{"id":"https://openalex.org/W4392168486","doi":"https://doi.org/10.1093/bioinformatics/btae110","title":"ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements","display_name":"ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements","publication_year":2024,"publication_date":"2024-02-24","ids":{"openalex":"https://openalex.org/W4392168486","doi":"https://doi.org/10.1093/bioinformatics/btae110","pmid":"https://pubmed.ncbi.nlm.nih.gov/38407414"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae110","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae110","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae110/56756167/btae110.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae110/56756167/btae110.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066616376","display_name":"Orit Adato","orcid":"https://orcid.org/0000-0002-2135-8947"},"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":"Orit Adato","raw_affiliation_strings":["The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat Gan, 5290002, Israel"],"affiliations":[{"raw_affiliation_string":"The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat Gan, 5290002, Israel","institution_ids":["https://openalex.org/I13955877"]}]},{"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, 5290002, Israel"],"affiliations":[{"raw_affiliation_string":"The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat Gan, 5290002, Israel","institution_ids":["https://openalex.org/I13955877"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5094005100","display_name":"Hodaya Komemi","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":"Hodaya Komemi","raw_affiliation_strings":["The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat Gan, 5290002, Israel"],"affiliations":[{"raw_affiliation_string":"The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat Gan, 5290002, Israel","institution_ids":["https://openalex.org/I13955877"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5092946009","display_name":"Ian M. Brabb","orcid":"https://orcid.org/0009-0006-8585-6319"},"institutions":[{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ian Brabb","raw_affiliation_strings":["School of Molecular Biosciences, College of Veterinary Medicine, Washington State University , Pullman, WA 99164, United States"],"affiliations":[{"raw_affiliation_string":"School of Molecular Biosciences, College of Veterinary Medicine, Washington State University , Pullman, WA 99164, United States","institution_ids":["https://openalex.org/I72951846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053327588","display_name":"Sascha H. Duttke","orcid":"https://orcid.org/0000-0003-4717-000X"},"institutions":[{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sascha Duttke","raw_affiliation_strings":["School of Molecular Biosciences, College of Veterinary Medicine, Washington State University , Pullman, WA 99164, United States"],"affiliations":[{"raw_affiliation_string":"School of Molecular Biosciences, College of Veterinary Medicine, Washington State University , Pullman, WA 99164, United States","institution_ids":["https://openalex.org/I72951846"]}]},{"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"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Philipp Bucher","raw_affiliation_strings":["Swiss Institute of Bioinformatics (SIB) , 1015 Lausanne, Switzerland"],"affiliations":[{"raw_affiliation_string":"Swiss Institute of Bioinformatics (SIB) , 1015 Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056692823","display_name":"Ron Unger","orcid":"https://orcid.org/0000-0003-4153-3922"},"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":"Ron Unger","raw_affiliation_strings":["The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat Gan, 5290002, Israel"],"affiliations":[{"raw_affiliation_string":"The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat Gan, 5290002, Israel","institution_ids":["https://openalex.org/I13955877"]}]},{"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":false,"raw_author_name":"Tamar Juven-Gershon","raw_affiliation_strings":["The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat Gan, 5290002, Israel"],"affiliations":[{"raw_affiliation_string":"The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat Gan, 5290002, Israel","institution_ids":["https://openalex.org/I13955877"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5066616376"],"corresponding_institution_ids":["https://openalex.org/I13955877"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.3738,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.79389959,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"40","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9994000196456909,"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":0.9994000196456909,"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/T11482","display_name":"RNA modifications and cancer","score":0.9994000196456909,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9976000189781189,"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/core","display_name":"Core (optical fiber)","score":0.6385788917541504},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5248425006866455},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5014669895172119},{"id":"https://openalex.org/keywords/element","display_name":"Element (criminal law)","score":0.4674704074859619},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.26587823033332825},{"id":"https://openalex.org/keywords/political-science","display_name":"Political science","score":0.07709068059921265}],"concepts":[{"id":"https://openalex.org/C2164484","wikidata":"https://www.wikidata.org/wiki/Q5170150","display_name":"Core (optical fiber)","level":2,"score":0.6385788917541504},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5248425006866455},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5014669895172119},{"id":"https://openalex.org/C200288055","wikidata":"https://www.wikidata.org/wiki/Q2621792","display_name":"Element (criminal law)","level":2,"score":0.4674704074859619},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26587823033332825},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.07709068059921265},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[{"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":"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":"D011401","descriptor_name":"Promoter Regions, 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":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, 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":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae110","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae110","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae110/56756167/btae110.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38407414","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38407414","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:10950481","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10950481","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10950481/pdf/btae110.pdf","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae110","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae110","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae110/56756167/btae110.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.4699999988079071}],"awards":[{"id":"https://openalex.org/G4359693134","display_name":null,"funder_award_id":"NIGMS","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4411139188","display_name":null,"funder_award_id":"NIGMS R00-GM135515","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8457414487","display_name":null,"funder_award_id":"R00-GM135515","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"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/W4392168486.pdf"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1950152486","https://openalex.org/W1971456303","https://openalex.org/W1972813594","https://openalex.org/W1980645953","https://openalex.org/W2033169664","https://openalex.org/W2038010573","https://openalex.org/W2045362835","https://openalex.org/W2057692691","https://openalex.org/W2067116931","https://openalex.org/W2083073732","https://openalex.org/W2091533196","https://openalex.org/W2097353028","https://openalex.org/W2097920884","https://openalex.org/W2121116352","https://openalex.org/W2124220434","https://openalex.org/W2124343649","https://openalex.org/W2125427542","https://openalex.org/W2133449910","https://openalex.org/W2147372875","https://openalex.org/W2148114118","https://openalex.org/W2149301312","https://openalex.org/W2157702310","https://openalex.org/W2274378441","https://openalex.org/W2578532919","https://openalex.org/W2730983731","https://openalex.org/W2942896967","https://openalex.org/W2982028528","https://openalex.org/W2988641336","https://openalex.org/W3013907744","https://openalex.org/W3201316962","https://openalex.org/W3215596355","https://openalex.org/W4213336556","https://openalex.org/W4306405496","https://openalex.org/W6770792585"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2143122080"],"abstract_inverted_index":{"ElemeNT":[0,15],"2023":[1,16],"is":[2],"freely":[3],"available":[4,18],"at":[5,19],"https://www.juven-gershonlab.org/resources/element-v2023/.":[6],"The":[7],"source":[8],"code":[9],"and":[10],"command":[11],"line":[12],"version":[13],"of":[14],"are":[17,24],"https://github.com/OritAdato/ElemeNT.":[20],"No":[21],"coding":[22],"skills":[23],"required":[25],"to":[26],"run":[27],"the":[28],"tool.":[29]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
