{"id":"https://openalex.org/W2143903417","doi":"https://doi.org/10.1145/2506583.2506626","title":"ChainKnot","display_name":"ChainKnot","publication_year":2013,"publication_date":"2013-09-22","ids":{"openalex":"https://openalex.org/W2143903417","doi":"https://doi.org/10.1145/2506583.2506626","mag":"2143903417"},"language":"en","primary_location":{"id":"doi:10.1145/2506583.2506626","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2506583.2506626","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5074646713","display_name":"Jikai Lei","orcid":"https://orcid.org/0000-0002-6081-2276"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jikai Lei","raw_affiliation_strings":["Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, U.S.A"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, U.S.A","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002806381","display_name":"Prapaporn Techa-Angkoon","orcid":null},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Prapaporn Techa-angkoon","raw_affiliation_strings":["Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, U.S.A"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, U.S.A","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081855118","display_name":"Yanni Sun","orcid":"https://orcid.org/0000-0003-1373-8023"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yanni Sun","raw_affiliation_strings":["Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, U.S.A"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, U.S.A","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049231974","display_name":"Rujira Achawanantakun","orcid":null},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rujira Achawanantakun","raw_affiliation_strings":["Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, U.S.A"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, U.S.A","institution_ids":["https://openalex.org/I87216513"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5074646713"],"corresponding_institution_ids":["https://openalex.org/I87216513"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.10500494,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"535","last_page":"544"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9997000098228455,"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":0.9975000023841858,"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":0.9804874062538147},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.599107027053833},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5990478992462158},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4561980366706848},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.45403429865837097},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.38614094257354736},{"id":"https://openalex.org/keywords/base-sequence","display_name":"Base sequence","score":0.1185421347618103},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11019644141197205},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07683184742927551}],"concepts":[{"id":"https://openalex.org/C105130999","wikidata":"https://www.wikidata.org/wiki/Q414976","display_name":"Pseudoknot","level":4,"score":0.9804874062538147},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.599107027053833},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5990478992462158},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4561980366706848},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.45403429865837097},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.38614094257354736},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.1185421347618103},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11019644141197205},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07683184742927551},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2506583.2506626","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2506583.2506626","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W938539187","https://openalex.org/W1542565836","https://openalex.org/W1950410402","https://openalex.org/W1967864248","https://openalex.org/W1984675364","https://openalex.org/W1990061958","https://openalex.org/W1994197834","https://openalex.org/W1996423252","https://openalex.org/W2007644443","https://openalex.org/W2060535707","https://openalex.org/W2074882547","https://openalex.org/W2076756368","https://openalex.org/W2086561953","https://openalex.org/W2099028333","https://openalex.org/W2102046276","https://openalex.org/W2104611815","https://openalex.org/W2105070391","https://openalex.org/W2106882534","https://openalex.org/W2115275409","https://openalex.org/W2121691652","https://openalex.org/W2124050695","https://openalex.org/W2127025444","https://openalex.org/W2134489577","https://openalex.org/W2138455866","https://openalex.org/W2141351700","https://openalex.org/W2153635508","https://openalex.org/W2156941119","https://openalex.org/W2163798335","https://openalex.org/W2168560548"],"related_works":["https://openalex.org/W2057901482","https://openalex.org/W2018280025","https://openalex.org/W1998399688","https://openalex.org/W2022565929","https://openalex.org/W2054306371","https://openalex.org/W2088188302","https://openalex.org/W2017993626","https://openalex.org/W2981287558","https://openalex.org/W2007550449","https://openalex.org/W2523675295"],"abstract_inverted_index":{"Pseudoknot":[0],"is":[1,17,149],"an":[2,36,62],"important":[3],"structural":[4,76],"motif":[5],"in":[6],"many":[7],"types":[8],"of":[9,14,84,98,108,116,147],"ncRNAs.":[10],"However,":[11],"the":[12,56,79,106,114,117,135],"accuracy":[13],"pseudoknot":[15,88,137],"derivation":[16,59],"still":[18],"not":[19],"satisfactory":[20],"even":[21],"for":[22,40],"simple":[23],"pseudoknotted":[24],"structures":[25,43],"and":[26,34,81,132],"short":[27],"sequences.":[28,53],"In":[29,67],"this":[30],"work,":[31],"we":[32],"design":[33],"implement":[35],"effective":[37],"pipeline,":[38],"ChainKnot,":[39],"deriving":[41],"secondary":[42],"containing":[44],"recursive":[45,141],"H-type":[46,142],"pseudoknots":[47],"from":[48,78,105],"two":[49],"or":[50],"multiple":[51,85],"ncRNA":[52],"ChainKnot":[54,69,148],"solves":[55],"consensus":[57],"structure":[58],"problem":[60],"using":[61,122],"extended":[63],"maximum-weighted":[64],"chain":[65],"algorithm.":[66],"addition,":[68],"tests":[70],"a":[71],"new":[72],"strategy":[73],"that":[74,102],"extracts":[75],"elements":[77],"optimal":[80],"sub-optimal":[82],"predictions":[83],"ab":[86,109],"initio":[87,110],"prediction":[89,118,138],"tools.":[90],"The":[91,144],"experimental":[92],"results":[93],"on":[94,140],"over":[95],"five":[96],"hundreds":[97],"pseudoknot-containing":[99],"ncRNAs":[100],"demonstrate":[101],"extracting":[103],"stems":[104],"output":[107],"tools":[111,139],"significantly":[112],"increases":[113],"performance":[115],"pipeline":[119],"compared":[120],"to":[121],"base-pairing":[123],"probability":[124],"matrices.":[125],"Our":[126],"approach":[127],"achieves":[128],"better":[129],"sensitivity,":[130],"PPV,":[131],"F-score":[133],"than":[134],"state-of-the-art":[136],"pseudoknots.":[143],"source":[145],"code":[146],"available":[150],"at":[151],"http://sourceforge.net/projects/chainknot":[152]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2016-06-24T00:00:00"}
