{"id":"https://openalex.org/W4390904763","doi":"https://doi.org/10.1371/journal.pcbi.1011802","title":"Transcription factor interactions explain the context-dependent activity of CRX binding sites","display_name":"Transcription factor interactions explain the context-dependent activity of CRX binding sites","publication_year":2024,"publication_date":"2024-01-16","ids":{"openalex":"https://openalex.org/W4390904763","doi":"https://doi.org/10.1371/journal.pcbi.1011802","pmid":"https://pubmed.ncbi.nlm.nih.gov/38227575"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011802","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011802","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011802&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.1011802&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053554337","display_name":"Kaiser Loell","orcid":"https://orcid.org/0000-0001-7076-6659"},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kaiser J. Loell","raw_affiliation_strings":["Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America","The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037912811","display_name":"Ryan Z. Friedman","orcid":"https://orcid.org/0000-0001-9013-8676"},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ryan Z. Friedman","raw_affiliation_strings":["Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America","The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-9013-8676","affiliations":[{"raw_affiliation_string":"Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108831754","display_name":"Connie A. Myers","orcid":null},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Connie A. Myers","raw_affiliation_strings":["Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060159232","display_name":"Joseph C. Corbo","orcid":"https://orcid.org/0000-0002-9323-7140"},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joseph C. Corbo","raw_affiliation_strings":["Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039532116","display_name":"Barak A. Cohen","orcid":"https://orcid.org/0000-0002-3350-2715"},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Barak A. Cohen","raw_affiliation_strings":["Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America","The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066016110","display_name":"Michael A. White","orcid":"https://orcid.org/0000-0001-8511-6026"},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michael A. White","raw_affiliation_strings":["Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America","The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-8511-6026","affiliations":[{"raw_affiliation_string":"Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5066016110"],"corresponding_institution_ids":["https://openalex.org/I204465549"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.2407,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.87963681,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"20","issue":"1","first_page":"e1011802","last_page":"e1011802"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10691","display_name":"Retinal Development and Disorders","score":0.9968000054359436,"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/T10691","display_name":"Retinal Development and Disorders","score":0.9968000054359436,"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/T12610","display_name":"RNA regulation and disease","score":0.9886999726295471,"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/T10617","display_name":"Cellular transport and secretion","score":0.9465000033378601,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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":0.6961871385574341},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5386126041412354},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.48895204067230225},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.4729311764240265},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4601500630378723},{"id":"https://openalex.org/keywords/plasma-protein-binding","display_name":"Plasma protein binding","score":0.41637688875198364},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3970698118209839},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.35787755250930786},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.26060551404953003},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1586971879005432},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1175483763217926},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.09054821729660034}],"concepts":[{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.6961871385574341},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5386126041412354},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.48895204067230225},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.4729311764240265},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4601500630378723},{"id":"https://openalex.org/C51639874","wikidata":"https://www.wikidata.org/wiki/Q167149","display_name":"Plasma protein