{"id":"https://openalex.org/W2146922921","doi":"https://doi.org/10.1089/106652703322756186","title":"Predicting RNA Secondary Structures with Arbitrary Pseudoknots by Maximizing the Number of Stacking Pairs","display_name":"Predicting RNA Secondary Structures with Arbitrary Pseudoknots by Maximizing the Number of Stacking Pairs","publication_year":2003,"publication_date":"2003-12-01","ids":{"openalex":"https://openalex.org/W2146922921","doi":"https://doi.org/10.1089/106652703322756186","mag":"2146922921","pmid":"https://pubmed.ncbi.nlm.nih.gov/14980021"},"language":"en","primary_location":{"id":"doi:10.1089/106652703322756186","is_oa":false,"landing_page_url":"https://doi.org/10.1089/106652703322756186","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022797064","display_name":"Samuel Ieong","orcid":null},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Samuel Ieong","raw_affiliation_strings":["Department of Computer Science, Yale University, New Haven, CT 06520"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Yale University, New Haven, CT 06520","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109219665","display_name":"Ming\u2010Yang Kao","orcid":null},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ming-Yang Kao","raw_affiliation_strings":["Department of Computer Science, Northwestern University, Evanston, IL 60201"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Northwestern University, Evanston, IL 60201","institution_ids":["https://openalex.org/I111979921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077116003","display_name":"Tak\u2010Wah Lam","orcid":"https://orcid.org/0000-0003-4676-8587"},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Tak-Wah Lam","raw_affiliation_strings":["Department of Computer Science, The University of Hong Kong, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, The University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012563463","display_name":"Wing\u2010Kin Sung","orcid":"https://orcid.org/0000-0001-7806-7086"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Wing-Kin Sung","raw_affiliation_strings":["Department of Computer Science, National University of Singapore, Singapore 117543"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, National University of Singapore, Singapore 117543","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5110500992","display_name":"Siu\u2010Ming Yiu","orcid":null},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Siu-Ming Yiu","raw_affiliation_strings":["Department of Computer Science, The University of Hong Kong, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, The University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.2602,"has_fulltext":false,"cited_by_count":61,"citation_normalized_percentile":{"value":0.78557218,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"10","issue":"6","first_page":"981","last_page":"995"},"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":0.996999979019165,"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":0.9876999855041504,"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/stacking","display_name":"Stacking","score":0.7475181818008423},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.6105362176895142},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.6070577502250671},{"id":"https://openalex.org/keywords/time-complexity","display_name":"Time complexity","score":0.603021502494812},{"id":"https://openalex.org/keywords/planar","display_name":"Planar","score":0.5860389471054077},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5452287197113037},{"id":"https://openalex.org/keywords/approximation-algorithm","display_name":"Approximation algorithm","score":0.5213426351547241},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5101369023323059},{"id":"https://openalex.org/keywords/pseudoknot","display_name":"Pseudoknot","score":0.508712112903595},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.48727524280548096},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.41876956820487976},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.39693307876586914},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.3457843065261841},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.2915399670600891},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.09839078783988953},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.06993675231933594}],"concepts":[{"id":"https://openalex.org/C33347731","wikidata":"https://www.wikidata.org/wiki/Q285210","display_name":"Stacking","level":2,"score":0.7475181818008423},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.6105362176895142},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.6070577502250671},{"id":"https://openalex.org/C311688","wikidata":"https://www.wikidata.org/wiki/Q2393193","display_name":"Time complexity","level":2,"score":0.603021502494812},{"id":"https://openalex.org/C134786449","wikidata":"https://www.wikidata.org/wiki/Q3391255","display_name":"Planar","level":2,"score":0.5860389471054077},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5452287197113037},{"id":"https://openalex.org/C148764684","wikidata":"https://www.wikidata.org/wiki/Q621751","display_name":"Approximation