{"id":"https://openalex.org/W2098793454","doi":"https://doi.org/10.1093/bioinformatics/bti256","title":"Transcription factor binding site identification using the self-organizing map","display_name":"Transcription factor binding site identification using the self-organizing map","publication_year":2005,"publication_date":"2005-01-12","ids":{"openalex":"https://openalex.org/W2098793454","doi":"https://doi.org/10.1093/bioinformatics/bti256","mag":"2098793454","pmid":"https://pubmed.ncbi.nlm.nih.gov/15647296"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti256","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti256","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/9/1807/48972707/bioinformatics_21_9_1807.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/21/9/1807/48972707/bioinformatics_21_9_1807.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077269033","display_name":"Shaun Mahony","orcid":"https://orcid.org/0000-0002-2641-1807"},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]}],"countries":["IE"],"is_corresponding":true,"raw_author_name":"S. Mahony","raw_affiliation_strings":["National Centre for Biomedical Engineering Science, NUI Galway, Ireland. shaun.mahony@nuigalway.ie","National Centre for Biomedical Engineering Science, NUI Galway Galway, Ireland#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Centre for Biomedical Engineering Science, NUI Galway, Ireland. shaun.mahony@nuigalway.ie","institution_ids":["https://openalex.org/I188760350"]},{"raw_affiliation_string":"National Centre for Biomedical Engineering Science, NUI Galway Galway, Ireland#TAB#","institution_ids":["https://openalex.org/I188760350"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005009833","display_name":"David A. Hendrix","orcid":"https://orcid.org/0000-0002-7285-1977"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"D. Hendrix","raw_affiliation_strings":["Department of Physics, University of California, Berkeley, CA 94720 (USA)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics, University of California, Berkeley, CA 94720 (USA)","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035389230","display_name":"Aaron Golden","orcid":"https://orcid.org/0000-0001-8208-4292"},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]},{"id":"https://openalex.org/I4210109397","display_name":"Centre for Biomedical Engineering and Physics","ror":"https://ror.org/01n5qfh17","country_code":"SE","type":"nonprofit","lineage":["https://openalex.org/I4210109397"]}],"countries":["IE","SE"],"is_corresponding":false,"raw_author_name":"A. Golden","raw_affiliation_strings":["Department of Information Technology, NUI Galway, Galway, Ireland,","National Centre for Biomedical Engineering Science and","National Centre for Biomedical Engineering Science, NUI Galway Galway, Ireland#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Technology, NUI Galway, Galway, Ireland,","institution_ids":["https://openalex.org/I188760350"]},{"raw_affiliation_string":"National Centre for Biomedical Engineering Science and","institution_ids":["https://openalex.org/I4210109397"]},{"raw_affiliation_string":"National Centre for Biomedical Engineering Science, NUI Galway Galway, Ireland#TAB#","institution_ids":["https://openalex.org/I188760350"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101903427","display_name":"Terry Smith","orcid":"https://orcid.org/0000-0002-4956-3299"},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]},{"id":"https://openalex.org/I4210109397","display_name":"Centre for Biomedical Engineering and Physics","ror":"https://ror.org/01n5qfh17","country_code":"SE","type":"nonprofit","lineage":["https://openalex.org/I4210109397"]}],"countries":["IE","SE"],"is_corresponding":false,"raw_author_name":"T. J. Smith","raw_affiliation_strings":["National Centre for Biomedical Engineering Science and","National Centre for Biomedical Engineering Science, NUI Galway Galway, Ireland#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Centre for Biomedical Engineering Science and","institution_ids":["https://openalex.org/I4210109397"]},{"raw_affiliation_string":"National Centre for Biomedical Engineering Science, NUI Galway Galway, Ireland#TAB#","institution_ids":["https://openalex.org/I188760350"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068564092","display_name":"Daniel S. Rokhsar","orcid":"https://orcid.org/0000-0002-8704-2224"},"institutions":[{"id":"https://openalex.org/I196679689","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I196679689","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I4210109258","display_name":"Innovative Genomics Institute","ror":"https://ror.org/01r4tcq81","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191","https://openalex.org/I4210109258","https://openalex.org/I95457486"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"D. S. Rokhsar","raw_affiliation_strings":["Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA and","Joint Genome Institute, Walnut Creek, CA 94598, USA","Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA and","institution_ids":["https://openalex.org/I4210109258","https://openalex.org/I95457486"]},{"raw_affiliation_string":"Joint Genome Institute, Walnut Creek, CA 94598, USA","institution_ids":["https://openalex.org/I196679689"]},{"raw_affiliation_string":"Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I4210109258","https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5077269033"],"corresponding_institution_ids":["https://openalex.org/I188760350"],"apc_list":null,"apc_paid":null,"fwci":2.5117,"has_fulltext":true,"cited_by_count":73,"citation_normalized_percentile":{"value":0.89127052,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"21","issue":"9","first_page":"1807","last_page":"1814"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9907000064849854,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9907000064849854,"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":0.9854000210762024,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9842000007629395,"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/computer-science","display_name":"Computer