{"id":"https://openalex.org/W2009818901","doi":"https://doi.org/10.1371/journal.pcbi.0020049","title":"Transcription Factor Map Alignment of Promoter Regions","display_name":"Transcription Factor Map Alignment of Promoter Regions","publication_year":2006,"publication_date":"2006-05-23","ids":{"openalex":"https://openalex.org/W2009818901","doi":"https://doi.org/10.1371/journal.pcbi.0020049","mag":"2009818901","pmid":"https://pubmed.ncbi.nlm.nih.gov/16733547"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.0020049","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0020049","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0020049&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0020049&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046391546","display_name":"Enrique Blanco","orcid":"https://orcid.org/0000-0001-6261-7370"},"institutions":[{"id":"https://openalex.org/I170486558","display_name":"Pompeu Fabra University","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Enrique Blanco","raw_affiliation_strings":["Research Group in Biomedical Informatics, Institut Municipal d'Investigaci\u00f3 M\u00e8dica/Universitat Pompeu Fabra, Barcelona, Catalonia, Spain","Grup d'Algor\u00edsmica i Gen\u00e8tica, Departament de Llenguatges i Sistemes Inform\u00e0tics, Universitat Polit\u00e8cnica de Catalunya, Barcelona, Catalonia, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Group in Biomedical Informatics, Institut Municipal d'Investigaci\u00f3 M\u00e8dica/Universitat Pompeu Fabra, Barcelona, Catalonia, Spain","institution_ids":["https://openalex.org/I170486558"]},{"raw_affiliation_string":"Grup d'Algor\u00edsmica i Gen\u00e8tica, Departament de Llenguatges i Sistemes Inform\u00e0tics, Universitat Polit\u00e8cnica de Catalunya, Barcelona, Catalonia, Spain","institution_ids":["https://openalex.org/I9617848"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068256758","display_name":"Xavier Messeguer","orcid":"https://orcid.org/0000-0001-7430-4857"},"institutions":[{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Xavier Messeguer","raw_affiliation_strings":["Grup d'Algor\u00edsmica i Gen\u00e8tica, Departament de Llenguatges i Sistemes Inform\u00e0tics, Universitat Polit\u00e8cnica de Catalunya, Barcelona, Catalonia, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Grup d'Algor\u00edsmica i Gen\u00e8tica, Departament de Llenguatges i Sistemes Inform\u00e0tics, Universitat Polit\u00e8cnica de Catalunya, Barcelona, Catalonia, Spain","institution_ids":["https://openalex.org/I9617848"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113513874","display_name":"Temple F. Smith","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Temple F Smith","raw_affiliation_strings":["Biomolecular Engineering Research Center, Boston University, Boston, Massachusetts, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomolecular Engineering Research Center, Boston University, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067701434","display_name":"Roderic Guig\u00f3","orcid":"https://orcid.org/0000-0002-5738-4477"},"institutions":[{"id":"https://openalex.org/I4210137962","display_name":"Centre for Genomic Regulation","ror":"https://ror.org/03wyzt892","country_code":"ES","type":"funder","lineage":["https://openalex.org/I4210132884","https://openalex.org/I4210137962","https://openalex.org/I4387153040"]},{"id":"https://openalex.org/I170486558","display_name":"Pompeu Fabra University","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Roderic Guig\u00f3","raw_affiliation_strings":["","Bioinformatics and Genomics Program, Centre de Regulaci\u00f3 Gen\u00f2mica, Barcelona, Catalonia, Spain","Research Group in Biomedical Informatics, Institut Municipal d'Investigaci\u00f3 M\u00e8dica/Universitat Pompeu Fabra, Barcelona, Catalonia, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"","institution_ids":[]},{"raw_affiliation_string":"Bioinformatics and Genomics Program, Centre de Regulaci\u00f3 Gen\u00f2mica, Barcelona, Catalonia, Spain","institution_ids":["https://openalex.org/I4210137962"]},{"raw_affiliation_string":"Research Group in Biomedical Informatics, Institut Municipal d'Investigaci\u00f3 M\u00e8dica/Universitat Pompeu Fabra, Barcelona, Catalonia, Spain","institution_ids":["https://openalex.org/I170486558"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5067701434"],"corresponding_institution_ids":["https://openalex.org/I170486558","https://openalex.org/I4210137962"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.0448,"has_fulltext":true,"cited_by_count":60,"citation_normalized_percentile":{"value":0.85329093,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"2","issue":"5","first_page":"e49","last_page":"e49"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9997000098228455,"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":0.9997000098228455,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9930999875068665,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9908000230789185,"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":0.7122634649276733},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.6237305402755737},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5753316879272461},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5711878538131714},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5628690719604492},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5486619472503662},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5456869602203369},{"id":"https://openalex.org/keywords/conserved-sequence","display_name":"Conserved