algorithm","level":2,"score":0.5213426351547241},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5101369023323059},{"id":"https://openalex.org/C105130999","wikidata":"https://www.wikidata.org/wiki/Q414976","display_name":"Pseudoknot","level":4,"score":0.508712112903595},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.48727524280548096},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.41876956820487976},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.39693307876586914},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.3457843065261841},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.2915399670600891},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.09839078783988953},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.06993675231933594},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","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":"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":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","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":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","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":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1089/106652703322756186","is_oa":false,"landing_page_url":"https://doi.org/10.1089/106652703322756186","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},{"id":"pmid:14980021","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14980021","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":"Journal of computational biology : a journal of computational molecular cell biology","raw_type":null},{"id":"pmh:oai:scholarbank.nus.edu.sg:10635/39233","is_oa":false,"landing_page_url":"http://scholarbank.nus.edu.sg/handle/10635/39233","pdf_url":null,"source":{"id":"https://openalex.org/S7407052290","display_name":"National University of Singapore","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Scopus","raw_type":"Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.341.5837","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.341.5837","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://arxiv.org/pdf/cs/0111051v1.pdf","raw_type":"text"},{"id":"pmh:oai:hub.hku.hk:10722/88933","is_oa":false,"landing_page_url":"http://hdl.handle.net/10722/88933","pdf_url":null,"source":{"id":"https://openalex.org/S4377196271","display_name":"The HKU Scholars Hub (University of Hong Kong)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I889458895","host_organization_name":"University of Hong Kong","host_organization_lineage":["https://openalex.org/I889458895"],"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":null,"sustainable_development_goals":[{"score":0.800000011920929,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W1589993665","https://openalex.org/W1968245790","https://openalex.org/W1971988254","https://openalex.org/W1987680287","https://openalex.org/W2011039300","https://openalex.org/W2041397659","https://openalex.org/W2054931730","https://openalex.org/W2061158331","https://openalex.org/W2076756368","https://openalex.org/W2086509077","https://openalex.org/W2109297587","https://openalex.org/W2123241418","https://openalex.org/W2171177497"],"related_works":["https://openalex.org/W2159621058","https://openalex.org/W1982134706","https://openalex.org/W2036643266","https://openalex.org/W1999060916","https://openalex.org/W1583489351","https://openalex.org/W2585053133","https://openalex.org/W2280924737","https://openalex.org/W2148725278","https://openalex.org/W1763957638","https://openalex.org/W2003956388"],"abstract_inverted_index":{"The":[0,11],"paper":[1],"investigates":[2],"the":[3,19,45,90,104,122,138],"computational":[4],"problem":[5,20],"of":[6,38,47,56,72,87,124],"predicting":[7,48],"RNA":[8,49,85],"secondary":[9,50,80,95,130],"structures.":[10],"general":[12,79,105,150],"belief":[13],"is":[14,134],"that":[15,102,114],"allowing":[16,60,115],"pseudoknots":[17,116],"makes":[18,117],"hard.":[21],"Existing":[22],"polynomial-time":[23],"algorithms":[24,27,67],"are":[25,145],"heuristic":[26],"with":[28,52,68,137],"no":[29],"performance":[30],"guarantee":[31],"and":[32,74,78,151],"can":[33],"handle":[34],"only":[35],"limited":[36],"types":[37],"pseudoknots.":[39,62],"In":[40],"this":[41],"paper,":[42],"we":[43,112],"initiate":[44],"study":[46],"structures":[51,96],"a":[53,128],"maximum":[54],"number":[55,123],"stacking":[57,125],"pairs":[58,126],"while":[59,101],"arbitrary":[61],"We":[63],"obtain":[64],"two":[65],"approximation":[66,70,91],"worst-case":[69],"ratios":[71],"1/2":[73],"1/3":[75],"for":[76,93,103],"planar":[77,94,129],"structures,":[81],"respectively.":[82],"For":[83],"an":[84],"sequence":[86],"n":[88],"bases,":[89],"algorithm":[92],"runs":[97,107],"in":[98,108,127,135],"O(n(3))":[99],"time":[100],"case":[106],"linear":[109],"time.":[110],"Furthermore,":[111],"prove":[113],"it":[118],"NP-hard":[119,140],"to":[120],"maximize":[121],"structure.":[131],"This":[132],"result":[133],"contrast":[136],"recent":[139],"results":[141],"on":[142,147],"psuedoknots":[143],"which":[144],"based":[146],"optimizing":[148],"some":[149],"complicated":[152],"energy":[153],"functions.":[154]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":4},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":3}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}