{"id":"https://openalex.org/W2166707334","doi":"https://doi.org/10.1007/11732990_13","title":"Structural Alignment of Pseudoknotted RNA","display_name":"Structural Alignment of Pseudoknotted RNA","publication_year":2006,"publication_date":"2006-01-01","ids":{"openalex":"https://openalex.org/W2166707334","doi":"https://doi.org/10.1007/11732990_13","mag":"2166707334"},"language":"en","primary_location":{"id":"doi:10.1007/11732990_13","is_oa":true,"landing_page_url":"https://doi.org/10.1007/11732990_13","pdf_url":"https://link.springer.com/content/pdf/10.1007%2F11732990_13.pdf","source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"type":"book-chapter","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://link.springer.com/content/pdf/10.1007%2F11732990_13.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073542996","display_name":"Banu Dost","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Banu Dost","raw_affiliation_strings":["Department of Computer Science and Engineering, University of California, San Diego, La Jolla, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of California, San Diego, La Jolla, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051872325","display_name":"Buhm Han","orcid":"https://orcid.org/0000-0002-2266-5164"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Buhm Han","raw_affiliation_strings":["Department of Computer Science and Engineering, University of California, San Diego, La Jolla, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of California, San Diego, La Jolla, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100768909","display_name":"Shaojie Zhang","orcid":"https://orcid.org/0000-0002-4051-5549"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shaojie Zhang","raw_affiliation_strings":["Department of Computer Science and Engineering, University of California, San Diego, La Jolla, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of California, San Diego, La Jolla, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028801735","display_name":"Vineet Bafna","orcid":"https://orcid.org/0000-0002-5810-6241"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vineet Bafna","raw_affiliation_strings":["Department of Computer Science and Engineering, University of California, San Diego, La Jolla, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of California, San Diego, La Jolla, USA","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5073542996"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":{"value":5000,"currency":"EUR","value_usd":5392},"apc_paid":null,"fwci":3.6869,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.93006823,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"143","last_page":"158"},"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":0.9987999796867371,"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":0.9987000226974487,"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/substring","display_name":"Substring","score":0.8221148252487183},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.6622397303581238},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.634758710861206},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6121683716773987},{"id":"https://openalex.org/keywords/non-coding-rna","display_name":"Non-coding RNA","score":0.5797519683837891},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5645135045051575},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.495489239692688},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4869895875453949},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.4709811210632324},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.43829256296157837},{"id":"https://openalex.org/keywords/homologous-chromosome","display_name":"Homologous chromosome","score":0.4254380762577057},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.40473514795303345},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3495258092880249},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.30424433946609497},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.24160242080688477},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2079978585243225},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.10915377736091614}],"concepts":[{"id":"https://openalex.org/C182407805","wikidata":"https://www.wikidata.org/wiki/Q2626534","display_name":"Substring","level":3,"score":0.8221148252487183},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.6622397303581238},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.634758710861206},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6121683716773987},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.5797519683837891},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5645135045051575},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.495489239692688},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4869895875453949},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.4709811210632324},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.43829256296157837},{"id":"https://openalex.org/C64894306","wikidata":"https://www.wikidata.org/wiki/Q849622","display_name":"Homologous chromosome","level":3,"score":0.4254380762577057},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.40473514795303345},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3495258092880249},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.30424433946609497},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.24160242080688477},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2079978585243225},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.10915377736091614},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1007/11732990_13","is_oa":true,"landing_page_url":"https://doi.org/10.1007/11732990_13","pdf_url":"https://link.springer.com/content/pdf/10.1007%2F11732990_13.pdf","source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.129.9152","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.129.9152","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cse.ucsd.edu/~shzhang/app/RECOMB2005_pseudoknot.pdf","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:7121381","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7121381","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Research in Computational Molecular Biology","raw_type":"Text"},{"id":"pmh:oai:s-space.snu.ac.kr:10371/191663","is_oa":false,"landing_page_url":"https://hdl.handle.net/10371/191663","pdf_url":null,"source":{"id":"https://openalex.org/S4306401345","display_name":"Seoul National University Open Repository (Seoul National University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139264467","host_organization_name":"Seoul National University","host_organization_lineage":["https://openalex.org/I139264467"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1007/11732990_13","is_oa":true,"landing_page_url":"https://doi.org/10.1007/11732990_13","pdf_url":"https://link.springer.com/content/pdf/10.1007%2F11732990_13.pdf","source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.7400000095367432,"id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G5699921400","display_name":"Novel Algorithms for NcRNA Discovery and RNA Structure Prediction","funder_award_id":"0516440","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2166707334.pdf","grobid_xml":"https://content.openalex.org/works/W2166707334.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W175036826","https://openalex.org/W1513047926","https://openalex.org/W1542426682","https://openalex.org/W1600401233","https://openalex.org/W1925397890","https://openalex.org/W1950410402","https://openalex.org/W1990549640","https://openalex.org/W1995403172","https://openalex.org/W1999410197","https://openalex.org/W2004812096","https://openalex.org/W2007550449","https://openalex.org/W2008288996","https://openalex.org/W2013195357","https://openalex.org/W2037722828","https://openalex.org/W2042881722","https://openalex.org/W2061158331","https://openalex.org/W2065225159","https://openalex.org/W2073865971","https://openalex.org/W2088938573","https://openalex.org/W2102066220","https://openalex.org/W2104141342","https://openalex.org/W2109297587","https://openalex.org/W2120523244","https://openalex.org/W2123241418","https://openalex.org/W2130978693","https://openalex.org/W2137677639","https://openalex.org/W2138452362","https://openalex.org/W2139993947","https://openalex.org/W2155058605","https://openalex.org/W2169751581","https://openalex.org/W4234667141","https://openalex.org/W4245668478"],"related_works":["https://openalex.org/W2120771433","https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W2162923930","https://openalex.org/W1482324242","https://openalex.org/W2133116680","https://openalex.org/W2029514038","https://openalex.org/W2149492307","https://openalex.org/W1985408726","https://openalex.org/W2055553856"],"abstract_inverted_index":null,"counts_by_year":[{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
