{"id":"https://openalex.org/W2065754412","doi":"https://doi.org/10.1109/cibcb.2014.6845526","title":"Side effect machine features for analysis and comparison of DNA promoter sequences","display_name":"Side effect machine features for analysis and comparison of DNA promoter sequences","publication_year":2014,"publication_date":"2014-05-01","ids":{"openalex":"https://openalex.org/W2065754412","doi":"https://doi.org/10.1109/cibcb.2014.6845526","mag":"2065754412"},"language":"en","primary_location":{"id":"doi:10.1109/cibcb.2014.6845526","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2014.6845526","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 IEEE Conference on Computational Intelligence in 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/A5066757355","display_name":"Wendy Ashlock","orcid":null},"institutions":[{"id":"https://openalex.org/I192455969","display_name":"York University","ror":"https://ror.org/05fq50484","country_code":"CA","type":"education","lineage":["https://openalex.org/I192455969"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Wendy Ashlock","raw_affiliation_strings":["Biology Department, York University, Toronto, Ontario, Canada","Biol. Dept., York Univ., Toronto, ON, Canada"],"affiliations":[{"raw_affiliation_string":"Biology Department, York University, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I192455969"]},{"raw_affiliation_string":"Biol. Dept., York Univ., Toronto, ON, Canada","institution_ids":["https://openalex.org/I192455969"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5066757355"],"corresponding_institution_ids":["https://openalex.org/I192455969"],"apc_list":null,"apc_paid":null,"fwci":1.227,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.84767512,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"19","issue":null,"first_page":"1","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9988999962806702,"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":0.9980000257492065,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.8903994560241699},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6138018369674683},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5838935375213623},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5476989150047302},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.5181854367256165},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5109297633171082},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.5098661184310913},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.505259096622467},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4995708465576172},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.477573424577713},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4641816020011902},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.443418025970459},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.15333890914916992}],"concepts":[{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.8903994560241699},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6138018369674683},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5838935375213623},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5476989150047302},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.5181854367256165},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5109297633171082},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.5098661184310913},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.505259096622467},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4995708465576172},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.477573424577713},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4641816020011902},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.443418025970459},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.15333890914916992},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cibcb.2014.6845526","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2014.6845526","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Zero hunger","id":"https://metadata.un.org/sdg/2","score":0.4699999988079071}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W139956475","https://openalex.org/W273955616","https://openalex.org/W1970679073","https://openalex.org/W1974524840","https://openalex.org/W1987122345","https://openalex.org/W1990987722","https://openalex.org/W2005986419","https://openalex.org/W2020879581","https://openalex.org/W2029480115","https://openalex.org/W2047749542","https://openalex.org/W2058777414","https://openalex.org/W2064604026","https://openalex.org/W2076871417","https://openalex.org/W2085380703","https://openalex.org/W2085707114","https://openalex.org/W2087058596","https://openalex.org/W2112348586","https://openalex.org/W2112814753","https://openalex.org/W2130886513","https://openalex.org/W2135030836","https://openalex.org/W2136711891","https://openalex.org/W2158714788","https://openalex.org/W2160877678","https://openalex.org/W2161849959","https://openalex.org/W2169251996","https://openalex.org/W4244030505","https://openalex.org/W6610017368","https://openalex.org/W6665453513","https://openalex.org/W6676606992"],"related_works":["https://openalex.org/W2139566393","https://openalex.org/W2901448061","https://openalex.org/W2124433786","https://openalex.org/W2162836426","https://openalex.org/W2734802753","https://openalex.org/W2149312834","https://openalex.org/W3089376739","https://openalex.org/W1534925089","https://openalex.org/W4200283209","https://openalex.org/W2143172590"],"abstract_inverted_index":{"Understanding":[0],"genomes":[1],"involves":[2,14],"more":[3],"than":[4],"just":[5],"knowing":[6,15],"what":[7,125],"all":[8,110],"the":[9,17,49,60,81,111,149,171,263,286,290],"genes":[10,18,34],"are.":[11],"It":[12],"also":[13],"how":[16],"are":[19,30,98,203,238],"regulated.":[20],"An":[21],"important":[22],"piece":[23],"of":[24,33,38,48,59,69,103,109,151,198],"this":[25,188],"concerns":[26],"gene":[27],"promoters.":[28,143,199],"These":[29,213],"regions":[31],"upstream":[32],"to":[35,45,87,89,121,134,141,169,177,194,261],"which":[36,108,137,142],"groups":[37],"protein":[39],"(transcription":[40],"factors)":[41],"bind":[42,88,120,140],"in":[43,73,117,124,182,223],"order":[44],"initiate":[46],"transcription":[47,83,112,138],"gene.":[50],"Much":[51],"work":[52,189],"has":[53],"focused":[54],"on":[55,174,285,289],"finding":[56],"sequence":[57,196,211,227],"properties":[58],"DNA":[61,210,226],"binding":[62,65,71,115],"sites,":[63],"called":[64],"motifs.":[66],"The":[67],"presence":[68],"a":[70,74,161,235,246,270,281],"motif":[72],"promoter":[75,104,266,274],"does":[76],"not,":[77],"however,":[78],"mean":[79],"that":[80,90,93,106,186,208,254,257,276],"associated":[82],"factor":[84],"is":[85,95,168,277],"likely":[86],"promoter,":[91],"only":[92,157],"it":[94,132],"possible.":[96],"There":[97],"other,":[99],"less":[100],"understood,":[101],"features":[102,197,214,256],"sequences":[105,275],"determine":[107,136],"factors":[113,139],"with":[114,218,220,280],"motifs":[116],"them":[118,122],"will":[119],"and":[123,148],"combinations.":[126],"Next":[127],"generation":[128],"sequencing":[129],"technologies":[130],"make":[131],"possible":[133],"experimentally":[135],"This":[144],"technology":[145],"requires":[146],"money":[147],"time":[150],"skilled":[152],"experimental":[153,172],"biologists.":[154],"Experiments":[155],"have":[156,215],"been":[158,216],"performed":[159],"for":[160,234,250],"few":[162],"select":[163],"model":[164],"organisms.":[165,184],"Our":[166],"goal":[167],"leverage":[170],"results":[173,222],"those":[175],"organisms":[176],"provide":[178],"information":[179],"about":[180],"promoters":[181],"other":[183],"Towards":[185],"end,":[187],"uses":[190],"side":[191,231,251],"effect":[192,201,232,252],"machines":[193,202,207,233,253],"find":[195],"Side":[200],"augmented":[204],"finite":[205],"state":[206],"compute":[209],"features.":[212],"used":[217,260],"classifiers":[219],"good":[221],"many":[224],"diverse":[225],"classification":[228],"problems.":[229],"Useful":[230],"given":[236],"problem":[237],"found":[239],"using":[240],"an":[241],"evolutionary":[242],"algorithm.":[243],"We":[244,268],"present":[245],"novel":[247],"fitness":[248],"function":[249],"produce":[255],"can":[258],"be":[259],"measure":[262,272,283],"similarity":[264],"between":[265,273],"sequences.":[267],"create":[269],"distance":[271,282],"significantly":[278],"correlated":[279],"based":[284],"experiments":[287],"done":[288],"yeast":[291],"genome.":[292]},"counts_by_year":[{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