science","score":0.6876063942909241},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4988274574279785},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.45142167806625366},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4413934051990509},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.35655122995376587},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.34535449743270874},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21331873536109924}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6876063942909241},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4988274574279785},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.45142167806625366},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4413934051990509},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.35655122995376587},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.34535449743270874},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21331873536109924},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","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":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","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},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/bti256","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti256","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/9/1807/48972707/bioinformatics_21_9_1807.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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:15647296","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15647296","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:aran.library.nuigalway.ie/:10379/4665","is_oa":false,"landing_page_url":"http://hdl.handle.net/10379/4665","pdf_url":null,"source":{"id":"https://openalex.org/S4377196322","display_name":"ARAN (University of Galway Research Repository) (Ollscoil na Gaillimhe \u2013 University of Galway)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I188760350","host_organization_name":"Ollscoil na Gaillimhe \u2013 University of Galway","host_organization_lineage":["https://openalex.org/I188760350"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:http://www.rian.ie/163088/","is_oa":false,"landing_page_url":"http://hdl.handle.net/10379/9478","pdf_url":null,"source":{"id":"https://openalex.org/S4306400033","display_name":"Arrow@dit (Dublin Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I115570527","host_organization_name":"Dublin Institute of Technology","host_organization_lineage":["https://openalex.org/I115570527"],"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:CiteSeerX.psu:10.1.1.104.3809","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.104.3809","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/cgi/reprint/bti256v1.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti256","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti256","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/9/1807/48972707/bioinformatics_21_9_1807.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320842","display_name":"Irish Research Council for Science, Engineering and Technology","ror":"https://ror.org/051xex213"},{"id":"https://openalex.org/F4320321056","display_name":"Irish Research Council","ror":"https://ror.org/051xex213"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2098793454.pdf","grobid_xml":"https://content.openalex.org/works/W2098793454.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1580213736","https://openalex.org/W1592870802","https://openalex.org/W1679913846","https://openalex.org/W1969698218","https://openalex.org/W2005244073","https://openalex.org/W2025540189","https://openalex.org/W2028903194","https://openalex.org/W2039286232","https://openalex.org/W2045342295","https://openalex.org/W2056134190","https://openalex.org/W2073850887","https://openalex.org/W2077606580","https://openalex.org/W2093901628","https://openalex.org/W2106104287","https://openalex.org/W2117131721","https://openalex.org/W2117549173","https://openalex.org/W2167630504","https://openalex.org/W2168157737","https://openalex.org/W2169001593"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W3046775127","https://openalex.org/W3107602296","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W2033914206","https://openalex.org/W4283697347"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,41],"automatic":[2],"identification":[3],"of":[4,11,30,43,77,89,106,121,144],"over-represented":[5],"motifs":[6,110],"present":[7,57,86,111],"in":[8,19,58,75,112],"a":[9,16,27,81,113],"collection":[10],"sequences":[12],"continues":[13],"to":[14,52,80],"be":[15,50,69],"challenging":[17],"problem":[18],"computational":[20],"biology.":[21],"In":[22],"this":[23,44,90],"paper,":[24],"we":[25],"propose":[26],"self-organizing":[28],"map":[29,95],"position":[31],"weight":[32],"matrices":[33],"as":[34],"an":[35,87],"alternative":[36],"method":[37],"for":[38,96],"motif":[39],"discovery.":[40],"advantage":[42],"approach":[45,123],"is":[46,104,141],"that":[47,65],"it":[48],"can":[49],"used":[51],"simultaneously":[53],"characterize":[54],"every":[55],"feature":[56],"the":[59,63,119],"dataset,":[60],"thus":[61],"lessening":[62],"chance":[64],"weaker":[66],"signals":[67],"will":[68],"missed.":[70],"Features":[71],"identified":[72],"are":[73,118],"ranked":[74],"terms":[76],"over-representation":[78],"relative":[79],"background":[82],"model.":[83],"RESULTS:":[84],"We":[85],"implementation":[88],"approach,":[91],"named":[92],"SOMBRERO":[93,140],"(self-organizing":[94],"biological":[97],"regulatory":[98],"element":[99],"recognition":[100],"and":[101,127,137],"ordering),":[102],"which":[103],"capable":[105],"discovering":[107],"multiple":[108],"distinct":[109],"single":[114],"dataset.":[115],"Demonstrated":[116],"here":[117],"advantages":[120],"our":[122],"on":[124],"various":[125],"datasets":[126],"SOMBRERO's":[128],"improved":[129],"performance":[130],"over":[131],"two":[132],"popular":[133],"motif-finding":[134],"programs,":[135],"MEME":[136],"AlignACE.":[138],"AVAILABILITY:":[139],"available":[142],"free":[143],"charge":[145],"from":[146],"http://bioinf.nuigalway.ie/sombrero":[147],"SUPPLEMENTARY":[148],"INFORMATION:":[149],"http://bioinf.nuigalway.ie/sombrero/additional.":[150]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":9}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}