{"id":"https://openalex.org/W2121983950","doi":"https://doi.org/10.1109/cibcb.2011.5948452","title":"Tackling the challenging motif problem through hybrid particle swarm optimized alignment clustering","display_name":"Tackling the challenging motif problem through hybrid particle swarm optimized alignment clustering","publication_year":2011,"publication_date":"2011-04-01","ids":{"openalex":"https://openalex.org/W2121983950","doi":"https://doi.org/10.1109/cibcb.2011.5948452","mag":"2121983950"},"language":"en","primary_location":{"id":"doi:10.1109/cibcb.2011.5948452","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2011.5948452","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2011 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)","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/A5111152604","display_name":"Chengpeng Bi","orcid":null},"institutions":[{"id":"https://openalex.org/I1328594524","display_name":"Children's Mercy Hospital","ror":"https://ror.org/04zfmcq84","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1328594524"]},{"id":"https://openalex.org/I75421653","display_name":"University of Missouri\u2013Kansas City","ror":"https://ror.org/01w0d5g70","country_code":"US","type":"education","lineage":["https://openalex.org/I75421653"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chengpeng Bi","raw_affiliation_strings":["Division of Clinical Pharmacology, Childrens Mercy Hospitals and Clinics, School of Medicine, School of Computing, University of Missouri, Kansas City, MO, USA","Division of Clinical Pharmacology, Children's Mercy Hospitals and Clinics, School of Medicine, School of Computing, University of Missouri, Kansas City, 64108 USA"],"affiliations":[{"raw_affiliation_string":"Division of Clinical Pharmacology, Childrens Mercy Hospitals and Clinics, School of Medicine, School of Computing, University of Missouri, Kansas City, MO, USA","institution_ids":["https://openalex.org/I1328594524","https://openalex.org/I75421653"]},{"raw_affiliation_string":"Division of Clinical Pharmacology, Children's Mercy Hospitals and Clinics, School of Medicine, School of Computing, University of Missouri, Kansas City, 64108 USA","institution_ids":["https://openalex.org/I75421653"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5111152604"],"corresponding_institution_ids":["https://openalex.org/I1328594524","https://openalex.org/I75421653"],"apc_list":null,"apc_paid":null,"fwci":0.1303,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.53088046,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9980000257492065,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9980000257492065,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.980400025844574,"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":0.9776999950408936,"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/cluster-analysis","display_name":"Cluster analysis","score":0.7552216649055481},{"id":"https://openalex.org/keywords/particle-swarm-optimization","display_name":"Particle swarm optimization","score":0.7543504238128662},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.7014784812927246},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6157051920890808},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5486168265342712},{"id":"https://openalex.org/keywords/gibbs-sampling","display_name":"Gibbs sampling","score":0.4617471992969513},{"id":"https://openalex.org/keywords/swarm-behaviour","display_name":"Swarm behaviour","score":0.41093724966049194},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.37504372000694275},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3572705388069153},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.28857773542404175}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.7552216649055481},{"id":"https://openalex.org/C85617194","wikidata":"https://www.wikidata.org/wiki/Q2072794","display_name":"Particle swarm optimization","level":2,"score":0.7543504238128662},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.7014784812927246},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6157051920890808},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5486168265342712},{"id":"https://openalex.org/C158424031","wikidata":"https://www.wikidata.org/wiki/Q1191905","display_name":"Gibbs