{"id":"https://openalex.org/W2135243774","doi":"https://doi.org/10.1093/bioinformatics/btl251","title":"Informative priors based on transcription factor structural class improve <i>de novo</i> motif discovery","display_name":"Informative priors based on transcription factor structural class improve <i>de novo</i> motif discovery","publication_year":2006,"publication_date":"2006-07-15","ids":{"openalex":"https://openalex.org/W2135243774","doi":"https://doi.org/10.1093/bioinformatics/btl251","mag":"2135243774","pmid":"https://pubmed.ncbi.nlm.nih.gov/16873497"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btl251","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl251","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/14/e384/616768/btl251.pdf","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/22/14/e384/616768/btl251.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078875370","display_name":"Leelavati Narlikar","orcid":"https://orcid.org/0000-0001-6820-1878"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Leelavati Narlikar","raw_affiliation_strings":["Department of Computer Science, Duke University 1 \u00a0 1 \u00a0 \u00a0 Durham, NC 27708"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Duke University 1 \u00a0 1 \u00a0 \u00a0 Durham, NC 27708","institution_ids":["https://openalex.org/I170897317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082030263","display_name":"Raluca Gord\u00e2n","orcid":"https://orcid.org/0000-0002-6404-6556"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Raluca Gord\u00e2n","raw_affiliation_strings":["Department of Computer Science, Duke University 1 \u00a0 1 \u00a0 \u00a0 Durham, NC 27708"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Duke University 1 \u00a0 1 \u00a0 \u00a0 Durham, NC 27708","institution_ids":["https://openalex.org/I170897317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000077668","display_name":"Uwe Ohler","orcid":"https://orcid.org/0000-0002-0881-3116"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Uwe Ohler","raw_affiliation_strings":["Department of Computer Science, Duke University 1 \u00a0 1 \u00a0 \u00a0 Durham, NC 27708","Institute for Genome Sciences and Policy, Duke University 2 \u00a0 2 \u00a0 \u00a0 Durham, NC 27708"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Duke University 1 \u00a0 1 \u00a0 \u00a0 Durham, NC 27708","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"Institute for Genome Sciences and Policy, Duke University 2 \u00a0 2 \u00a0 \u00a0 Durham, NC 27708","institution_ids":["https://openalex.org/I170897317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026273992","display_name":"Alexander J. Hartemink","orcid":"https://orcid.org/0000-0002-1292-2606"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Alexander J. Hartemink","raw_affiliation_strings":["Department of Computer Science, Duke University 1 \u00a0 1 \u00a0 \u00a0 Durham, NC 27708","Institute for Genome Sciences and Policy, Duke University 2 \u00a0 2 \u00a0 \u00a0 Durham, NC 27708"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Duke University 1 \u00a0 1 \u00a0 \u00a0 Durham, NC 27708","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"Institute for Genome Sciences and Policy, Duke University 2 \u00a0 2 \u00a0 \u00a0 Durham, NC 27708","institution_ids":["https://openalex.org/I170897317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5000077668","https://openalex.org/A5026273992","https://openalex.org/A5078875370","https://openalex.org/A5082030263"],"corresponding_institution_ids":["https://openalex.org/I170897317"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.7261,"has_fulltext":true,"cited_by_count":57,"citation_normalized_percentile":{"value":0.9003546,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"22","issue":"14","first_page":"e384","last_page":"e392"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9822999835014343,"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":0.9822999835014343,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.004800000227987766,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.004699999932199717,"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/transcription-factor","display_name":"Transcription factor","score":0.6537171602249146},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6355085372924805},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.6224815249443054},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.6154036521911621},{"id":"https://openalex.org/keywords/basic-helix-loop-helix","display_name":"Basic helix-loop-helix","score":0.5998642444610596},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.5087049603462219},{"id":"https://openalex.org/keywords/structural-motif","display_name":"Structural motif","score":0.4930536448955536},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.4863896667957306},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4655146598815918},{"id":"https://openalex.org/keywords/prior-probability","display_name":"Prior probability","score":0.43240252137184143},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.4320959448814392},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4136640429496765},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.39830726385116577},{"id":"https://openalex.org/keywords/dna-binding-protein","display_name":"DNA-binding protein","score":0.32158321142196655},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18641811609268188},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.17666855454444885},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.14028966426849365}],"concepts":[{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.6537171602249146},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6355085372924805},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.6224815249443054},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.6154036521911621},{"id":"https://openalex.org/C6174537","wikidata":"https://www.wikidata.org/wiki/Q377955","display_name":"Basic helix-loop-helix","level":5,"score":0.5998642444610596},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.5087049603462219},{"id":"https://openalex.org/C132677234","wikidata":"https://www.wikidata.org/wiki/Q3273544","display_name":"Structural motif","level":2,"score":0.4930536448955536},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.4863896667957306},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4655146598815918},{"id":"https://openalex.org/C177769412","wikidata":"https://www.wikidata.org/wiki/Q278090","display_name":"Prior