sequence","score":0.5261282920837402},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.48487505316734314},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.4837910830974579},{"id":"https://openalex.org/keywords/cis-regulatory-module","display_name":"Cis-regulatory module","score":0.4755663275718689},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.44816210865974426},{"id":"https://openalex.org/keywords/regulatory-sequence","display_name":"Regulatory sequence","score":0.44533589482307434},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.44081854820251465},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.4294721484184265},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.23984888195991516},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.19754058122634888},{"id":"https://openalex.org/keywords/base-sequence","display_name":"Base sequence","score":0.1268453598022461},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.12560933828353882},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.11275598406791687}],"concepts":[{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.7122634649276733},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.6237305402755737},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5753316879272461},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5711878538131714},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5628690719604492},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5486619472503662},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5456869602203369},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.5261282920837402},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.48487505316734314},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.4837910830974579},{"id":"https://openalex.org/C190796033","wikidata":"https://www.wikidata.org/wiki/Q1093165","display_name":"Cis-regulatory module","level":5,"score":0.4755663275718689},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.44816210865974426},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.44533589482307434},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.44081854820251465},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.4294721484184265},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.23984888195991516},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.19754058122634888},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.1268453598022461},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.12560933828353882},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.11275598406791687}],"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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015183","descriptor_name":"Restriction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015183","descriptor_name":"Restriction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015183","descriptor_name":"Restriction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":10,"locations":[{"id":"doi:10.1371/journal.pcbi.0020049","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0020049","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0020049&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:16733547","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16733547","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:recercat.cat:2072/213170","is_oa":true,"landing_page_url":"http://hdl.handle.net/10230/13156","pdf_url":null,"source":{"id":"https://openalex.org/S4306402147","display_name":"RECERCAT (Consorci de Serveis Universitaris de Catalunya)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210090028","host_organization_name":"Consorci de Serveis Universitaris de Catalunya","host_organization_lineage":["https://openalex.org/I4210090028"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:www.recercat.cat:2072/211159","is_oa":true,"landing_page_url":"http://hdl.handle.net/2445/43418","pdf_url":null,"source":{"id":"https://openalex.org/S4306402147","display_name":"RECERCAT (Consorci de Serveis Universitaris de Catalunya)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210090028","host_organization_name":"Consorci de Serveis Universitaris de Catalunya","host_organization_lineage":["https://openalex.org/I4210090028"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.275.8345","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.275.8345","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/31/9f/PLoS_Comput_Biol_2006_May_26_2(5)_e49.tar.gz","raw_type":"text"},{"id":"pmh:oai:RePEc:plo:pcbi00:0020049","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0020049","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"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":"article"},{"id":"pmh:oai:doaj.org/article:92f2634ebf954388ab246f1dca6c9ca2","is_oa":true,"landing_page_url":"https://doaj.org/article/92f2634ebf954388ab246f1dca6c9ca2","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 2, Iss 5, p e49 (2006)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/152947","is_oa":true,"landing_page_url":"https://figshare.com/articles/Transcription_Factor_Map_Alignment_of_Promoter_Regions/152947","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"},{"id":"pmh:oai:open.bu.edu:2144/3442","is_oa":false,"landing_page_url":"https://hdl.handle.net/2144/3442","pdf_url":null,"source":{"id":"https://openalex.org/S4306402183","display_name":"OpenBU/Boston University Institutional Repository (Boston University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I111088046","host_organization_name":"Boston University","host_organization_lineage":["https://openalex.org/I111088046"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1464811","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1464811","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.0020049","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0020049","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0020049&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.7099999785423279}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2009818901.pdf","grobid_xml":"https://content.openalex.org/works/W2009818901.grobid-xml"},"referenced_works_count":52,"referenced_works":["https://openalex.org/W1592870802","https://openalex.org/W1600463518","https://openalex.org/W1964823180","https://openalex.org/W1980809845","https://openalex.org/W1987122345","https://openalex.org/W2001785106","https://openalex.org/W2006101746","https://openalex.org/W2041726559","https://openalex.org/W2041877620","https://openalex.org/W2042784621","https://openalex.org/W2055043387","https://openalex.org/W2068011423","https://openalex.org/W2070373973","https://openalex.org/W2073783949","https://openalex.org/W2075363163","https://openalex.org/W2083648095","https://openalex.org/W2084620487","https://openalex.org/W2084908610","https://openalex.org/W2085538975","https://openalex.org/W2103017472","https://openalex.org/W2103465619","https://openalex.org/W2106882534","https://openalex.org/W2107432340","https://openalex.org/W2107903949","https://openalex.org/W2110291136","https://openalex.org/W2116688916","https://openalex.org/W2130035151","https://openalex.org/W2133147430","https://openalex.org/W2135722286","https://openalex.org/W2137427011","https://openalex.org/W2137458297","https://openalex.org/W2141408320","https://openalex.org/W2141885858","https://openalex.org/W2144857133","https://openalex.org/W2146453000","https://openalex.org/W2147154551","https://openalex.org/W2149754027","https://openalex.org/W2149769193","https://openalex.org/W2151464048","https://openalex.org/W2152295114","https://openalex.org/W2154514071","https://openalex.org/W2155144061","https://openalex.org/W2155997603","https://openalex.org/W2166898290","https://openalex.org/W2168148721","https://openalex.org/W2169351355","https://openalex.org/W2170698318","https://openalex.org/W2798682151","https://openalex.org/W4210400672","https://openalex.org/W4230932396","https://openalex.org/W4233051382","https://openalex.org/W4292239814"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W2162923930","https://openalex.org/W1985408726","https://openalex.org/W1482324242","https://openalex.org/W2759306076","https://openalex.org/W1981307089","https://openalex.org/W2029514038","https://openalex.org/W2117549173","https://openalex.org/W1502510273"],"abstract_inverted_index":{"We":[0,112],"address":[1],"the":[2,8,27,48,64,68,71,77,93,115,118,145,164],"problem":[3,21],"of":[4,11,30,51,58,70,80,97,117,126],"comparing":[5],"and":[6,75],"characterizing":[7],"promoter":[9,28],"regions":[10,29],"genes":[12,32],"with":[13,67],"similar":[14],"expression":[15],"patterns.":[16],"This":[17],"remains":[18],"a":[19,121],"challenging":[20],"in":[22,120,132,138],"sequence":[23,37,50,166],"analysis,":[24],"because":[25],"often":[26],"co-expressed":[31],"do":[33],"not":[34,45],"show":[35],"discernible":[36],"conservation.":[38],"In":[39],"our":[40],"approach,":[41],"thus,":[42],"we":[43,54,83,100],"have":[44,55,101,113],"directly":[46],"compared":[47],"nucleotide":[49],"promoters.":[52],"Instead,":[53],"obtained":[56],"predictions":[57],"transcription":[59,87],"factor":[60,88],"binding":[61,73],"sites,":[62],"annotated":[63],"predicted":[65],"sites":[66],"labels":[69],"corresponding":[72],"factors,":[74],"aligned":[76],"resulting":[78],"sequences":[79],"labels--to":[81],"which":[82,159],"refer":[84],"here":[85],"as":[86,135,137],"maps":[89],"(TF-maps).":[90],"To":[91],"obtain":[92],"global":[94],"pairwise":[95],"alignment":[96],"two":[98],"TF-maps,":[99],"adapted":[102],"an":[103,139],"algorithm":[104,119],"initially":[105],"developed":[106],"to":[107,154],"align":[108],"restriction":[109],"enzyme":[110],"maps.":[111],"optimized":[114],"parameters":[116],"small,":[122],"but":[123],"well-curated,":[124],"collection":[125],"human-mouse":[127],"orthologous":[128],"gene":[129],"pairs.":[130],"Results":[131],"this":[133],"dataset,":[134],"well":[136],"independent":[140],"much":[141],"larger":[142],"dataset":[143],"from":[144],"CISRED":[146],"database,":[147],"indicate":[148],"that":[149],"TF-map":[150],"alignments":[151],"are":[152],"able":[153],"uncover":[155],"conserved":[156],"regulatory":[157],"elements,":[158],"cannot":[160],"be":[161],"detected":[162],"by":[163],"typical":[165],"alignments.":[167]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":4},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":9}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}