{"id":"https://openalex.org/W1975420528","doi":"https://doi.org/10.1371/journal.pcbi.1000039","title":"Statistical Modeling of Transcription Factor Binding Affinities Predicts Regulatory Interactions","display_name":"Statistical Modeling of Transcription Factor Binding Affinities Predicts Regulatory Interactions","publication_year":2008,"publication_date":"2008-03-20","ids":{"openalex":"https://openalex.org/W1975420528","doi":"https://doi.org/10.1371/journal.pcbi.1000039","mag":"1975420528","pmid":"https://pubmed.ncbi.nlm.nih.gov/18369429"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1000039","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000039","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000039&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.1000039&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060587616","display_name":"Thomas Manke","orcid":"https://orcid.org/0000-0003-3702-0868"},"institutions":[{"id":"https://openalex.org/I149899117","display_name":"Max Planck Society","ror":"https://ror.org/01hhn8329","country_code":"DE","type":"funder","lineage":["https://openalex.org/I149899117"]},{"id":"https://openalex.org/I4210142260","display_name":"Max Planck Institute for Molecular Genetics","ror":"https://ror.org/03ate3e03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210142260"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Thomas Manke","raw_affiliation_strings":["Max Planck Institute for Molecular Genetics, Berlin, Germany. manke@molgen.mpg.de","Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society"],"affiliations":[{"raw_affiliation_string":"Max Planck Institute for Molecular Genetics, Berlin, Germany. manke@molgen.mpg.de","institution_ids":["https://openalex.org/I4210142260"]},{"raw_affiliation_string":"Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society","institution_ids":["https://openalex.org/I4210142260","https://openalex.org/I149899117"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047866999","display_name":"Helge G. Roider","orcid":"https://orcid.org/0000-0002-4614-5219"},"institutions":[{"id":"https://openalex.org/I4210142260","display_name":"Max Planck Institute for Molecular Genetics","ror":"https://ror.org/03ate3e03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210142260"]},{"id":"https://openalex.org/I149899117","display_name":"Max Planck Society","ror":"https://ror.org/01hhn8329","country_code":"DE","type":"funder","lineage":["https://openalex.org/I149899117"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Helge G. Roider","raw_affiliation_strings":["Max Planck Institute for Molecular Genetics, Berlin, Germany","Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society"],"affiliations":[{"raw_affiliation_string":"Max Planck Institute for Molecular Genetics, Berlin, Germany","institution_ids":["https://openalex.org/I4210142260"]},{"raw_affiliation_string":"Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society","institution_ids":["https://openalex.org/I4210142260","https://openalex.org/I149899117"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009628707","display_name":"Martin Vingron","orcid":"https://orcid.org/0000-0002-1765-4241"},"institutions":[{"id":"https://openalex.org/I149899117","display_name":"Max Planck Society","ror":"https://ror.org/01hhn8329","country_code":"DE","type":"funder","lineage":["https://openalex.org/I149899117"]},{"id":"https://openalex.org/I4210142260","display_name":"Max Planck Institute for Molecular Genetics","ror":"https://ror.org/03ate3e03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210142260"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Martin Vingron","raw_affiliation_strings":["Max Planck Institute for Molecular Genetics, Berlin, Germany","Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society"],"affiliations":[{"raw_affiliation_string":"Max Planck Institute for Molecular Genetics, Berlin, Germany","institution_ids":["https://openalex.org/I4210142260"]},{"raw_affiliation_string":"Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society","institution_ids":["https://openalex.org/I4210142260","https://openalex.org/I149899117"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5060587616"],"corresponding_institution_ids":["https://openalex.org/I149899117","https://openalex.org/I4210142260"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.3512,"has_fulltext":true,"cited_by_count":63,"citation_normalized_percentile":{"value":0.87955278,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"4","issue":"3","first_page":"e1000039","last_page":"e1000039"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9987999796867371,"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":0.9987999796867371,"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":0.982699990272522,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.970300018787384,"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/affinities","display_name":"Affinities","score":0.7413153648376465},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5250280499458313},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.4916728138923645},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49009621143341064},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.4835350513458252},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.4732556641101837},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.4660642743110657},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4560754597187042},{"id":"https://openalex.org/keywords/statistical-model","display_name":"Statistical model","score":0.4548126459121704},{"id":"https://openalex.org/keywords/binding-affinities","display_name":"Binding affinities","score":0.43049126863479614},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4217302203178406},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.359480082988739},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.32602620124816895},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.3072729706764221},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.20680251717567444},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.183040052652359},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.07165321707725525}],"concepts":[{"id":"https://openalex.org/C2780283098","wikidata":"https://www.wikidata.org/wiki/Q4688960","display_name":"Affinities","level":2,"score":0.7413153648376465},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5250280499458313},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.4916728138923645},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49009621143341064},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.4835350513458252},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.4732556641101837},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.4660642743110657},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4560754597187042},{"id":"https://openalex.org/C114289077","wikidata":"https://www.wikidata.org/wiki/Q3284399","display_name":"Statistical model","level":2,"score":0.4548126459121704},{"id":"https://openalex.org/C3018795828","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Binding