{"id":"https://openalex.org/W2002586473","doi":"https://doi.org/10.1142/s0219720005001508","title":"RANDOMIZED ALGORITHMS FOR MOTIF DETECTION","display_name":"RANDOMIZED ALGORITHMS FOR MOTIF DETECTION","publication_year":2005,"publication_date":"2005-10-01","ids":{"openalex":"https://openalex.org/W2002586473","doi":"https://doi.org/10.1142/s0219720005001508","mag":"2002586473","pmid":"https://pubmed.ncbi.nlm.nih.gov/16278946"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720005001508","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720005001508","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5065315257","display_name":"Lusheng Wang","orcid":"https://orcid.org/0000-0002-4344-8791"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"LUSHENG WANG","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, P. R. China","Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, P.R. China#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, P. R. China","institution_ids":["https://openalex.org/I168719708"]},{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, P.R. China#TAB#","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"last","author":{"id":null,"display_name":"LIANG DONG","orcid":null},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"LIANG DONG","raw_affiliation_strings":["Department of Computer Science, Peking University, Beijing 100871, P. R. China","Department of Computer Science, Peking University, Beijing, 100871, P.R. China,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Peking University, Beijing 100871, P. R. China","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"Department of Computer Science, Peking University, Beijing, 100871, P.R. China,","institution_ids":["https://openalex.org/I20231570"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.5023,"has_fulltext":false,"cited_by_count":26,"citation_normalized_percentile":{"value":0.62258038,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"03","issue":"05","first_page":"1039","last_page":"1052"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.48019999265670776,"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":0.48019999265670776,"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/T12029","display_name":"DNA and Biological Computing","score":0.1331000030040741,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.055399999022483826,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.6047481894493103},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5998159646987915},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5770396590232849},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5515215992927551},{"id":"https://openalex.org/keywords/randomized-algorithm","display_name":"Randomized algorithm","score":0.4945802390575409}],"concepts":[{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.6047481894493103},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5998159646987915},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5770396590232849},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5515215992927551},{"id":"https://openalex.org/C128669082","wikidata":"https://www.wikidata.org/wiki/Q583461","display_name":"Randomized algorithm","level":2,"score":0.4945802390575409},{"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}],"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":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1142/s0219720005001508","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720005001508","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:16278946","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16278946","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":"Journal of bioinformatics and computational biology","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.407.9706","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.407.9706","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.cityu.edu.hk/~lwang/research/issac04.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W938539187","https://openalex.org/W2028904582","https://openalex.org/W2047386086","https://openalex.org/W2048869777","https://openalex.org/W2053743126","https://openalex.org/W2056002855","https://openalex.org/W2070310544","https://openalex.org/W2092006839","https://openalex.org/W2117168988","https://openalex.org/W2171614937"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W3170299350","https://openalex.org/W2368410102","https://openalex.org/W2368037387","https://openalex.org/W190186656","https://openalex.org/W2377079823","https://openalex.org/W2902352756","https://openalex.org/W2605676258","https://openalex.org/W2599962286","https://openalex.org/W2319582300"],"abstract_inverted_index":{"MOTIVATION:":[0],"Motif":[1],"detection":[2],"for":[3,51,78,155,186],"DNA":[4],"sequences":[5],"has":[6],"many":[7],"important":[8],"applications":[9],"in":[10,68],"biological":[11],"studies,":[12],"e.g.":[13],"locating":[14],"binding":[15],"sites":[16],"regulatory":[17],"signals,":[18],"designing":[19],"genetic":[20],"probes":[21],"etc.":[22],"In":[23],"this":[24],"paper,":[25],"we":[26],"propose":[27],"a":[28,41,48,66,115],"randomized":[29,49,63,122],"algorithm,":[30],"design":[31,47,101],"an":[32,102],"improved":[33,103,131],"EM":[34,104,110,132],"algorithm":[35,50,64,105,123,133],"and":[36,89,128,143,173],"combine":[37],"them":[38],"to":[39,124,134,149,191],"form":[40],"software":[42,116,154],"tool.":[43],"RESULTS:":[44],"(1)":[45],"We":[46,55,100,113,138],"consensus":[52],"pattern":[53,67,168,178],"problem.":[54],"can":[56,90],"show":[57,159],"that":[58,106,119,160],"with":[59,71,141],"high":[60],"probability,":[61],"our":[62,121],"finds":[65],"polynomial":[69],"time":[70],"cost":[72],"error":[73],"at":[74,188],"most":[75],"x":[76],"l":[77,82],"each":[79],"string,":[80],"where":[81],"is":[83,147,162,170,184],"the":[84,87,97,108,130,151,167,177],"length":[85,169,179],"of":[86],"motif":[88,156],"be":[91,150],"any":[92],"positive":[93],"number":[94],"given":[95],"by":[96],"user.":[98],"(2)":[99],"outperforms":[107,174],"original":[109],"algorithm.":[111],"(3)":[112],"develop":[114],"tool,":[117],"MotifDetector,":[118],"uses":[120,129],"find":[125],"good":[126],"seeds":[127],"do":[135],"local":[136],"search.":[137],"compare":[139],"MotifDetector":[140,161],"Buhler":[142],"Tompa's":[144],"PROJECTION":[145,165,175],"which":[146],"considered":[148],"best":[152],"known":[153],"detection.":[157],"Simulations":[158],"slower":[163],"than":[164],"when":[166,176],"relatively":[171],"small,":[172],"becomes":[180],"large.":[181],"AVAILABILITY:":[182],"It":[183],"available":[185],"free":[187],"http://www.cs.cityu.edu.hk/~lwang/software/motif/index.html,":[189],"subject":[190],"copyright":[192],"restrictions.":[193]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
