{"id":"https://openalex.org/W3189024040","doi":"https://doi.org/10.1371/journal.pcbi.1009256","title":"Computational identification and experimental characterization of preferred downstream positions in human core promoters","display_name":"Computational identification and experimental characterization of preferred downstream positions in human core promoters","publication_year":2021,"publication_date":"2021-08-12","ids":{"openalex":"https://openalex.org/W3189024040","doi":"https://doi.org/10.1371/journal.pcbi.1009256","mag":"3189024040","pmid":"https://pubmed.ncbi.nlm.nih.gov/34383743"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1009256","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009256","pdf_url":null,"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://doi.org/10.1371/journal.pcbi.1009256","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017962316","display_name":"Ren\u00e9 Dreos","orcid":"https://orcid.org/0000-0002-0816-7775"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Ren\u00e9 Dreos","raw_affiliation_strings":["Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-0816-7775","affiliations":[{"raw_affiliation_string":"Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076096212","display_name":"Anna Sloutskin","orcid":"https://orcid.org/0000-0003-2076-1141"},"institutions":[{"id":"https://openalex.org/I13955877","display_name":"Bar-Ilan University","ror":"https://ror.org/03kgsv495","country_code":"IL","type":"education","lineage":["https://openalex.org/I13955877"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Anna Sloutskin","raw_affiliation_strings":["The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel"],"raw_orcid":"https://orcid.org/0000-0003-2076-1141","affiliations":[{"raw_affiliation_string":"The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel","institution_ids":["https://openalex.org/I13955877"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006982391","display_name":"Nati Malachi","orcid":"https://orcid.org/0009-0005-5790-0311"},"institutions":[{"id":"https://openalex.org/I13955877","display_name":"Bar-Ilan University","ror":"https://ror.org/03kgsv495","country_code":"IL","type":"education","lineage":["https://openalex.org/I13955877"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Nati Malachi","raw_affiliation_strings":["The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel","institution_ids":["https://openalex.org/I13955877"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022454722","display_name":"Diana Ideses","orcid":null},"institutions":[{"id":"https://openalex.org/I13955877","display_name":"Bar-Ilan University","ror":"https://ror.org/03kgsv495","country_code":"IL","type":"education","lineage":["https://openalex.org/I13955877"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Diana Ideses","raw_affiliation_strings":["The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel","institution_ids":["https://openalex.org/I13955877"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103270230","display_name":"Philipp B\u00fccher","orcid":"https://orcid.org/0000-0003-4824-885X"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Philipp Bucher","raw_affiliation_strings":["School of Life Sciences, Swiss Federal Institute of Technology, Lausanne, Switzerland","Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland"],"raw_orcid":"https://orcid.org/0000-0003-4824-885X","affiliations":[{"raw_affiliation_string":"School of Life Sciences, Swiss Federal Institute of Technology, Lausanne, Switzerland","institution_ids":["https://openalex.org/I5124864"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020739453","display_name":"Tamar Juven\u2010Gershon","orcid":"https://orcid.org/0000-0003-2607-5476"},"institutions":[{"id":"https://openalex.org/I13955877","display_name":"Bar-Ilan University","ror":"https://ror.org/03kgsv495","country_code":"IL","type":"education","lineage":["https://openalex.org/I13955877"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Tamar Juven-Gershon","raw_affiliation_strings":["The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel"],"raw_orcid":"https://orcid.org/0000-0003-2607-5476","affiliations":[{"raw_affiliation_string":"The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel","institution_ids":["https://openalex.org/I13955877"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5020739453","https://openalex.org/A5103270230"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I13955877","https://openalex.org/I5124864"],"apc_list":{"value":2575,"currency":"USD","value_usd":2575},"apc_paid":{"value":2575,"currency":"USD","value_usd":2575},"fwci":0.2984,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.52516839,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":97},"biblio":{"volume":"17","issue":"8","first_page":"e1009256","last_page":"e1009256"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":1.0,"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":1.0,"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":0.9987000226974487,"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/T10604","display_name":"RNA Research and Splicing","score":0.9970999956130981,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.9130244851112366},{"id":"https://openalex.org/keywords/rna-polymerase-ii","display_name":"RNA polymerase II","score":0.6445509195327759},{"id":"https://openalex.org/keywords/tata-box","display_name":"TATA