binding","level":2,"score":0.41637688875198364},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3970698118209839},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.35787755250930786},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.26060551404953003},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1586971879005432},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1175483763217926},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.09054821729660034},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012160","descriptor_name":"Retina","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012160","descriptor_name":"Retina","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012160","descriptor_name":"Retina","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012160","descriptor_name":"Retina","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012160","descriptor_name":"Retina","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012160","descriptor_name":"Retina","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015534","descriptor_name":"Trans-Activators","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015534","descriptor_name":"Trans-Activators","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015534","descriptor_name":"Trans-Activators","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015534","descriptor_name":"Trans-Activators","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015534","descriptor_name":"Trans-Activators","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015534","descriptor_name":"Trans-Activators","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D018398","descriptor_name":"Homeodomain Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018398","descriptor_name":"Homeodomain Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018398","descriptor_name":"Homeodomain Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018398","descriptor_name":"Homeodomain Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018398","descriptor_name":"Homeodomain Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018398","descriptor_name":"Homeodomain Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1011802","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011802","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011802&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:38227575","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38227575","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:pubmedcentral.nih.gov:10817189","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10817189","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10817189/pdf/pcbi.1011802.pdf","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"},{"id":"pmh:oai:digitalcommons.wustl.edu:oa_4-4092","is_oa":true,"landing_page_url":"https://digitalcommons.wustl.edu/oa_4/3105","pdf_url":null,"source":{"id":"https://openalex.org/S4306400764","display_name":"Digital Commons@Becker (Washington University School of Medicine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I204465549","host_organization_name":"Washington University in St. Louis","host_organization_lineage":["https://openalex.org/I204465549"],"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":"2020-Current year OA Pubs","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:23ab48da7da341368da6f3e8978fd5ec","is_oa":true,"landing_page_url":"https://doaj.org/article/23ab48da7da341368da6f3e8978fd5ec","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 20, Iss 1, p e1011802 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011802","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011802","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011802&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":[{"id":"https://openalex.org/G1007394735","display_name":null,"funder_award_id":"EY030075","funder_id":"https://openalex.org/F4320337350","funder_display_name":"National Eye Institute"},{"id":"https://openalex.org/G1233985242","display_name":null,"funder_award_id":"R01 GM092910","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2018256535","display_name":"DISCOVERY OF DNA DETERMINANTS OF TRANSCRIPTION FACTOR BINDING AND FUNCTION IN PHO","funder_award_id":"5r01gm121755-05","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2653103420","display_name":null,"funder_award_id":"GM121755","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3230965671","display_name":null,"funder_award_id":"HL149961","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G5178570048","display_name":null,"funder_award_id":"F31 HG011431","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G5276146136","display_name":"Elucidating the cis-regulatory grammar of human photoreceptors","funder_award_id":"5r01ey030075-04","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5450694340","display_name":null,"funder_award_id":"R01 EY030075","funder_id":"https://openalex.org/F4320337350","funder_display_name":"National Eye Institute"},{"id":"https://openalex.org/G567085343","display_name":null,"funder_award_id":"MH122451","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"},{"id":"https://openalex.org/G6463630380","display_name":null,"funder_award_id":"R01 HL149961","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G651082115","display_name":"Analysis of combinatorial cis-regulation in synthetic and genomic promoters","funder_award_id":"2r01gm092910-13","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7026665502","display_name":null,"funder_award_id":"R01 MH122451","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"},{"id":"https://openalex.org/G7030179470","display_name":null,"funder_award_id":"R01 GM121755","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7436242911","display_name":null,"funder_award_id":"HG011431","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G8694168126","display_name":null,"funder_award_id":"GM092910","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337350","display_name":"National Eye