sampling","level":3,"score":0.4617471992969513},{"id":"https://openalex.org/C181335050","wikidata":"https://www.wikidata.org/wiki/Q14915018","display_name":"Swarm behaviour","level":2,"score":0.41093724966049194},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.37504372000694275},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3572705388069153},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.28857773542404175},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cibcb.2011.5948452","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2011.5948452","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2011 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W1486659038","https://openalex.org/W1486759576","https://openalex.org/W1498410508","https://openalex.org/W1580213736","https://openalex.org/W1592870802","https://openalex.org/W1970525478","https://openalex.org/W1991248646","https://openalex.org/W1991293339","https://openalex.org/W1998300401","https://openalex.org/W2002638840","https://openalex.org/W2015416439","https://openalex.org/W2017746806","https://openalex.org/W2022116091","https://openalex.org/W2028904582","https://openalex.org/W2029722028","https://openalex.org/W2048869777","https://openalex.org/W2059054592","https://openalex.org/W2059699217","https://openalex.org/W2063447456","https://openalex.org/W2076749179","https://openalex.org/W2080286449","https://openalex.org/W2103903744","https://openalex.org/W2104865962","https://openalex.org/W2114454601","https://openalex.org/W2123734457","https://openalex.org/W2129795133","https://openalex.org/W2136534018","https://openalex.org/W2145234224","https://openalex.org/W2149769193","https://openalex.org/W2152195021","https://openalex.org/W2163133632","https://openalex.org/W2171111703","https://openalex.org/W2402846924","https://openalex.org/W2543580944","https://openalex.org/W6628970866","https://openalex.org/W6629008406","https://openalex.org/W6634719314","https://openalex.org/W6635200387","https://openalex.org/W6677231972","https://openalex.org/W6679880933","https://openalex.org/W6681739218"],"related_works":["https://openalex.org/W3170299350","https://openalex.org/W2368410102","https://openalex.org/W4288714711","https://openalex.org/W2368037387","https://openalex.org/W3200708550","https://openalex.org/W2736680465","https://openalex.org/W2771637876","https://openalex.org/W190186656","https://openalex.org/W2902352756","https://openalex.org/W2377079823"],"abstract_inverted_index":{"Previous":[0],"studies":[1],"show":[2,127],"that":[3,128],"Gibbs":[4,26,60],"sampling":[5],"methods":[6],"and":[7,75,118,124,139],"the":[8,14,39,120,129,146],"like":[9],"desperately":[10],"failed":[11],"to":[12,37,97,109,144,161],"solve":[13,38,145],"challenging":[15,40,147],"motif":[16,33,41,64,91,113,148],"problem.":[17],"This":[18],"paper":[19],"proposes":[20],"a":[21,46,58,69,80,86,100],"new":[22,130,154],"hybrid":[23,105,131,155],"algorithm,":[24],"integrated":[25],"with":[27,90,150],"particle":[28],"swarm":[29],"optimization":[30],"(PSO)":[31],"based":[32],"alignment":[34,92],"clustering":[35,93,119],"(PSO-MAC),":[36],"problem":[42,149],"by":[43,115],"iteratively":[44],"refining":[45,117],"population":[47,81,101],"of":[48,82,102],"potential":[49,83],"solutions.":[50,103],"The":[51,104,153],"PSO-MAC":[52,106],"algorithm":[53,107,132,156],"is":[54,71,95,142,157],"closely":[55],"incorporated":[56],"into":[57],"variant":[59],"called":[61],"pseudo-Gibbs":[62],"(pGibbs)":[63],"sampler.":[65],"Notably,":[66],"pGibbs":[67],"as":[68],"forerunner":[70],"executed":[72],"multiple":[73],"times":[74],"hence":[76],"it":[77,141],"brings":[78],"about":[79],"alignments.":[84],"Then,":[85],"PSO":[87],"procedure":[88],"coupled":[89],"(MAC)":[94],"developed":[96],"fine-tune":[98],"such":[99],"aims":[108],"glean":[110],"high":[111,151],"quality":[112],"solutions":[114],"cyclically":[116],"solution":[121],"pool.":[122],"Simulation":[123],"experimental":[125],"results":[126],"performs":[133],"markedly":[134],"better":[135],"than":[136],"others":[137],"tested,":[138],"surprisingly":[140],"able":[143],"precision.":[152],"also":[158],"successfully":[159],"applied":[160],"large-scale":[162],"ChIP-Seq":[163],"data":[164],"sets.":[165]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
