{"id":"https://openalex.org/W1970871448","doi":"https://doi.org/10.1186/1471-2105-9-89","title":"An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance","display_name":"An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance","publication_year":2008,"publication_date":"2008-02-07","ids":{"openalex":"https://openalex.org/W1970871448","doi":"https://doi.org/10.1186/1471-2105-9-89","mag":"1970871448","pmid":"https://pubmed.ncbi.nlm.nih.gov/18257925"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-9-89","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-89","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-89","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-89","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037378656","display_name":"Ana Casimiro","orcid":"https://orcid.org/0000-0001-6001-6803"},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Ana C Casimiro","raw_affiliation_strings":["INESC-ID/IST, Rua Alves Redol, 9 1000-029 Lisboa, Portugal. ana.casimiro@gmail.com","INESC-ID/IST, Rua Alves Redol, 9, 1000-029, Lisboa, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INESC-ID/IST, Rua Alves Redol, 9 1000-029 Lisboa, Portugal. ana.casimiro@gmail.com","institution_ids":["https://openalex.org/I121345201"]},{"raw_affiliation_string":"INESC-ID/IST, Rua Alves Redol, 9, 1000-029, Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005271169","display_name":"Susana Vinga","orcid":"https://orcid.org/0000-0002-1954-5487"},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I4210160579","display_name":"Ordem dos M\u00e9dicos","ror":"https://ror.org/05n5mpz07","country_code":"PT","type":"government","lineage":["https://openalex.org/I4210160579"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Susana Vinga","raw_affiliation_strings":["FCM/UNL, Campo dos M\u00e1rtires da P\u00e1tria 130, 1169-056, Lisboa, Portugal","INESC-ID/IST, Rua Alves Redol, 9, 1000-029, Lisboa, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"FCM/UNL, Campo dos M\u00e1rtires da P\u00e1tria 130, 1169-056, Lisboa, Portugal","institution_ids":["https://openalex.org/I4210160579"]},{"raw_affiliation_string":"INESC-ID/IST, Rua Alves Redol, 9, 1000-029, Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083766796","display_name":"Ana T. Freitas","orcid":"https://orcid.org/0000-0002-2997-5990"},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Ana T Freitas","raw_affiliation_strings":["INESC-ID/IST, Rua Alves Redol, 9, 1000-029, Lisboa, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INESC-ID/IST, Rua Alves Redol, 9, 1000-029, Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001327675","display_name":"Arlindo L. Oliveira","orcid":"https://orcid.org/0000-0001-8638-5594"},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Arlindo L Oliveira","raw_affiliation_strings":["INESC-ID/IST, Rua Alves Redol, 9, 1000-029, Lisboa, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INESC-ID/IST, Rua Alves Redol, 9, 1000-029, Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5001327675"],"corresponding_institution_ids":["https://openalex.org/I121345201"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.2997,"has_fulltext":true,"cited_by_count":22,"citation_normalized_percentile":{"value":0.7802472,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"9","issue":"1","first_page":"89","last_page":"89"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.8055999875068665,"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":0.8055999875068665,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.156700000166893,"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/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.005799999926239252,"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/computational-biology","display_name":"Computational biology","score":0.5999377369880676},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.5806869268417358},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.5399461388587952},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5346779823303223},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5029358267784119},{"id":"https://openalex.org/keywords/homo-sapiens","display_name":"Homo sapiens","score":0.47732287645339966},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4667855501174927},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4663374125957489},{"id":"https://openalex.org/keywords/statistical-hypothesis-testing","display_name":"Statistical hypothesis testing","score":0.4422897398471832},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.4318038821220398},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.4139770269393921},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.35289162397384644},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2199704647064209},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.13112667202949524},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.09965658187866211}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5999377369880676},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.5806869268417358},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.5399461388587952},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5346779823303223},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5029358267784119},{"id":"https://openalex.org/C2777938546","wikidata":"https://www.wikidata.org/wiki/Q5","display_name":"Homo sapiens","level":2,"score":0.47732287645339966},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4667855501174927},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4663374125957489},{"id":"https://openalex.org/C87007009","wikidata":"https://www.wikidata.org/wiki/Q210832","display_name":"Statistical hypothesis testing","level":2,"score":0.4422897398471832},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.4318038821220398},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.4139770269393921},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.35289162397384644},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2199704647064209},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.13112667202949524},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.09965658187866211},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"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":[{"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":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"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":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":"D016008","descriptor_name":"Statistical