{"id":"https://openalex.org/W2145234224","doi":"https://doi.org/10.1109/cibcb.2007.4221233","title":"A Genetic-Based EM Motif-Finding Algorithm for Biological Sequence Analysis","display_name":"A Genetic-Based EM Motif-Finding Algorithm for Biological Sequence Analysis","publication_year":2007,"publication_date":"2007-04-01","ids":{"openalex":"https://openalex.org/W2145234224","doi":"https://doi.org/10.1109/cibcb.2007.4221233","mag":"2145234224"},"language":"en","primary_location":{"id":"doi:10.1109/cibcb.2007.4221233","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2007.4221233","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology","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/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]},{"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":["Children's Mercy Hospitals and Clinics Schools of Medicine Computing and Engineering, University of Missouri, Kansas City, MO, USA","Schools of Medicine, Comput. & Eng., Missouri Univ., Kansas City, MO"],"affiliations":[{"raw_affiliation_string":"Children's Mercy Hospitals and Clinics Schools of Medicine Computing and Engineering, University of Missouri, Kansas City, MO, USA","institution_ids":["https://openalex.org/I1328594524","https://openalex.org/I75421653"]},{"raw_affiliation_string":"Schools of Medicine, Comput. & Eng., Missouri Univ., Kansas City, MO","institution_ids":["https://openalex.org/I76835614"]}]}],"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","https://openalex.org/I76835614"],"apc_list":null,"apc_paid":null,"fwci":1.3389,"has_fulltext":false,"cited_by_count":19,"citation_normalized_percentile":{"value":0.79934609,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"275","last_page":"282"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9990000128746033,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9990000128746033,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9970999956130981,"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":0.9958000183105469,"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/motif","display_name":"Motif (music)","score":0.7811186909675598},{"id":"https://openalex.org/keywords/initialization","display_name":"Initialization","score":0.7391288876533508},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.60709547996521},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5670101046562195},{"id":"https://openalex.org/keywords/fitness-function","display_name":"Fitness function","score":0.45180901885032654},{"id":"https://openalex.org/keywords/expectation\u2013maximization-algorithm","display_name":"Expectation\u2013maximization algorithm","score":0.43509384989738464},{"id":"https://openalex.org/keywords/maximization","display_name":"Maximization","score":0.4180399477481842},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.41729307174682617},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.41370728611946106},{"id":"https://openalex.org/keywords/genetic-algorithm","display_name":"Genetic algorithm","score":0.4064229428768158},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24468979239463806},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.23172423243522644},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.1859307587146759},{"id":"https://openalex.org/keywords/maximum-likelihood","display_name":"Maximum likelihood","score":0.1700151562690735},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.16066905856132507},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15364030003547668},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1369883418083191}],"concepts":[{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.7811186909675598},{"id":"https://openalex.org/C114466953","wikidata":"https://www.wikidata.org/wiki/Q6034165","display_name":"Initialization","level":2,"score":0.7391288876533508},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.60709547996521},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5670101046562195},{"id":"https://openalex.org/C176066374","wikidata":"https://www.wikidata.org/wiki/Q629118","display_name":"Fitness function","level":3,"score":0.45180901885032654},{"id":"https://openalex.org/C182081679","wikidata":"https://www.wikidata.org/wiki/Q1275153","display_name":"Expectation\u2013maximization algorithm","level":3,"score":0.43509384989738464},{"id":"https://openalex.org/C2776330181","wikidata":"https://www.wikidata.org/wiki/Q18358244","display_name":"Maximization","level":2,"score":0.4180399477481842},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.41729307174682617},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.41370728611946106},{"id":"https://openalex.org/C8880873","wikidata":"https://www.wikidata.org/wiki/Q187787","display_name":"Genetic