{"id":"https://openalex.org/W1936745395","doi":"https://doi.org/10.1109/cec.2004.1331093","title":"A computational approach to detect regulatory elements in Dictyostelium discoideum","display_name":"A computational approach to detect regulatory elements in Dictyostelium discoideum","publication_year":2005,"publication_date":"2005-01-17","ids":{"openalex":"https://openalex.org/W1936745395","doi":"https://doi.org/10.1109/cec.2004.1331093","mag":"1936745395"},"language":"en","primary_location":{"id":"doi:10.1109/cec.2004.1331093","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cec.2004.1331093","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2004 Congress on Evolutionary Computation (IEEE Cat. No.04TH8753)","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/A5026855776","display_name":"Daekwan Seo","orcid":"https://orcid.org/0000-0002-8628-6120"},"institutions":[{"id":"https://openalex.org/I102401767","display_name":"University of Arkansas at Little Rock","ror":"https://ror.org/04fttyv97","country_code":"US","type":"education","lineage":["https://openalex.org/I102401767"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Daekwan Seo","raw_affiliation_strings":["Applied Science Department, University of Arkansas, Little Rock, Little Rock, AR, USA"],"affiliations":[{"raw_affiliation_string":"Applied Science Department, University of Arkansas, Little Rock, Little Rock, AR, USA","institution_ids":["https://openalex.org/I102401767"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051774299","display_name":"Masahiro Yasunaga","orcid":"https://orcid.org/0000-0003-3356-0197"},"institutions":[{"id":"https://openalex.org/I146399215","display_name":"University of Tsukuba","ror":"https://ror.org/02956yf07","country_code":"JP","type":"education","lineage":["https://openalex.org/I146399215"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"M. Yasunaga","raw_affiliation_strings":["Institute of Information Sciences and Electronics, University of Tsukuba, Tsukuba, Japan"],"affiliations":[{"raw_affiliation_string":"Institute of Information Sciences and Electronics, University of Tsukuba, Tsukuba, Japan","institution_ids":["https://openalex.org/I146399215"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100360483","display_name":"Jung Hwan Kim","orcid":"https://orcid.org/0000-0001-8548-4435"},"institutions":[{"id":"https://openalex.org/I102401767","display_name":"University of Arkansas at Little Rock","ror":"https://ror.org/04fttyv97","country_code":"US","type":"education","lineage":["https://openalex.org/I102401767"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jung Hwan Kim","raw_affiliation_strings":["Systems Engineering Department, University of Arkansas, Little Rock, Little Rock, AR, USA"],"affiliations":[{"raw_affiliation_string":"Systems Engineering Department, University of Arkansas, Little Rock, Little Rock, AR, USA","institution_ids":["https://openalex.org/I102401767"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5026855776"],"corresponding_institution_ids":["https://openalex.org/I102401767"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0664083,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"1994","issue":null,"first_page":"1647","last_page":"1653"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10379","display_name":"Cellular Mechanics and Interactions","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/T10379","display_name":"Cellular Mechanics and Interactions","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9944999814033508,"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/dictyostelium-discoideum","display_name":"Dictyostelium discoideum","score":0.7095471024513245},{"id":"https://openalex.org/keywords/dictyostelium","display_name":"Dictyostelium","score":0.5377472043037415},{"id":"https://openalex.org/keywords/class","display_name":"Class (philosophy)","score":0.5302619338035583},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.525137186050415},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5236108899116516},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4956015348434448},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.48184406757354736},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.47843435406684875},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.4306229054927826},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.34918463230133057},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.26812565326690674},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23752444982528687},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.07966729998588562}],"concepts":[{"id":"https://openalex.org/C2775969001","wikidata":"https://www.wikidata.org/wiki/Q134351","display_name":"Dictyostelium