box","score":0.5598785877227783},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5413340330123901},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5018365383148193},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4936128854751587},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.48730766773223877},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.456053227186203},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.44041356444358826},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.4314311742782593},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.29161521792411804},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.12065878510475159}],"concepts":[{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.9130244851112366},{"id":"https://openalex.org/C64350747","wikidata":"https://www.wikidata.org/wiki/Q15334993","display_name":"RNA polymerase II","level":5,"score":0.6445509195327759},{"id":"https://openalex.org/C65888428","wikidata":"https://www.wikidata.org/wiki/Q1413955","display_name":"TATA box","level":5,"score":0.5598785877227783},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5413340330123901},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5018365383148193},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4936128854751587},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.48730766773223877},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.456053227186203},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.44041356444358826},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.4314311742782593},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.29161521792411804},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.12065878510475159},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"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":"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":"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":"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":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012319","descriptor_name":"RNA Polymerase II","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012319","descriptor_name":"RNA Polymerase II","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012319","descriptor_name":"RNA Polymerase II","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","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":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016385","descriptor_name":"TATA Box","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016385","descriptor_name":"TATA Box","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016385","descriptor_name":"TATA Box","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057809","descriptor_name":"HEK293 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057809","descriptor_name":"HEK293 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057809","descriptor_name":"HEK293 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1009256","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009256","pdf_url":null,"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:34383743","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34383743","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":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8384218","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8384218","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1009256","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009256","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:a78d4bd839e24933a5d03afa2c49c7c6","is_oa":true,"landing_page_url":"https://doaj.org/article/a78d4bd839e24933a5d03afa2c49c7c6","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 17, Iss 8, p e1009256 (2021)","raw_type":"article"},{"id":"pmh:oai:infoscience.epfl.ch:288112","is_oa":true,"landing_page_url":"http://infoscience.epfl.ch/record/288112","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I5124864","host_organization_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","host_organization_lineage":["https://openalex.org/I5124864"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"research article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1009256","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009256","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.5199999809265137,"id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G3211312752","display_name":null,"funder_award_id":"798/10","funder_id":"https://openalex.org/F4320322252","funder_display_name":"Israel Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320321449","display_name":"Bar-Ilan University","ror":"https://ror.org/03kgsv495"},{"id":"https://openalex.org/F4320322252","display_name":"Israel Science