algorithm","level":2,"score":0.4064229428768158},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24468979239463806},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.23172423243522644},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.1859307587146759},{"id":"https://openalex.org/C49781872","wikidata":"https://www.wikidata.org/wiki/Q1045555","display_name":"Maximum likelihood","level":2,"score":0.1700151562690735},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.16066905856132507},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15364030003547668},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1369883418083191},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cibcb.2007.4221233","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2007.4221233","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology","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":26,"referenced_works":["https://openalex.org/W1498410508","https://openalex.org/W1580213736","https://openalex.org/W1592870802","https://openalex.org/W1970525478","https://openalex.org/W1998300401","https://openalex.org/W2041397659","https://openalex.org/W2041877620","https://openalex.org/W2048869777","https://openalex.org/W2050341350","https://openalex.org/W2050802973","https://openalex.org/W2053742104","https://openalex.org/W2056002855","https://openalex.org/W2059579283","https://openalex.org/W2073850887","https://openalex.org/W2097571405","https://openalex.org/W2102941368","https://openalex.org/W2109619915","https://openalex.org/W2112444654","https://openalex.org/W2121298930","https://openalex.org/W2124369546","https://openalex.org/W2135729552","https://openalex.org/W2141408320","https://openalex.org/W2151638714","https://openalex.org/W2157076973","https://openalex.org/W2158266834","https://openalex.org/W2159831212"],"related_works":["https://openalex.org/W2368486525","https://openalex.org/W2041758614","https://openalex.org/W2025031893","https://openalex.org/W2361119249","https://openalex.org/W104157611","https://openalex.org/W2010454570","https://openalex.org/W2124815120","https://openalex.org/W2060868730","https://openalex.org/W2145234224","https://openalex.org/W2074530889"],"abstract_inverted_index":{"Motif-finding":[0],"in":[1,8,47,61,81,113,171],"biological":[2,154],"sequence":[3,155,175],"analysis":[4,156],"remains":[5],"a":[6,69,89,101,105],"challenge":[7],"computational":[9],"biology.":[10],"Many":[11],"algorithms":[12,50,180],"and":[13,56,67,152,177],"software":[14],"packages":[15],"have":[16],"been":[17],"developed":[18],"to":[19,76],"address":[20],"the":[21,35,78,114,124,141,146,163,172],"problem.":[22],"The":[23,133],"expectation":[24],"maximization":[25],"(EM)-type":[26],"motif":[27,40,83,147,174],"algorithm":[28,73,135,169],"such":[29],"as":[30,44,123,181],"MEME":[31],"is":[32,98,128,149],"one":[33],"of":[34,91,96,166],"most":[36],"popular":[37],"de":[38],"novo":[39],"discovery":[41,84],"methods.":[42],"However,":[43],"pointed":[45],"out":[46],"literature,":[48],"EM":[49,71,82,167],"largely":[51],"depend":[52],"on":[53,100],"their":[54],"initialization":[55],"can":[57],"be":[58],"easily":[59],"trapped":[60],"local":[62,93],"optima.":[63],"This":[64],"paper":[65],"proposes":[66],"implements":[68],"genetic-based":[70],"motif-finding":[72,168],"(GEMFA)":[74],"aiming":[75],"overcome":[77],"drawbacks":[79],"inherent":[80],"algorithms.":[85],"It":[86],"first":[87],"initializes":[88],"population":[90,139],"multiple":[92],"alignments":[94],"each":[95],"which":[97,127,145],"encoded":[99],"chromosome":[102],"that":[103,158],"represents":[104],"potential":[106],"solution.":[107],"GEMFA":[108,159],"then":[109],"performs":[110],"heuristic":[111],"search":[112],"whole":[115],"alignment":[116,143,176],"space":[117],"using":[118],"minimum":[119],"distance":[120],"length":[121],"(MDL)":[122],"fitness":[125],"function":[126],"generalized":[129],"from":[130,144],"maximum":[131],"log-likelihood.":[132],"genetic":[134],"gradually":[136],"moves":[137],"this":[138],"towards":[140],"best":[142],"model":[148],"derived.":[150],"Simulated":[151],"real":[153],"showed":[157],"performed":[160],"better":[161],"than":[162],"simple":[164],"multiple-restart":[165],"especially":[170],"subtle":[173],"other":[178],"similar":[179],"well":[182]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-03-18T14:38:29.013473","created_date":"2025-10-10T00:00:00"}