{"id":"https://openalex.org/W4223591415","doi":"https://doi.org/10.1093/bib/bbac121","title":"Multiobjective optimization-driven primer design mechanism: towards user-specified parameters of PCR primer","display_name":"Multiobjective optimization-driven primer design mechanism: towards user-specified parameters of PCR primer","publication_year":2022,"publication_date":"2022-03-17","ids":{"openalex":"https://openalex.org/W4223591415","doi":"https://doi.org/10.1093/bib/bbac121","pmid":"https://pubmed.ncbi.nlm.nih.gov/35397164"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac121","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac121","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5065832977","display_name":"Cheng\u2010Hong Yang","orcid":"https://orcid.org/0000-0002-2741-0072"},"institutions":[{"id":"https://openalex.org/I152743029","display_name":"Kaohsiung Medical University","ror":"https://ror.org/03gk81f96","country_code":"TW","type":"education","lineage":["https://openalex.org/I152743029"]},{"id":"https://openalex.org/I4387154394","display_name":"National Kaohsiung University of Science and Technology","ror":"https://ror.org/00hfj7g70","country_code":null,"type":"education","lineage":["https://openalex.org/I4387154394"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Cheng-Hong Yang","raw_affiliation_strings":["Department of Electronic Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, 80778, Taiwan","Ph. D. Program in Biomedical Engineering, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan","School of Dentistry, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan"],"affiliations":[{"raw_affiliation_string":"Department of Electronic Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, 80778, Taiwan","institution_ids":["https://openalex.org/I4387154394","https://openalex.org/I4387154394"]},{"raw_affiliation_string":"Ph. D. Program in Biomedical Engineering, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan","institution_ids":["https://openalex.org/I152743029"]},{"raw_affiliation_string":"School of Dentistry, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan","institution_ids":["https://openalex.org/I152743029"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014905668","display_name":"Yu\u2010Huei Cheng","orcid":"https://orcid.org/0000-0002-1468-6686"},"institutions":[{"id":"https://openalex.org/I126145234","display_name":"Chaoyang University of Technology","ror":"https://ror.org/04xwksx09","country_code":"TW","type":"education","lineage":["https://openalex.org/I126145234"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Yu-Huei Cheng","raw_affiliation_strings":["Department of Information and Communication Engineering, Chaoyang University of Technology, Taichung, 413310, Taiwan"],"affiliations":[{"raw_affiliation_string":"Department of Information and Communication Engineering, Chaoyang University of Technology, Taichung, 413310, Taiwan","institution_ids":["https://openalex.org/I126145234"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052675204","display_name":"Emirlyn Cheng Yang","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":"Emirlyn Cheng Yang","raw_affiliation_strings":["Department of Biochemistry, The University of Hong Kong, Pok Fu Lam, Hong Kong"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, The University of Hong Kong, Pok Fu Lam, Hong Kong","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034774683","display_name":"Li\u2010Yeh Chuang","orcid":"https://orcid.org/0000-0002-9817-5102"},"institutions":[{"id":"https://openalex.org/I98298690","display_name":"I-Shou University","ror":"https://ror.org/04d7e4m76","country_code":"TW","type":"education","lineage":["https://openalex.org/I98298690"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Li-Yeh Chuang","raw_affiliation_strings":["Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, 84001, Taiwan"],"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, 84001, Taiwan","institution_ids":["https://openalex.org/I98298690"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068361665","display_name":"Yu\u2010Da Lin","orcid":"https://orcid.org/0000-0001-5100-6072"},"institutions":[{"id":"https://openalex.org/I32078218","display_name":"National Penghu University of Science and Technology","ror":"https://ror.org/03fxxpd92","country_code":"TW","type":"education","lineage":["https://openalex.org/I32078218"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Yu-Da Lin","raw_affiliation_strings":["Department of Computer Science and Information Engineering, National Penghu University of Science and Technology, Penghu, 880011, Taiwan"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Engineering, National Penghu University of Science and Technology, Penghu, 880011, Taiwan","institution_ids":["https://openalex.org/I32078218"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5034774683","https://openalex.org/A5068361665"],"corresponding_institution_ids":["https://openalex.org/I32078218","https://openalex.org/I98298690"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.4289,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.57267253,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"23","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9995999932289124,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9995999932289124,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9948999881744385,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9883999824523926,"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/primer","display_name":"Primer (cosmetics)","score":0.8635326027870178},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6301607489585876},{"id":"https://openalex.org/keywords/particle-swarm-optimization","display_name":"Particle swarm optimization","score":0.5677254796028137},{"id":"https://openalex.org/keywords/fitness-function","display_name":"Fitness function","score":0.5078492760658264},{"id":"https://openalex.org/keywords/genetic-algorithm","display_name":"Genetic algorithm","score":0.45479467511177063},{"id":"https://openalex.org/keywords/constraint","display_name":"Constraint (computer-aided