{"id":"https://openalex.org/W1976996978","doi":"https://doi.org/10.1108/17563781111136685","title":"Particle swarm optimization for finding RNA secondary structures","display_name":"Particle swarm optimization for finding RNA secondary structures","publication_year":2011,"publication_date":"2011-06-07","ids":{"openalex":"https://openalex.org/W1976996978","doi":"https://doi.org/10.1108/17563781111136685","mag":"1976996978"},"language":"en","primary_location":{"id":"doi:10.1108/17563781111136685","is_oa":false,"landing_page_url":"https://doi.org/10.1108/17563781111136685","pdf_url":null,"source":{"id":"https://openalex.org/S124503262","display_name":"International Journal of Intelligent Computing and Cybernetics","issn_l":"1756-378X","issn":["1756-378X","1756-3798"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319811","host_organization_name":"Emerald Publishing Limited","host_organization_lineage":["https://openalex.org/P4310319811"],"host_organization_lineage_names":["Emerald Publishing Limited"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Intelligent Computing and Cybernetics","raw_type":"journal-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/A5080590604","display_name":"Michael L. Geis","orcid":null},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Michael Geis","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016253883","display_name":"Martin Middendorf","orcid":"https://orcid.org/0000-0002-5426-1092"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Martin Middendorf","raw_affiliation_strings":["Parallel Computing and Complex Systems Group, Department of Computer Science, University of Leipzig, Leipzig, Germany","#N##TAB##TAB##TAB##TAB# Leipzig University#N##TAB##TAB##TAB#"],"affiliations":[{"raw_affiliation_string":"Parallel Computing and Complex Systems Group, Department of Computer Science, University of Leipzig, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]},{"raw_affiliation_string":"#N##TAB##TAB##TAB##TAB# Leipzig University#N##TAB##TAB##TAB#","institution_ids":["https://openalex.org/I926574661"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5080590604"],"corresponding_institution_ids":["https://openalex.org/I926574661"],"apc_list":null,"apc_paid":null,"fwci":0.452,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.62906556,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"4","issue":"2","first_page":"160","last_page":"186"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998000264167786,"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":0.9998000264167786,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.989300012588501,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9598000049591064,"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/rna","display_name":"RNA","score":0.654451847076416},{"id":"https://openalex.org/keywords/particle-swarm-optimization","display_name":"Particle swarm optimization","score":0.6114603281021118},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5940927863121033},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.5674647688865662},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.542956531047821},{"id":"https://openalex.org/keywords/centroid","display_name":"Centroid","score":0.4665355980396271},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15148398280143738},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09648570418357849},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.06997200846672058}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.654451847076416},{"id":"https://openalex.org/C85617194","wikidata":"https://www.wikidata.org/wiki/Q2072794","display_name":"Particle swarm optimization","level":2,"score":0.6114603281021118},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5940927863121033},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.5674647688865662},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.542956531047821},{"id":"https://openalex.org/C146599234","wikidata":"https://www.wikidata.org/wiki/Q511093","display_name":"Centroid","level":2,"score":0.4665355980396271},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15148398280143738},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09648570418357849},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06997200846672058},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1108/17563781111136685","is_oa":false,"landing_page_url":"https://doi.org/10.1108/17563781111136685","pdf_url":null,"source":{"id":"https://openalex.org/S124503262","display_name":"International Journal of Intelligent Computing and Cybernetics","issn_l":"1756-378X","issn":["1756-378X","1756-3798"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319811","host_organization_name":"Emerald Publishing Limited","host_organization_lineage":["https://openalex.org/P4310319811"],"host_organization_lineage_names":["Emerald Publishing Limited"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Intelligent