Distributions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016008","descriptor_name":"Statistical Distributions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016008","descriptor_name":"Statistical Distributions","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":5,"locations":[{"id":"doi:10.1186/1471-2105-9-89","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-89","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-89","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18257925","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18257925","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:6631b049c18a4c089585a39dcf020b0f","is_oa":false,"landing_page_url":"https://doaj.org/article/6631b049c18a4c089585a39dcf020b0f","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 9, Iss 1, p 89 (2008)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2375121","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2375121","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:run.unl.pt:10362/23352","is_oa":true,"landing_page_url":"http://hdl.handle.net/10362/23352","pdf_url":null,"source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null}],"best_oa_location":{"id":"doi:10.1186/1471-2105-9-89","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-89","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-89","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.6700000166893005}],"awards":[],"funders":[{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1970871448.pdf","grobid_xml":"https://content.openalex.org/works/W1970871448.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W178414959","https://openalex.org/W634757314","https://openalex.org/W938539187","https://openalex.org/W1571839798","https://openalex.org/W1592870802","https://openalex.org/W1815199292","https://openalex.org/W1990987722","https://openalex.org/W1999966058","https://openalex.org/W2016786878","https://openalex.org/W2020830418","https://openalex.org/W2029873987","https://openalex.org/W2054984882","https://openalex.org/W2062372788","https://openalex.org/W2076313473","https://openalex.org/W2096210973","https://openalex.org/W2097879961","https://openalex.org/W2097920884","https://openalex.org/W2101025813","https://openalex.org/W2101163218","https://openalex.org/W2112139159","https://openalex.org/W2118640842","https://openalex.org/W2119022656","https://openalex.org/W2134193442","https://openalex.org/W2135243774","https://openalex.org/W2141437736","https://openalex.org/W2154854793","https://openalex.org/W2158470315","https://openalex.org/W2168157737","https://openalex.org/W2510854709","https://openalex.org/W2610179052","https://openalex.org/W4255852734","https://openalex.org/W4298872162"],"related_works":["https://openalex.org/W2468279273","https://openalex.org/W2354198838","https://openalex.org/W1989130879","https://openalex.org/W2103419012","https://openalex.org/W3170299350","https://openalex.org/W2368410102","https://openalex.org/W2368037387","https://openalex.org/W122800452","https://openalex.org/W190186656","https://openalex.org/W2377079823"],"abstract_inverted_index":{"BACKGROUND:":[0],"Motif":[1],"finding":[2],"algorithms":[3],"have":[4,106],"developed":[5],"in":[6,17,56,126,139,155,197],"their":[7],"ability":[8],"to":[9,14,36,85,93,118,144,218],"use":[10],"computationally":[11],"efficient":[12],"methods":[13],"detect":[15],"patterns":[16,79],"biological":[18,39,212],"sequences.":[19],"However":[20],"the":[21,25,38,42,49,57,66,75,95,98,127,134,146,156,183,198,229,233],"posterior":[22],"classification":[23,99],"of":[24,41,51,54,74,97,100,130,149,159,201,211],"output":[26],"still":[27],"suffers":[28],"from":[29],"some":[30],"limitations,":[31],"which":[32,60],"makes":[33],"it":[34],"difficult":[35],"assess":[37,119],"significance":[40],"motifs":[43,55,193],"found.":[44],"Previous":[45],"work":[46],"has":[47],"highlighted":[48],"existence":[50],"positional":[52,147],"bias":[53],"DNA":[58],"sequences,":[59],"might":[61],"indicate":[62],"not":[63],"only":[64],"that":[65,136,177,189,205],"pattern":[67],"is":[68,180,207],"important,":[69],"but":[70],"also":[71],"provide":[72],"hints":[73],"positions":[76],"where":[77],"these":[78],"occur":[80],"preferentially.":[81],"RESULTS:":[82],"We":[83,187],"propose":[84],"integrate":[86],"position":[87,178],"uniformity":[88],"tests":[89,92,111,221],"and":[90,114,170,203,214],"over-representation":[91,220],"improve":[94],"accuracy":[96],"motifs.":[101],"Using":[102,133],"artificial":[103],"data,":[104],"we":[105,142,227],"compared":[107],"three":[108],"different":[109,160],"statistical":[110],"(Chi-Square,":[112],"Kolmogorov-Smirnov":[113],"a":[115,121,131,208],"Chi-Square":[116],"bootstrap)":[117],"whether":[120],"given":[122],"motif":[123],"occurs":[124],"uniformly":[125],"promoter":[128,157,199],"region":[129,200],"gene.":[132],"test":[135],"performed":[137],"better":[138],"this":[140,225],"dataset,":[141],"proceeded":[143],"study":[145],"distribution":[148],"several":[150,171],"well":[151],"known":[152],"cis-regulatory":[153],"elements,":[154],"sequences":[158],"organisms":[161],"(S.":[162],"cerevisiae,":[163],"H.":[164],"sapiens,":[165],"D.":[166],"melanogaster,":[167],"E.":[168],"coli":[169],"Dicotyledons":[172],"plants).":[173],"The":[174],"results":[175,230],"show":[176],"conservation":[179],"relevant":[181,192],"for":[182,232],"transcriptional":[184],"machinery.":[185],"CONCLUSION:":[186],"conclude":[188],"many":[190],"biologically":[191],"appear":[194],"heterogeneously":[195],"distributed":[196],"genes,":[202],"therefore,":[204],"non-uniformity":[206],"good":[209],"indicator":[210],"relevance":[213],"can":[215],"be":[216],"used":[217],"complement":[219],"commonly":[222],"used.":[223],"In":[224],"article":[226],"present":[228],"obtained":[231],"S.":[234],"cerevisiae":[235],"data":[236],"sets.":[237]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}