design)","score":0.42739975452423096},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.3783978521823883},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32155442237854004},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.24607130885124207},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2183871567249298}],"concepts":[{"id":"https://openalex.org/C2777563447","wikidata":"https://www.wikidata.org/wiki/Q7243397","display_name":"Primer (cosmetics)","level":2,"score":0.8635326027870178},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6301607489585876},{"id":"https://openalex.org/C85617194","wikidata":"https://www.wikidata.org/wiki/Q2072794","display_name":"Particle swarm optimization","level":2,"score":0.5677254796028137},{"id":"https://openalex.org/C176066374","wikidata":"https://www.wikidata.org/wiki/Q629118","display_name":"Fitness function","level":3,"score":0.5078492760658264},{"id":"https://openalex.org/C8880873","wikidata":"https://www.wikidata.org/wiki/Q187787","display_name":"Genetic algorithm","level":2,"score":0.45479467511177063},{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.42739975452423096},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.3783978521823883},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32155442237854004},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.24607130885124207},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2183871567249298},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac121","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac121","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35397164","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35397164","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2104059527","display_name":null,"funder_award_id":"108-2221-E-214-019-MY3","funder_id":"https://openalex.org/F4320325390","funder_display_name":"Ministry of Science and Technology, Government of the People\u2019s Republic of Bangladesh"},{"id":"https://openalex.org/G4248021448","display_name":null,"funder_award_id":"108-2221-E-992-031-MY3","funder_id":"https://openalex.org/F4320325390","funder_display_name":"Ministry of Science and Technology, Government of the People\u2019s Republic of Bangladesh"},{"id":"https://openalex.org/G869239069","display_name":null,"funder_award_id":"110-2222-E-346-002","funder_id":"https://openalex.org/F4320325390","funder_display_name":"Ministry of Science and Technology, Government of the People\u2019s Republic of Bangladesh"}],"funders":[{"id":"https://openalex.org/F4320325390","display_name":"Ministry of Science and Technology, Government of the People\u2019s Republic of Bangladesh","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W1499500424","https://openalex.org/W1915267438","https://openalex.org/W1983055623","https://openalex.org/W1991452997","https://openalex.org/W1991719135","https://openalex.org/W1997495012","https://openalex.org/W2032019813","https://openalex.org/W2033630480","https://openalex.org/W2055043387","https://openalex.org/W2071151181","https://openalex.org/W2078204597","https://openalex.org/W2087525580","https://openalex.org/W2120865268","https://openalex.org/W2125882871","https://openalex.org/W2138833955","https://openalex.org/W2140609744","https://openalex.org/W2140841059","https://openalex.org/W2143434226","https://openalex.org/W2148312059","https://openalex.org/W2162098634","https://openalex.org/W2169245194","https://openalex.org/W2214790705","https://openalex.org/W2296457500","https://openalex.org/W2323555810","https://openalex.org/W2505614110","https://openalex.org/W2543580944","https://openalex.org/W2600619218","https://openalex.org/W2789393753","https://openalex.org/W2793388751","https://openalex.org/W2801615337","https://openalex.org/W2893529647","https://openalex.org/W2895902242","https://openalex.org/W2944767271","https://openalex.org/W2980245990","https://openalex.org/W2989658305","https://openalex.org/W6629874611","https://openalex.org/W6640051865","https://openalex.org/W6682642761"],"related_works":["https://openalex.org/W2114356839","https://openalex.org/W3134384462","https://openalex.org/W2125094050","https://openalex.org/W2540137049","https://openalex.org/W2106492215","https://openalex.org/W2326694407","https://openalex.org/W2082859007","https://openalex.org/W2378719652","https://openalex.org/W2115729582","https://openalex.org/W2164831575"],"abstract_inverted_index":{"Primers":[0],"are":[1],"critical":[2],"for":[3,148],"polymerase":[4],"chain":[5],"reaction":[6],"(PCR)":[7],"and":[8,18,54,100,127,170],"influence":[9],"PCR":[10,30,168],"experimental":[11],"outcomes.":[12],"Designing":[13],"numerous":[14],"combinations":[15],"of":[16,76],"forward":[17],"reverse":[19],"primers":[20,176],"involves":[21],"various":[22],"primer":[23,31,60,77,89,105,128,150],"constraints,":[24],"posing":[25],"a":[26,59,103],"computational":[27],"challenge.":[28],"Most":[29],"design":[32,61,78,106],"methods":[33],"limit":[34],"parameters":[35,53,126,139],"because":[36],"the":[37,56,65,74,121,124,141,167],"available":[38],"algorithms":[39,132,142],"use":[40],"general":[41,145],"fitness":[42,48,92,135,146],"functions.":[43],"This":[44],"study":[45],"designed":[46],"new":[47],"functions":[49,57,93,136,147],"based":[50,63,87,108,133,143,177],"on":[51,64,88,109,134,144,178],"user-specified":[52,80,125,138,179],"used":[55],"in":[58,157],"approach":[62,107],"multiobjective":[66],"particle":[67],"swarm":[68],"optimization":[69,110],"(MOPSO)":[70],"algorithm":[71],"to":[72,119,165],"address":[73],"challenge":[75],"with":[79,102,137],"parameters.":[81,180],"Multicriteria":[82],"evaluation":[83],"was":[84,115,163],"conducted":[85,164],"simultaneously":[86],"constraints.":[90,151],"The":[91,131],"were":[94],"evaluated":[95],"using":[96],"7425":[97],"DNA":[98,113],"sequences":[99],"compared":[101],"predominant":[104],"algorithms.":[111],"Each":[112],"sequence":[114],"run":[116],"100":[117],"times":[118],"calculate":[120],"difference":[122],"between":[123],"constraint":[129],"values.":[130],"outperformed":[140],"11":[149],"Moreover,":[152],"MOPSO":[153,173],"exhibited":[154],"superior":[155],"implementation":[156],"all":[158],"experiments.":[159],"Practical":[160],"gel":[161],"electrophoresis":[162],"verify":[166],"experiments":[169],"established":[171],"that":[172],"effectively":[174],"designs":[175]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