discoideum","level":3,"score":0.7095471024513245},{"id":"https://openalex.org/C2775889303","wikidata":"https://www.wikidata.org/wiki/Q17146891","display_name":"Dictyostelium","level":3,"score":0.5377472043037415},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.5302619338035583},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.525137186050415},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5236108899116516},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4956015348434448},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48184406757354736},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.47843435406684875},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.4306229054927826},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.34918463230133057},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.26812565326690674},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23752444982528687},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.07966729998588562}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cec.2004.1331093","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cec.2004.1331093","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2004 Congress on Evolutionary Computation (IEEE Cat. No.04TH8753)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W178414959","https://openalex.org/W1489860517","https://openalex.org/W1956090332","https://openalex.org/W1968233665","https://openalex.org/W2003967338","https://openalex.org/W2021282293","https://openalex.org/W2037307974","https://openalex.org/W2046484221","https://openalex.org/W2047007462","https://openalex.org/W2051151530","https://openalex.org/W2058511877","https://openalex.org/W2102122585","https://openalex.org/W2104992468","https://openalex.org/W2108774839","https://openalex.org/W2132536544","https://openalex.org/W2142446963","https://openalex.org/W2144242878","https://openalex.org/W2152893838","https://openalex.org/W2162828041","https://openalex.org/W2169351355","https://openalex.org/W2610179052","https://openalex.org/W3189823449","https://openalex.org/W4252019831","https://openalex.org/W4292024674","https://openalex.org/W6624626827","https://openalex.org/W6629198963","https://openalex.org/W6641001594","https://openalex.org/W6676214501","https://openalex.org/W6679876871","https://openalex.org/W7029391333"],"related_works":["https://openalex.org/W2034720620","https://openalex.org/W3015698348","https://openalex.org/W2519058576","https://openalex.org/W3209588668","https://openalex.org/W2015897732","https://openalex.org/W2399065385","https://openalex.org/W2066066606","https://openalex.org/W1825029112","https://openalex.org/W2394887779","https://openalex.org/W4206010648"],"abstract_inverted_index":{"Finding":[0],"transcription":[1],"regulatory":[2,24],"elements":[3],"(TREs)":[4],"is":[5,18,34],"one":[6],"of":[7,26,31,43,63,85,100,165],"most":[8],"important":[9],"tasks":[10],"in":[11,47,95,110,115,118,122,143,149,155,161],"current":[12],"bioinformatics":[13],"and":[14,17,120,141,147,153,159],"functional":[15],"genomics":[16],"the":[19,71,81,104],"first":[20],"step":[21],"to":[22,35,59,103,130],"discover":[23],"mechanisms":[25],"gene":[27],"expression.":[28],"The":[29],"goal":[30],"this":[32],"paper":[33],"detect":[36],"class-specific":[37,90,126],"TREs":[38,91,94],"associated":[39],"with":[40,51,65,107,179],"four":[41],"classes":[42],"developmentally":[44,97],"regulated":[45,98],"genes":[46],"Dictyostelium":[48],"discoideum":[49],"(Dd)":[50],"statistically":[52],"significant":[53],"measure.":[54],"Applying":[55],"a":[56,131],"DP":[57],"matching":[58],"5'":[60],"UTR":[61],"sequences":[62,109],"Dd":[64],"generated":[66],"candidate":[67,77,93],"TREs,":[68,86,128],"we":[69,87,124],"calculate":[70],"evaluation":[72],"score":[73],"(E-score)":[74],"for":[75],"given":[76],"TREs.":[78],"Based":[79],"on":[80],"proposed":[82],"selection":[83],"criteria":[84],"choose":[88],"putative":[89,127],"among":[92],"each":[96],"class":[99],"Dd.":[101,166],"According":[102],"simulation":[105],"result":[106],"49":[108],"V":[111],"expression":[112,163],"stage,":[113],"43":[114],"A,":[116,150],"42":[117],"S,":[119,156],"47":[121],"C,":[123],"predicted":[125],"corresponding":[129],"P":[132],"/spl":[133],"les/":[134],"10/sup":[135],"-3/":[136],"such":[137],"as":[138],"\"aataattt\",":[139],"\"attacaaa\",":[140],"\"attaatat\"":[142],"V,":[144],"\"ttattcta\",":[145],"\"atgtgtta\",":[146],"\"aaaattga\"":[148],"\"atttcaat\",":[151],"\"aataattg\",":[152],"\"acaacaac\"":[154],"\"aaaaaatt\",":[157],"\"ttaataat\",":[158],"\"atagtttt\"":[160],"C":[162],"stage":[164],"We":[167],"could":[168],"achieve":[169],"17.8":[170],"times":[171],"faster":[172],"TRE":[173],"detection":[174],"via":[175],"parallel":[176],"computing":[177],"algorithm":[178],"32":[180],"processor":[181],"machines.":[182]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
