{"id":"https://openalex.org/W2124823957","doi":"https://doi.org/10.1093/bioinformatics/btu163","title":"Improving MEME via a two-tiered significance analysis","display_name":"Improving MEME via a two-tiered significance analysis","publication_year":2014,"publication_date":"2014-03-24","ids":{"openalex":"https://openalex.org/W2124823957","doi":"https://doi.org/10.1093/bioinformatics/btu163","mag":"2124823957","pmid":"https://pubmed.ncbi.nlm.nih.gov/24665130"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu163","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu163","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5038453269","display_name":"Emi Tanaka","orcid":"https://orcid.org/0000-0002-1455-259X"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]},{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]},{"id":"https://openalex.org/I204824540","display_name":"University of Wollongong","ror":"https://ror.org/00jtmb277","country_code":"AU","type":"education","lineage":["https://openalex.org/I204824540"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Emi Tanaka","raw_affiliation_strings":["1 School of Mathematics and Statistics, University of Sydney, Sydney 2006, 2 School of Mathematics and Applied Statistics, University of Wollongong, Wollongong 2522, New South Wales and 3 Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Mathematics and Statistics, University of Sydney, Sydney 2006, 2 School of Mathematics and Applied Statistics, University of Wollongong, Wollongong 2522, New South Wales and 3 Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia","institution_ids":["https://openalex.org/I204824540","https://openalex.org/I165143802","https://openalex.org/I129604602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017222669","display_name":"Timothy L. Bailey","orcid":"https://orcid.org/0000-0002-7018-9342"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]},{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]},{"id":"https://openalex.org/I204824540","display_name":"University of Wollongong","ror":"https://ror.org/00jtmb277","country_code":"AU","type":"education","lineage":["https://openalex.org/I204824540"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Timothy L. Bailey","raw_affiliation_strings":["1 School of Mathematics and Statistics, University of Sydney, Sydney 2006, 2 School of Mathematics and Applied Statistics, University of Wollongong, Wollongong 2522, New South Wales and 3 Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Mathematics and Statistics, University of Sydney, Sydney 2006, 2 School of Mathematics and Applied Statistics, University of Wollongong, Wollongong 2522, New South Wales and 3 Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia","institution_ids":["https://openalex.org/I204824540","https://openalex.org/I165143802","https://openalex.org/I129604602"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068879102","display_name":"Uri Keich","orcid":"https://orcid.org/0000-0002-3209-5011"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]},{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]},{"id":"https://openalex.org/I204824540","display_name":"University of Wollongong","ror":"https://ror.org/00jtmb277","country_code":"AU","type":"education","lineage":["https://openalex.org/I204824540"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Uri Keich","raw_affiliation_strings":["1 School of Mathematics and Statistics, University of Sydney, Sydney 2006, 2 School of Mathematics and Applied Statistics, University of Wollongong, Wollongong 2522, New South Wales and 3 Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Mathematics and Statistics, University of Sydney, Sydney 2006, 2 School of Mathematics and Applied Statistics, University of Wollongong, Wollongong 2522, New South Wales and 3 Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia","institution_ids":["https://openalex.org/I204824540","https://openalex.org/I165143802","https://openalex.org/I129604602"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.9665,"has_fulltext":false,"cited_by_count":24,"citation_normalized_percentile":{"value":0.93297776,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"30","issue":"14","first_page":"1965","last_page":"1973"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10799","display_name":"Data Visualization and Analytics","score":0.22349999845027924,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"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/T10799","display_name":"Data Visualization and Analytics","score":0.22349999845027924,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"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/T11574","display_name":"Artificial Intelligence in Games","score":0.12409999966621399,"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/T10538","display_name":"Data Mining Algorithms and Applications","score":0.04230000078678131,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.8435485363006592},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.694231390953064},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4430266320705414},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3357221186161041}],"concepts":[{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.8435485363006592},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.694231390953064},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4430266320705414},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3357221186161041},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"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":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/btu163","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu163","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:24665130","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24665130","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:ro.uow.edu.au:eispapers-4485","is_oa":false,"landing_page_url":"https://ro.uow.edu.au/eispapers/3468","pdf_url":null,"source":{"id":"https://openalex.org/S4306400510","display_name":"Research