affinities","level":3,"score":0.43049126863479614},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4217302203178406},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.359480082988739},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.32602620124816895},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.3072729706764221},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.20680251717567444},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.183040052652359},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.07165321707725525},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"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":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"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":"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":"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":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.pcbi.1000039","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000039","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000039&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:18369429","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18369429","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:pure.mpg.de:item_1584573","is_oa":true,"landing_page_url":"http://hdl.handle.net/11858/00-001M-0000-0010-8029-2","pdf_url":"https://hdl.handle.net/11858/00-001M-0000-0010-8028-4","source":{"id":"https://openalex.org/S4306400654","display_name":"MPG.PuRe (Max Planck Society)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:RePEc:plo:pcbi00:1000039","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000039","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:9c6f280385624fc6ab8c58e93a32beb7","is_oa":true,"landing_page_url":"https://doaj.org/article/9c6f280385624fc6ab8c58e93a32beb7","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"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 4, Iss 3, p e1000039 (2008)","raw_type":"article"},{"id":"pmh:oai:edoc.mpg.de:404420","is_oa":true,"landing_page_url":"http://edoc.mpg.de/404420","pdf_url":null,"source":{"id":"https://openalex.org/S4406922265","display_name":"Max Planck Institute for Plasma Physics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, v.4, e1000039-e1000039 (2008)","raw_type":"Article"},{"id":"pmh:oai:figshare.com:article/150774","is_oa":true,"landing_page_url":"https://figshare.com/articles/Statistical_Modeling_of_Transcription_Factor_Binding_Affinities_Predicts_Regulatory_Interactions/150774","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:pubmedcentral.nih.gov:2266803","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2266803","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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.1000039","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000039","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000039&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":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1975420528.pdf","grobid_xml":"https://content.openalex.org/works/W1975420528.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1498410508","https://openalex.org/W1500657154","https://openalex.org/W1753000577","https://openalex.org/W1984450450","https://openalex.org/W1986841498","https://openalex.org/W1989080074","https://openalex.org/W2004563262","https://openalex.org/W2015502807","https://openalex.org/W2049672602","https://openalex.org/W2053126761","https://openalex.org/W2079321730","https://openalex.org/W2100305057","https://openalex.org/W2108595723","https://openalex.org/W2111919009","https://openalex.org/W2118628540","https://openalex.org/W2126602684","https://openalex.org/W2127021450","https://openalex.org/W2137428312","https://openalex.org/W2137961581","https://openalex.org/W2141222206","https://openalex.org/W2166898290","https://openalex.org/W2751862591","https://openalex.org/W4210241463","https://openalex.org/W4248318091","https://openalex.org/W4299432846","https://openalex.org/W7038906009"],"related_works":["https://openalex.org/W3187200704","https://openalex.org/W2031259671","https://openalex.org/W3112966125","https://openalex.org/W2108080735","https://openalex.org/W1990832091","https://openalex.org/W2095596733","https://openalex.org/W4240532245","https://openalex.org/W1961356786","https://openalex.org/W1966443150","https://openalex.org/W4248477353"],"abstract_inverted_index":{"Recent":[0],"experimental":[1],"and":[2,135,205,220],"theoretical":[3],"efforts":[4],"have":[5],"highlighted":[6],"the":[7,39,55,74,87,113,191,197,244],"fact":[8],"that":[9,86,143],"binding":[10,26,36,40,58,141,182,228],"of":[11,24,35,57,90,103,149,177,186,202,242],"transcription":[12,94,137,164,214],"factors":[13,95,138,165,215],"to":[14,53,72,132,161,233,249],"DNA":[15],"can":[16,42,96,144,222,246],"be":[17,43,97,145,223,247],"more":[18],"accurately":[19],"described":[20,146],"by":[21,100,174],"continuous":[22],"measures":[23],"their":[25],"affinities,":[27],"rather":[28],"than":[29],"a":[30,46,69,101,150,158,209,217],"discrete":[31],"description":[32],"in":[33,147],"terms":[34,148],"sites.":[37],"While":[38],"affinities":[41,59],"predicted":[44],"from":[45],"physical":[47,203],"model,":[48],"it":[49],"is":[50,130,172],"often":[51],"desirable":[52],"know":[54],"distribution":[56,76,89,115],"for":[60,77,116,184,216],"specific":[61],"sequence":[62,78,117],"backgrounds.":[63],"In":[64],"this":[65,109],"paper,":[66],"we":[67,188],"present":[68],"statistical":[70,154,206],"approach":[71,129],"derive":[73],"exact":[75],"models":[79],"with":[80,119,139,166,180,196,226],"fixed":[81],"GC":[82,121],"content.":[83],"We":[84],"demonstrate":[85],"affinity":[88,114,169],"almost":[91],"all":[92,136],"known":[93,140,181,192],"effectively":[98],"parametrized":[99],"class":[102],"generalized":[104],"extreme":[105],"value":[106],"distributions.":[107,170],"Moreover,":[108],"parameterization":[110],"also":[111,156],"describes":[112],"backgrounds":[118],"variable":[120],"content,":[122],"such":[123],"as":[124,194,238],"human":[125,178,234],"promoter":[126,235],"sequences.":[127,251],"Our":[128],"applicable":[131],"arbitrary":[133],"sequences":[134,236],"preferences":[142],"motif":[151],"matrix.":[152],"The":[153,200],"treatment":[155],"provides":[157,208],"proper":[159],"framework":[160],"directly":[162,225],"compare":[163],"very":[167],"different":[168],"This":[171],"illustrated":[173],"our":[175],"analysis":[176],"promoters":[179],"sites,":[183],"many":[185],"which":[187,212,221],"could":[189],"identify":[190],"regulators":[193],"those":[195],"highest":[198],"affinity.":[199],"combination":[201],"model":[204],"normalization":[207],"quantitative":[210],"measure":[211],"ranks":[213],"given":[218],"sequence,":[219],"compared":[224],"large-scale":[227],"data.":[229],"Its":[230],"successful":[231],"application":[232],"serves":[237],"an":[239],"encouraging":[240],"example":[241],"how":[243],"method":[245],"applied":[248],"other":[250]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":3}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