Computing and Cybernetics","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.6700000166893005}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":55,"referenced_works":["https://openalex.org/W17748033","https://openalex.org/W68587524","https://openalex.org/W99032621","https://openalex.org/W113288072","https://openalex.org/W141039805","https://openalex.org/W149500278","https://openalex.org/W1516301787","https://openalex.org/W1538689496","https://openalex.org/W1541914161","https://openalex.org/W1543796220","https://openalex.org/W1574643310","https://openalex.org/W1576426930","https://openalex.org/W1859892029","https://openalex.org/W1971443922","https://openalex.org/W1971883398","https://openalex.org/W1989296116","https://openalex.org/W1990411923","https://openalex.org/W2003956388","https://openalex.org/W2007799540","https://openalex.org/W2009265617","https://openalex.org/W2009818318","https://openalex.org/W2010352098","https://openalex.org/W2024734101","https://openalex.org/W2030640142","https://openalex.org/W2040015982","https://openalex.org/W2044595289","https://openalex.org/W2048796447","https://openalex.org/W2051713039","https://openalex.org/W2061158331","https://openalex.org/W2075702353","https://openalex.org/W2091735434","https://openalex.org/W2098818780","https://openalex.org/W2102528857","https://openalex.org/W2102934142","https://openalex.org/W2118684341","https://openalex.org/W2121492055","https://openalex.org/W2122534713","https://openalex.org/W2131281445","https://openalex.org/W2137677829","https://openalex.org/W2139138332","https://openalex.org/W2141157874","https://openalex.org/W2142056356","https://openalex.org/W2147416962","https://openalex.org/W2150174329","https://openalex.org/W2152195021","https://openalex.org/W2158746132","https://openalex.org/W2164618041","https://openalex.org/W2164943294","https://openalex.org/W2976664243","https://openalex.org/W3041019241","https://openalex.org/W3175596131","https://openalex.org/W4237234846","https://openalex.org/W4255486187","https://openalex.org/W4285719527","https://openalex.org/W6600210833"],"related_works":["https://openalex.org/W2381926679","https://openalex.org/W2007009951","https://openalex.org/W2082644203","https://openalex.org/W2350539780","https://openalex.org/W3165040664","https://openalex.org/W2051487156","https://openalex.org/W4242386713","https://openalex.org/W3122652148","https://openalex.org/W1583866266","https://openalex.org/W2996505764"],"abstract_inverted_index":{"Purpose":[0],"The":[1,177],"purpose":[2],"of":[3,40,59,68,104,157],"this":[4],"paper":[5],"is":[6,62,74,89,127,132,160,212],"to":[7,33,46,124,171],"present":[8],"a":[9,27,56,66,80,208,215],"new":[10,178],"particle":[11],"swarm":[12,217],"optimization":[13],"(PSO)":[14],"algorithm":[15,180,196],"called":[16],"HelixPSO":[17,41,61,78,118,135,158,181,198],"for":[18,99,169,182],"finding":[19,183],"ribonucleic":[20],"acid":[21],"(RNA)":[22],"secondary":[23,185],"structures":[24,186],"that":[25,77,134,162],"have":[26],"low":[28],"energy":[29],"and":[30,44,53,86,88,94,111,126,138,211],"are":[31,42,116],"similar":[32,123],"the":[34,47,60,142,150,154,192,205],"native":[35],"structure.":[36],"Design/methodology/approach":[37],"Two":[38],"variants":[39],"described":[43],"compared":[45],"recent":[48],"algorithms":[49,143],"Rna\u2010Predict,":[50],"SARNA\u2010Predict,":[51],"SetPSO":[52,87],"RNAfold.":[54,95],"Furthermore,":[55],"parallel":[57,155],"version":[58,156],"proposed.":[63],"Findings":[64],"For":[65,153],"set":[67],"standard":[69],"RNA":[70,184],"test":[71],"sequences":[72],"it":[73,159],"shown":[75,133,161],"experimentally":[76],"obtains":[79],"better":[81,120],"average":[82],"sensitivity":[83],"than":[84,121,191],"SARNA\u2010Predict":[85,139],"as":[90,92,202,204,207],"good":[91,163],"RNA\u2010Predict":[93,137],"When":[96],"best":[97],"values":[98,165],"different":[100,147,188],"measures":[101],"(e.g.":[102],"number":[103],"correctly":[105],"predicted":[106],"base":[107],"pairs,":[108],"false":[109],"positives":[110],"sensitivity)":[112],"over":[113],"several":[114],"runs":[115],"compared,":[117],"performs":[119],"RNAfold,":[122],"RNA\u2010Predict,":[125],"outperformed":[128],"by":[129],"SARNA\u2010Predict.":[130],"It":[131],"complements":[136],"well":[140,203],"since":[141],"show":[144],"often":[145],"very":[146],"behavior":[148],"on":[149,214],"same":[151],"sequence.":[152],"speedup":[164],"can":[166],"be":[167],"obtained":[168],"small":[170],"medium":[172],"size":[173],"PC":[174],"clusters.":[175],"Originality/value":[176],"PSO":[179,195],"uses":[187,199],"algorithmic":[189],"ideas":[190],"other":[193],"existing":[194],"SetPSO.":[197],"thermodynamic":[200],"information":[201],"centroid":[206],"reference":[209],"structure":[210],"based":[213],"multiple":[216],"approach.":[218]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2013,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