probability","level":3,"score":0.43240252137184143},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4320959448814392},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4136640429496765},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39830726385116577},{"id":"https://openalex.org/C94966510","wikidata":"https://www.wikidata.org/wiki/Q2252764","display_name":"DNA-binding protein","level":4,"score":0.32158321142196655},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18641811609268188},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.17666855454444885},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.14028966426849365},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"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":"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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000145","qualifier_name":"classification","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":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btl251","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl251","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/14/e384/616768/btl251.pdf","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16873497","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16873497","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btl251","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl251","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/14/e384/616768/btl251.pdf","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6671297155","display_name":null,"funder_award_id":"CAREER","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2135243774.pdf","grobid_xml":"https://content.openalex.org/works/W2135243774.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W1530964327","https://openalex.org/W1544729927","https://openalex.org/W1592870802","https://openalex.org/W1975036436","https://openalex.org/W1987122345","https://openalex.org/W1996270170","https://openalex.org/W2007969038","https://openalex.org/W2025868820","https://openalex.org/W2027662098","https://openalex.org/W2033765726","https://openalex.org/W2035564383","https://openalex.org/W2049633694","https://openalex.org/W2054624670","https://openalex.org/W2073850887","https://openalex.org/W2077013196","https://openalex.org/W2078143516","https://openalex.org/W2080498142","https://openalex.org/W2081189755","https://openalex.org/W2083875149","https://openalex.org/W2084620487","https://openalex.org/W2084908610","https://openalex.org/W2088228878","https://openalex.org/W2092742937","https://openalex.org/W2101025813","https://openalex.org/W2103325210","https://openalex.org/W2103453943","https://openalex.org/W2110403456","https://openalex.org/W2121356022","https://openalex.org/W2140115103","https://openalex.org/W2145218186","https://openalex.org/W2146393977","https://openalex.org/W2148711195","https://openalex.org/W2150579376","https://openalex.org/W2162829784","https://openalex.org/W2166740584","https://openalex.org/W2610493035","https://openalex.org/W2900434634","https://openalex.org/W3139846067","https://openalex.org/W4249255000","https://openalex.org/W4298255402","https://openalex.org/W4302434451","https://openalex.org/W6602670149","https://openalex.org/W6604813197"],"related_works":["https://openalex.org/W2044328609","https://openalex.org/W2145627818","https://openalex.org/W2127161698","https://openalex.org/W3089376739","https://openalex.org/W2951273973","https://openalex.org/W2019160435","https://openalex.org/W2473539711","https://openalex.org/W2048594737","https://openalex.org/W4288716296","https://openalex.org/W2135243774"],"abstract_inverted_index":{"MOTIVATION:":[0],"An":[1],"important":[2],"problem":[3],"in":[4,41,72,174],"molecular":[5],"biology":[6],"is":[7,49],"to":[8,19,28,51,79,148,167,176,180,197,208,221],"identify":[9],"the":[10,42,53,57,122,217,226,230,233],"locations":[11,71],"at":[12,116,245],"which":[13,70],"a":[14,22,46,111,131,177,190],"transcription":[15],"factor":[16],"(TF)":[17],"binds":[18,60],"DNA,":[20],"given":[21],"set":[23],"of":[24,45,56,85,124,152,183,192,199,229],"DNA":[25,43,74],"sequences":[26],"believed":[27],"be":[29,80,101,209,243],"bound":[30,81,210],"by":[31,82,104,206,211],"that":[32,39,59,66,92,110,203],"TF.":[33],"In":[34,62],"previous":[35],"work,":[36],"we":[37,67,90,128,144],"showed":[38],"information":[40],"sequence":[44,75,118],"binding":[47,113,150,235],"site":[48,114],"sufficient":[50],"predict":[52,69],"structural":[54,227],"class":[55,228],"TF":[58,112,231],"it.":[61],"particular,":[63],"this":[64],"suggests":[65],"can":[68,100,242],"any":[73],"are":[76,165,204],"more":[77],"likely":[78],"certain":[83],"classes":[84],"TFs":[86,182],"than":[87],"others.":[88],"Here,":[89],"argue":[91],"traditional":[93],"methods":[94,219],"for":[95],"de":[96,134],"novo":[97,135],"motif":[98,136,194],"finding":[99,137,195],"significantly":[102],"improved":[103],"adopting":[105],"an":[106,126],"informative":[107],"prior":[108,179],"probability":[109],"occurs":[115],"each":[117],"location.":[119],"To":[120],"demonstrate":[121],"utility":[123],"such":[125],"approach,":[127],"present":[129],"priority,":[130],"powerful":[132],"new":[133],"algorithm.":[138],"RESULTS:":[139],"Using":[140],"data":[141],"from":[142],"TRANSFAC,":[143],"train":[145],"three":[146,171],"classifiers":[147,164],"recognize":[149],"sites":[151],"basic":[153,158],"leucine":[154],"zipper,":[155],"forkhead,":[156],"and":[157,189,223,240],"helix":[159,161],"loop":[160],"TFs.":[162,213],"These":[163],"used":[166],"equip":[168],"priority":[169,188,214],"with":[170],"class-specific":[172],"priors,":[173],"addition":[175],"default":[178],"handle":[181],"other":[184,218],"classes.":[185],"We":[186],"apply":[187],"number":[191],"popular":[193],"programs":[196],"sets":[198],"yeast":[200],"intergenic":[201],"regions":[202],"reported":[205],"ChIP-chip":[207],"particular":[212],"identifies":[215],"motifs":[216],"fail":[220],"identify,":[222],"correctly":[224],"predicts":[225],"recognizing":[232],"identified":[234],"sites.":[236],"AVAILABILITY:":[237],"Supplementary":[238],"material":[239],"code":[241],"found":[244],"http://www.cs.duke.edu/~amink/.":[246]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":10}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2016-06-24T00:00:00"}