{"id":"https://openalex.org/W2096016699","doi":"https://doi.org/10.1093/bioinformatics/btp282","title":"Affinity Density: a novel genomic approach to the identification of transcription factor regulatory targets","display_name":"Affinity Density: a novel genomic approach to the identification of transcription factor regulatory targets","publication_year":2009,"publication_date":"2009-04-28","ids":{"openalex":"https://openalex.org/W2096016699","doi":"https://doi.org/10.1093/bioinformatics/btp282","mag":"2096016699","pmid":"https://pubmed.ncbi.nlm.nih.gov/19401399"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp282","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp282","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/13/1617/48996743/bioinformatics_25_13_1617.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/25/13/1617/48996743/bioinformatics_25_13_1617.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050826378","display_name":"Dennis J. Hazelett","orcid":"https://orcid.org/0000-0003-0749-9935"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dennis J. Hazelett","raw_affiliation_strings":["1 Integrative Biosciences, Oregon Health and Science University (OHSU), 611 SW Campus Dr SOD705, Portland, OR 97239, 2Independent Consultant, Los Angeles, CA and 3Department of Cardiology, Oregon Health and Science University (OHSU), 3303 SW Bond Ave CHH14W, Portland, OR 97239, USA"],"affiliations":[{"raw_affiliation_string":"1 Integrative Biosciences, Oregon Health and Science University (OHSU), 611 SW Campus Dr SOD705, Portland, OR 97239, 2Independent Consultant, Los Angeles, CA and 3Department of Cardiology, Oregon Health and Science University (OHSU), 3303 SW Bond Ave CHH14W, Portland, OR 97239, USA","institution_ids":["https://openalex.org/I165690674"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025929318","display_name":"Daniel L. Lakeland","orcid":"https://orcid.org/0000-0002-8204-4933"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel L. Lakeland","raw_affiliation_strings":["1 Integrative Biosciences, Oregon Health and Science University (OHSU), 611 SW Campus Dr SOD705, Portland, OR 97239, 2Independent Consultant, Los Angeles, CA and 3Department of Cardiology, Oregon Health and Science University (OHSU), 3303 SW Bond Ave CHH14W, Portland, OR 97239, USA"],"affiliations":[{"raw_affiliation_string":"1 Integrative Biosciences, Oregon Health and Science University (OHSU), 611 SW Campus Dr SOD705, Portland, OR 97239, 2Independent Consultant, Los Angeles, CA and 3Department of Cardiology, Oregon Health and Science University (OHSU), 3303 SW Bond Ave CHH14W, Portland, OR 97239, USA","institution_ids":["https://openalex.org/I165690674"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102976996","display_name":"Joseph B. Weiss","orcid":"https://orcid.org/0000-0003-3348-338X"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joseph B. Weiss","raw_affiliation_strings":["1 Integrative Biosciences, Oregon Health and Science University (OHSU), 611 SW Campus Dr SOD705, Portland, OR 97239, 2Independent Consultant, Los Angeles, CA and 3Department of Cardiology, Oregon Health and Science University (OHSU), 3303 SW Bond Ave CHH14W, Portland, OR 97239, USA"],"affiliations":[{"raw_affiliation_string":"1 Integrative Biosciences, Oregon Health and Science University (OHSU), 611 SW Campus Dr SOD705, Portland, OR 97239, 2Independent Consultant, Los Angeles, CA and 3Department of Cardiology, Oregon Health and Science University (OHSU), 3303 SW Bond Ave CHH14W, Portland, OR 97239, USA","institution_ids":["https://openalex.org/I165690674"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5050826378"],"corresponding_institution_ids":["https://openalex.org/I165690674"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.1344,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.5506202,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"25","issue":"13","first_page":"1617","last_page":"1624"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9994999766349792,"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":0.9994999766349792,"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/T12929","display_name":"Animal Genetics and Reproduction","score":0.9973999857902527,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.9951000213623047,"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/biology","display_name":"Biology","score":0.6571182012557983},{"id":"https://openalex.org/keywords/drosophila-melanogaster","display_name":"Drosophila melanogaster","score":0.597252607345581},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5927895307540894},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5657589435577393},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.526854395866394},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5162646770477295},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4748792052268982},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.20989465713500977},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.11847278475761414}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6571182012557983},{"id":"https://openalex.org/C2780104201","wikidata":"https://www.wikidata.org/wiki/Q130888","display_name":"Drosophila melanogaster","level":3,"score":0.597252607345581},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5927895307540894},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5657589435577393},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.526854395866394},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5162646770477295},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4748792052268982},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.20989465713500977},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.11847278475761414}],"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":"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":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btp282","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp282","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/13/1617/48996743/bioinformatics_25_13_1617.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19401399","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19401399","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:pubmedcentral.nih.gov:2732317","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2732317","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp282","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp282","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/13/1617/48996743/bioinformatics_25_13_1617.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.7300000190734863,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2096016699.pdf","grobid_xml":"https://content.openalex.org/works/W2096016699.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W17849359","https://openalex.org/W1898282649","https://openalex.org/W1964244769","https://openalex.org/W1964773110","https://openalex.org/W1972553552","https://openalex.org/W1973476220","https://openalex.org/W1973738440","https://openalex.org/W1975538460","https://openalex.org/W1980253661","https://openalex.org/W1980366949","https://openalex.org/W1983075472","https://openalex.org/W1999555880","https://openalex.org/W2008448536","https://openalex.org/W2012040988","https://openalex.org/W2017746806","https://openalex.org/W2022342905","https://openalex.org/W2034719432","https://openalex.org/W2040686597","https://openalex.org/W2042524484","https://openalex.org/W2045310150","https://openalex.org/W2058552632","https://openalex.org/W2061772063","https://openalex.org/W2070630477","https://openalex.org/W2080071785","https://openalex.org/W2093008096","https://openalex.org/W2105796031","https://openalex.org/W2107768450","https://openalex.org/W2109412588","https://openalex.org/W2111525541","https://openalex.org/W2112221859","https://openalex.org/W2117549173","https://openalex.org/W2117904145","https://openalex.org/W2120610134","https://openalex.org/W2135720963","https://openalex.org/W2142946358","https://openalex.org/W2148944713","https://openalex.org/W2155717510","https://openalex.org/W2157674573","https://openalex.org/W2293599327","https://openalex.org/W2343326981"],"related_works":["https://openalex.org/W2587366952","https://openalex.org/W2393920775","https://openalex.org/W2944994818","https://openalex.org/W2379997263","https://openalex.org/W2367493320","https://openalex.org/W2112717966","https://openalex.org/W2131580913","https://openalex.org/W2125854412","https://openalex.org/W3083097828","https://openalex.org/W2499916532"],"abstract_inverted_index":{"Algorithms":[0],"were":[1],"implemented":[2],"in":[3],"Python,":[4],"LISP,":[5],"R":[6],"and":[7,22,31],"maxima,":[8],"using":[9],"MySQL":[10],"to":[11],"access":[12],"locally":[13],"mirrored":[14],"sequence":[15],"data":[16],"from":[17],"Ensembl":[18],"(D.melanogaster":[19],"release":[20],"4.3)":[21],"flybase":[23],"(D.pseudoobscura).":[24],"All":[25],"code":[26],"is":[27],"licensed":[28],"under":[29],"GPL":[30],"freely":[32],"available":[33],"at":[34],"http://www.ohsu.edu/cellbio/dev_biol_prog/affinitydensity/.":[35]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}