Online (University of Wollongong)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I204824540","host_organization_name":"University of Wollongong","host_organization_lineage":["https://openalex.org/I204824540"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty of Engineering and Information Sciences - Papers: Part A","raw_type":"article"},{"id":"pmh:oai:espace.library.uq.edu.au:UQ:330847","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402388","display_name":"Queensland's institutional digital repository (The University of Queensland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165143802","host_organization_name":"The University of Queensland","host_organization_lineage":["https://openalex.org/I165143802"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:3464875","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4080741","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:openresearch-repository.anu.edu.au:1885/733800123","is_oa":false,"landing_page_url":"https://hdl.handle.net/1885/733800123","pdf_url":null,"source":{"id":"https://openalex.org/S4306402539","display_name":"ANU Open Research (Australian National University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I118347636","host_organization_name":"Australian National University","host_organization_lineage":["https://openalex.org/I118347636"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Journal article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W1549994062","https://openalex.org/W1592870802","https://openalex.org/W1837699063","https://openalex.org/W1981093360","https://openalex.org/W1991567646","https://openalex.org/W2003967338","https://openalex.org/W2038963685","https://openalex.org/W2049633694","https://openalex.org/W2055043387","https://openalex.org/W2080498142","https://openalex.org/W2097175728","https://openalex.org/W2098885692","https://openalex.org/W2103630240","https://openalex.org/W2103777723","https://openalex.org/W2110403456","https://openalex.org/W2113117122","https://openalex.org/W2116402745","https://openalex.org/W2128757772","https://openalex.org/W2130063415","https://openalex.org/W2132909884","https://openalex.org/W2133540950","https://openalex.org/W2148032724","https://openalex.org/W2149769193","https://openalex.org/W2154412571","https://openalex.org/W2158714788","https://openalex.org/W2188937707","https://openalex.org/W2522049477","https://openalex.org/W2522401206","https://openalex.org/W2951079730","https://openalex.org/W6635200387","https://openalex.org/W6638990142","https://openalex.org/W6675084509"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W3170299350","https://openalex.org/W2368410102","https://openalex.org/W2605676258","https://openalex.org/W2368037387","https://openalex.org/W190186656","https://openalex.org/W2902352756","https://openalex.org/W2377079823"],"abstract_inverted_index":{"MOTIVATION:":[0],"With":[1],"over":[2],"9000":[3],"unique":[4],"users":[5],"recorded":[6],"in":[7,121,128,167],"the":[8,17,26,34,69,76,100,119,123,150,171],"first":[9],"half":[10],"of":[11,16,25,29,36,65,78],"2013,":[12],"MEME":[13,56,96],"is":[14,43,166],"one":[15],"most":[18],"popular":[19],"motif-finding":[20,70,144],"tools":[21],"available.":[22],"Reliable":[23],"estimates":[24],"statistical":[27,132],"significance":[28,81,114,155],"motifs":[30,61],"can":[31,117],"greatly":[32],"increase":[33],"usefulness":[35],"any":[37],"motif":[38,126],"finder.":[39],"By":[40],"analogy,":[41],"it":[42],"difficult":[44],"to":[45,68,103],"imagine":[46],"evaluating":[47,129],"a":[48,87,112,153],"BLAST":[49],"result":[50],"without":[51],"its":[52,58,92,130],"accompanying":[53],"E-value.":[54],"Currently":[55],"evaluates":[57],"EM-generated":[59],"candidate":[60,106,125],"using":[62],"an":[63],"extension":[64],"BLAST's":[66],"E-value":[67,101,120,174],"context.":[71],"Although":[72],"we":[73,83,110],"previously":[74],"indicated":[75],"drawbacks":[77],"MEME's":[79,143],"current":[80],"evaluation,":[82],"did":[84],"not":[85],"offer":[86,111],"practical":[88],"substitute":[89],"suited":[90],"for":[91,159],"needs,":[93],"especially":[94],"because":[95],"also":[97,148],"relies":[98],"on":[99],"internally":[102],"rank":[104],"competing":[105],"motifs.":[107],"RESULTS:":[108],"Here":[109],"two-tiered":[113],"analysis":[115],"that":[116,136],"replace":[118],"selecting":[122],"best":[124],"and":[127,146],"overall":[131],"significance.":[133],"We":[134],"show":[135],"our":[137,163],"new":[138,164],"approach":[139,165],"could":[140],"substantially":[141],"improve":[142],"performance":[145],"would":[147],"provide":[149],"user":[151],"with":[152],"reliable":[154],"analysis.":[156,175],"In":[157],"addition,":[158],"large":[160],"input":[161],"sets,":[162],"fact":[168],"faster":[169],"than":[170],"currently":[172],"implemented":[173]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":3}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