Institute","ror":"https://ror.org/03wkg3b53"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4390904763.pdf"},"referenced_works_count":105,"referenced_works":["https://openalex.org/W1525882285","https://openalex.org/W1585313030","https://openalex.org/W1844738640","https://openalex.org/W1962652794","https://openalex.org/W1964629749","https://openalex.org/W1974913126","https://openalex.org/W1980504985","https://openalex.org/W1980507776","https://openalex.org/W1981411229","https://openalex.org/W1993392563","https://openalex.org/W1997767982","https://openalex.org/W2001770641","https://openalex.org/W2002964220","https://openalex.org/W2008047506","https://openalex.org/W2017244785","https://openalex.org/W2017826121","https://openalex.org/W2022891974","https://openalex.org/W2024520070","https://openalex.org/W2027066480","https://openalex.org/W2027368464","https://openalex.org/W2027469999","https://openalex.org/W2036363416","https://openalex.org/W2045362835","https://openalex.org/W2049890303","https://openalex.org/W2056026334","https://openalex.org/W2059344357","https://openalex.org/W2062075767","https://openalex.org/W2067899297","https://openalex.org/W2072414883","https://openalex.org/W2081710784","https://openalex.org/W2083823883","https://openalex.org/W2086411786","https://openalex.org/W2086876386","https://openalex.org/W2099105062","https://openalex.org/W2111760909","https://openalex.org/W2112500061","https://openalex.org/W2114715558","https://openalex.org/W2125427437","https://openalex.org/W2125716773","https://openalex.org/W2136899592","https://openalex.org/W2141215651","https://openalex.org/W2142644426","https://openalex.org/W2143855992","https://openalex.org/W2145674897","https://openalex.org/W2145694460","https://openalex.org/W2147635933","https://openalex.org/W2150796809","https://openalex.org/W2153115129","https://openalex.org/W2154840766","https://openalex.org/W2155015939","https://openalex.org/W2157191738","https://openalex.org/W2159864583","https://openalex.org/W2159933659","https://openalex.org/W2166691503","https://openalex.org/W2168735550","https://openalex.org/W2307093200","https://openalex.org/W2337928212","https://openalex.org/W2475324019","https://openalex.org/W2536763320","https://openalex.org/W2556513628","https://openalex.org/W2565717971","https://openalex.org/W2581468399","https://openalex.org/W2591919483","https://openalex.org/W2620848075","https://openalex.org/W2760114054","https://openalex.org/W2769983384","https://openalex.org/W2784779095","https://openalex.org/W2888553721","https://openalex.org/W2889201683","https://openalex.org/W2901183331","https://openalex.org/W2946122061","https://openalex.org/W2951045203","https://openalex.org/W2953306855","https://openalex.org/W2997652628","https://openalex.org/W2998961866","https://openalex.org/W3000870857","https://openalex.org/W3006431270","https://openalex.org/W3008725968","https://openalex.org/W3015016698","https://openalex.org/W3023043220","https://openalex.org/W3045747015","https://openalex.org/W3045910546","https://openalex.org/W3046196569","https://openalex.org/W3092493149","https://openalex.org/W3103238209","https://openalex.org/W3125946770","https://openalex.org/W3133716533","https://openalex.org/W3133944950","https://openalex.org/W3134994147","https://openalex.org/W3137739829","https://openalex.org/W3192469487","https://openalex.org/W3197459873","https://openalex.org/W4213140257","https://openalex.org/W4226162236","https://openalex.org/W4280563114","https://openalex.org/W4291019836","https://openalex.org/W4294897896","https://openalex.org/W4294898368","https://openalex.org/W4308774215","https://openalex.org/W4312062050","https://openalex.org/W4362607738","https://openalex.org/W4366372506","https://openalex.org/W4366769693","https://openalex.org/W4378551232","https://openalex.org/W4391805471"],"related_works":["https://openalex.org/W2036927633","https://openalex.org/W2152664145","https://openalex.org/W2153561273","https://openalex.org/W2079197459","https://openalex.org/W2379997263","https://openalex.org/W2165899269","https://openalex.org/W2236968607","https://openalex.org/W1570348606","https://openalex.org/W1557222478","https://openalex.org/W2131580913"],"abstract_inverted_index":{"The":[0,84,116,145],"effects":[1,117],"of":[2,11,56,66,77,81,108,118,128,148,163,174],"transcription":[3,29,57],"factor":[4,30],"binding":[5,25,49,89],"sites":[6,26,50,90,104,111,137,150],"(TFBSs)":[7],"on":[8,17],"the":[9,18,28,42,63,75,126,155],"activity":[10,65,147,175],"a":[12],"cis-regulatory":[13],"element":[14],"(CRE)":[15],"depend":[16],"local":[19],"sequence":[20,43],"context.":[21],"In":[22],"rod":[23],"photoreceptors,":[24],"for":[27],"(TF)":[31],"Cone-rod":[32],"homeobox":[33],"(CRX)":[34],"occur":[35],"in":[36],"both":[37],"enhancers":[38,179,185],"and":[39,165,180,182],"silencers,":[40,181],"but":[41],"context":[44],"that":[45,87,131,184],"determines":[46],"whether":[47],"CRX":[48,67,88,110,136,149],"contribute":[51],"to":[52,74,96,112,143,190],"activation":[53],"or":[54,138],"repression":[55],"is":[58,151],"not":[59],"understood.":[60],"To":[61],"investigate":[62],"context-dependent":[64,146],"sites,":[68],"we":[69],"fit":[70],"neural":[71],"network-based":[72],"models":[73,85],"activities":[76],"synthetic":[78],"CREs":[79,106],"composed":[80,107],"photoreceptor":[82],"TFBSs.":[83,196],"revealed":[86],"consistently":[91],"make":[92,139],"positive,":[93],"independent":[94,140,161],"contributions":[95,142,162],"CRE":[97],"activity,":[98],"while":[99],"negative":[100,119,166,192],"homotypic":[101,120,167,193],"interactions":[102,121,194],"between":[103,157,195],"cause":[105],"multiple":[109],"function":[113],"as":[114],"silencers.":[115],"can":[122],"be":[123],"overcome":[124,191],"by":[125,154],"presence":[127],"other":[129],"TFBSs":[130,189],"either":[132],"interact":[133],"cooperatively":[134],"with":[135],"positive":[141,158],"activity.":[144],"thus":[152],"determined":[153],"balance":[156],"heterotypic":[159],"interactions,":[160],"TFBSs,":[164],"interactions.":[168],"Our":[169],"findings":[170],"explain":[171],"observed":[172],"patterns":[173],"among":[176],"genomic":[177],"CRX-bound":[178],"suggest":[183],"may":[186],"require":[187],"diverse":[188]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":1}],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2025-10-10T00:00:00"}
