-article"},{"id":"pmh:oai:openscholarship.wustl.edu:cse_research-2089","is_oa":false,"landing_page_url":"https://openscholarship.wustl.edu/cse_research/1088","pdf_url":null,"source":{"id":"https://openalex.org/S4377196400","display_name":"Open Scholarship Institutional Repository (Washington University in St. Louis)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I204465549","host_organization_name":"Washington University in St. Louis","host_organization_lineage":["https://openalex.org/I204465549"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"All Computer Science and Engineering Research","raw_type":"text"},{"id":"doi:10.7936/k7h993k8","is_oa":true,"landing_page_url":"https://doi.org/10.7936/k7h993k8","pdf_url":null,"source":{"id":"https://openalex.org/S7407053377","display_name":"Washington University in St. Louis Libraries","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.7936/k7h993k8","is_oa":true,"landing_page_url":"https://doi.org/10.7936/k7h993k8","pdf_url":null,"source":{"id":"https://openalex.org/S7407053377","display_name":"Washington University in St. Louis Libraries","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":50,"referenced_works":["https://openalex.org/W140117565","https://openalex.org/W1537127938","https://openalex.org/W1543796220","https://openalex.org/W1725615870","https://openalex.org/W1757958358","https://openalex.org/W1881326155","https://openalex.org/W1978202265","https://openalex.org/W1983806762","https://openalex.org/W1984675364","https://openalex.org/W1993968482","https://openalex.org/W2009736453","https://openalex.org/W2009818318","https://openalex.org/W2011039300","https://openalex.org/W2011368877","https://openalex.org/W2014989101","https://openalex.org/W2017313617","https://openalex.org/W2018216725","https://openalex.org/W2023206235","https://openalex.org/W2025763720","https://openalex.org/W2028574527","https://openalex.org/W2034762276","https://openalex.org/W2039915263","https://openalex.org/W2040015982","https://openalex.org/W2053620236","https://openalex.org/W2054931730","https://openalex.org/W2075702353","https://openalex.org/W2076756368","https://openalex.org/W2077237370","https://openalex.org/W2086509077","https://openalex.org/W2095145214","https://openalex.org/W2098341656","https://openalex.org/W2099359200","https://openalex.org/W2100271852","https://openalex.org/W2102046276","https://openalex.org/W2107432340","https://openalex.org/W2109297587","https://openalex.org/W2113368761","https://openalex.org/W2123241418","https://openalex.org/W2134453550","https://openalex.org/W2140651796","https://openalex.org/W2142056356","https://openalex.org/W2144399441","https://openalex.org/W2144660787","https://openalex.org/W2145972251","https://openalex.org/W2151538750","https://openalex.org/W2166412654","https://openalex.org/W2169239541","https://openalex.org/W4246308822","https://openalex.org/W4285719527","https://openalex.org/W6681001129"],"related_works":["https://openalex.org/W24774503","https://openalex.org/W2014821076","https://openalex.org/W1990620319","https://openalex.org/W1965744717","https://openalex.org/W2111234595","https://openalex.org/W3216334292","https://openalex.org/W1883238101","https://openalex.org/W2481821631","https://openalex.org/W1536525683","https://openalex.org/W1972035260"],"abstract_inverted_index":{"In":[0,82],"this":[1],"paper":[2],"we":[3],"present":[4],"a":[5],"heuristic":[6],"algorithm,":[7],"iterative":[8],"loop":[9],"matching,":[10],"for":[11,31,50],"predicting":[12],"RNA":[13],"pseudoknots.":[14],"The":[15],"method":[16],"can":[17,90],"utilize":[18],"either":[19],"thermodynamic":[20],"or":[21,24],"comparative":[22],"information":[23],"both,":[25],"thus":[26],"is":[27,73,86],"able":[28],"to":[29,93,96],"predict":[30],"both":[32],"aligned":[33],"and":[34,53,76,89],"individual":[35],"sequences.":[36],"Using":[37],"8-12":[38],"homologous":[39],"sequences,":[40],"the":[41],"algorithm":[42,72,85],"correctly":[43,57],"identifies":[44],"more":[45,74,77],"than":[46,79],"90%":[47],"of":[48,99],"base-pairs":[49],"short":[51],"sequences":[52,94],"80%":[54],"overall.":[55],"It":[56],"predicts":[58],"nearly":[59],"all":[60],"pseudoknots,":[61],"while":[62],"having":[63],"very":[64,87],"few":[65],"false":[66],"predictions.":[67],"Comparisons":[68],"show":[69],"that":[70],"our":[71,84],"sensitive":[75],"specific":[78],"existing":[80],"methods.":[81],"addition,":[83],"efficient":[88],"be":[91],"applied":[92],"up":[95],"several":[97],"thousands":[98],"bases":[100],"long.":[101]},"counts_by_year":[],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}