Foundation","ror":"https://ror.org/04sazxf24"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":72,"referenced_works":["https://openalex.org/W1562374859","https://openalex.org/W1841597658","https://openalex.org/W1950152486","https://openalex.org/W1971456303","https://openalex.org/W1972813594","https://openalex.org/W1979028385","https://openalex.org/W1980645953","https://openalex.org/W1986223165","https://openalex.org/W2028381655","https://openalex.org/W2029492292","https://openalex.org/W2029947491","https://openalex.org/W2034785524","https://openalex.org/W2038010573","https://openalex.org/W2047366906","https://openalex.org/W2057692691","https://openalex.org/W2064390432","https://openalex.org/W2070170431","https://openalex.org/W2077132193","https://openalex.org/W2079124813","https://openalex.org/W2083073732","https://openalex.org/W2086916162","https://openalex.org/W2094385715","https://openalex.org/W2094972443","https://openalex.org/W2097140065","https://openalex.org/W2097353028","https://openalex.org/W2097920884","https://openalex.org/W2099397128","https://openalex.org/W2101079676","https://openalex.org/W2101794645","https://openalex.org/W2102473929","https://openalex.org/W2104467425","https://openalex.org/W2108712717","https://openalex.org/W2115358825","https://openalex.org/W2116453847","https://openalex.org/W2117757143","https://openalex.org/W2120761571","https://openalex.org/W2124220434","https://openalex.org/W2126119172","https://openalex.org/W2126354232","https://openalex.org/W2132327671","https://openalex.org/W2133449910","https://openalex.org/W2137670824","https://openalex.org/W2140600399","https://openalex.org/W2146975493","https://openalex.org/W2147372875","https://openalex.org/W2153007310","https://openalex.org/W2161711244","https://openalex.org/W2162026806","https://openalex.org/W2163542423","https://openalex.org/W2216978877","https://openalex.org/W2269336305","https://openalex.org/W2308896320","https://openalex.org/W2527951543","https://openalex.org/W2531296558","https://openalex.org/W2552377493","https://openalex.org/W2558947257","https://openalex.org/W2615878271","https://openalex.org/W2746992081","https://openalex.org/W2766287235","https://openalex.org/W2794084858","https://openalex.org/W2810754857","https://openalex.org/W2883251903","https://openalex.org/W2900044275","https://openalex.org/W2900974706","https://openalex.org/W2938996079","https://openalex.org/W2942896967","https://openalex.org/W2961211115","https://openalex.org/W2969984773","https://openalex.org/W2970073459","https://openalex.org/W2988716798","https://openalex.org/W2990523642","https://openalex.org/W3084020252"],"related_works":["https://openalex.org/W2134002428","https://openalex.org/W1989509859","https://openalex.org/W1991259976","https://openalex.org/W3163988421","https://openalex.org/W4245957168","https://openalex.org/W186167790","https://openalex.org/W1871847816","https://openalex.org/W2133676917","https://openalex.org/W1993786842","https://openalex.org/W2039269859"],"abstract_inverted_index":{"Metazoan":[0],"core":[1,21,32,273],"promoters,":[2,274],"which":[3,36],"direct":[4],"the":[5,25,41,61,67,73,79,103,155,183,189,214,217,222,234,237,254,260,276],"initiation":[6],"of":[7,63,110,188,216,224,233,253,278],"transcription":[8,43,81],"by":[9,78,241],"RNA":[10],"polymerase":[11],"II":[12,39],"(Pol":[13],"II),":[14],"may":[15],"contain":[16,91,116],"short":[17],"sequence":[18,191],"motifs":[19,192,280],"termed":[20],"promoter":[22,33,168,247],"elements/motifs":[23],"(e.g.":[24],"TATA":[26],"box,":[27],"initiator":[28],"(Inr)":[29],"and":[30,49,66,120,165,239],"downstream":[31,93,147,185,219,269],"element":[34,94],"(DPE)),":[35],"recruit":[37],"Pol":[38],"via":[40],"general":[42],"machinery.":[44],"The":[45],"DPE":[46,75],"was":[47],"discovered":[48,145,256],"extensively":[50],"characterized":[51],"in":[52,150,182,245,281],"Drosophila,":[53],"where":[54],"it":[55,83],"is":[56,76,84,96],"strictly":[57],"dependent":[58],"on":[59,139,259],"both":[60],"presence":[62],"an":[64],"Inr":[65,238],"precise":[68],"spacing":[69,235,251],"from":[70],"it.":[71],"Since":[72],"Drosophila":[74,104,156,164],"recognized":[77],"human":[80,89,111,125,151,166,226,257,272,282],"machinery,":[82],"most":[85],"likely":[86],"that":[87,95,153,163,199,231],"some":[88],"promoters":[90,112,127,152,202],"a":[92,108,117,133,194,250],"similar,":[97],"though":[98],"not":[99,171],"necessarily":[100],"identical,":[101],"to":[102,115,122,178,206,221],"DPE.":[105,157],"However,":[106],"only":[107,172],"couple":[109],"were":[113],"shown":[114],"functional":[118,268],"DPE,":[119],"attempts":[121],"computationally":[123],"detect":[124],"DPE-containing":[126],"have":[128],"mostly":[129],"been":[130],"unsuccessful.":[131],"Using":[132,209],"newly-designed":[134],"motif":[135],"discovery":[136],"strategy":[137,265],"based":[138],"Expectation-Maximization":[140],"probabilistic":[141],"partitioning":[142],"algorithms,":[143],"we":[144,212,229],"preferred":[146],"positions":[148,220,270],"(PDP)":[149],"resemble":[154],"Available":[158],"chromatin":[159],"accessibility":[160],"footprints":[161],"revealed":[162],"Inr+DPE":[167,201],"classes":[169],"are":[170],"highly":[173],"structured,":[174],"but":[175],"also":[176],"similar":[177],"each":[179],"other,":[180],"particularly":[181],"proximal":[184],"region.":[186],"Clustering":[187],"corresponding":[190],"using":[193],"neighbor-joining":[195],"algorithm":[196],"strongly":[197],"suggests":[198],"canonical":[200],"could":[203],"be":[204],"common":[205],"metazoan":[207],"species.":[208],"reporter":[210],"assays":[211],"demonstrate":[213],"contribution":[215],"identified":[218,266],"function":[223],"multiple":[225],"promoters.":[227,283],"Furthermore,":[228],"show":[230],"alteration":[232],"between":[236],"PDP":[240,258],"two":[242],"nucleotides":[243],"results":[244],"reduced":[246],"activity,":[248],"suggesting":[249],"dependency":[252],"newly":[255],"Inr.":[261],"Taken":[262],"together,":[263],"our":[264],"novel":[267],"within":[271],"supporting":[275],"existence":[277],"DPE-like":[279]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2}],"updated_date":"2026-08-28T12:50:07.497085","created_date":"2025-10-10T00:00:00"}
