{"id":"https://openalex.org/W4399676687","doi":"https://doi.org/10.1093/bioinformatics/btae367","title":"Supervised learning of enhancer\u2013promoter specificity based on genome-wide perturbation studies highlights areas for improvement in learning","display_name":"Supervised learning of enhancer\u2013promoter specificity based on genome-wide perturbation studies highlights areas for improvement in learning","publication_year":2024,"publication_date":"2024-06-01","ids":{"openalex":"https://openalex.org/W4399676687","doi":"https://doi.org/10.1093/bioinformatics/btae367","pmid":"https://pubmed.ncbi.nlm.nih.gov/38870532"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae367","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae367","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae367/58230312/btae367.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/btae367/58230312/btae367.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010625037","display_name":"Dylan Barth","orcid":null},"institutions":[{"id":"https://openalex.org/I133999245","display_name":"University of Nevada, Las Vegas","ror":"https://ror.org/0406gha72","country_code":"US","type":"education","lineage":["https://openalex.org/I133999245"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dylan Barth","raw_affiliation_strings":["Nevada Institute of Personalized Medicine, University of Nevada , Las Vegas, NV 89154, United States","School of Life Sciences, University of Nevada , Las Vegas, NV 89154, United States"],"affiliations":[{"raw_affiliation_string":"Nevada Institute of Personalized Medicine, University of Nevada , Las Vegas, NV 89154, United States","institution_ids":["https://openalex.org/I133999245"]},{"raw_affiliation_string":"School of Life Sciences, University of Nevada , Las Vegas, NV 89154, United States","institution_ids":["https://openalex.org/I133999245"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055517021","display_name":"Richard Van","orcid":"https://orcid.org/0000-0002-0870-4788"},"institutions":[{"id":"https://openalex.org/I133999245","display_name":"University of Nevada, Las Vegas","ror":"https://ror.org/0406gha72","country_code":"US","type":"education","lineage":["https://openalex.org/I133999245"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard Van","raw_affiliation_strings":["Nevada Institute of Personalized Medicine, University of Nevada , Las Vegas, NV 89154, United States","School of Life Sciences, University of Nevada , Las Vegas, NV 89154, United States"],"affiliations":[{"raw_affiliation_string":"Nevada Institute of Personalized Medicine, University of Nevada , Las Vegas, NV 89154, United States","institution_ids":["https://openalex.org/I133999245"]},{"raw_affiliation_string":"School of Life Sciences, University of Nevada , Las Vegas, NV 89154, United States","institution_ids":["https://openalex.org/I133999245"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025427625","display_name":"Jonathan Cardwell","orcid":null},"institutions":[{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan Cardwell","raw_affiliation_strings":["Department of Medicine, University of Colorado School of Medicine , Denver, CO 80045, United States"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of Colorado School of Medicine , Denver, CO 80045, United States","institution_ids":["https://openalex.org/I921990950"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080164890","display_name":"Mira Han","orcid":"https://orcid.org/0000-0002-0488-1170"},"institutions":[{"id":"https://openalex.org/I133999245","display_name":"University of Nevada, Las Vegas","ror":"https://ror.org/0406gha72","country_code":"US","type":"education","lineage":["https://openalex.org/I133999245"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mira V Han","raw_affiliation_strings":["Nevada Institute of Personalized Medicine, University of Nevada , Las Vegas, NV 89154, United States","School of Life Sciences, University of Nevada , Las Vegas, NV 89154, United States"],"affiliations":[{"raw_affiliation_string":"Nevada Institute of Personalized Medicine, University of Nevada , Las Vegas, NV 89154, United States","institution_ids":["https://openalex.org/I133999245"]},{"raw_affiliation_string":"School of Life Sciences, University of Nevada , Las Vegas, NV 89154, United States","institution_ids":["https://openalex.org/I133999245"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5010625037"],"corresponding_institution_ids":["https://openalex.org/I133999245"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.08603512,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"40","issue":"6","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":0.9997000098228455,"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":0.9997000098228455,"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":0.9980000257492065,"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/T11103","display_name":"Antimicrobial Peptides and Activities","score":0.9908000230789185,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/enhancer","display_name":"Enhancer","score":0.8980913162231445},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6439281702041626},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5438114404678345},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.49681833386421204},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4826510548591614},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.4659140408039093},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4304999113082886},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.30192598700523376},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2795451283454895}],"concepts":[{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.8980913162231445},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6439281702041626},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5438114404678345},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.49681833386421204},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4826510548591614},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.4659140408039093},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4304999113082886},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.30192598700523376},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2795451283454895}],"mesh":[{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":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":"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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"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":"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":"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":"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae367","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae367","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae367/58230312/btae367.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:38870532","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38870532","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:11211214","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11211214","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11211214/pdf/btae367.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/btae367","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae367","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae367/58230312/btae367.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":[],"awards":[{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8771448163","display_name":null,"funder_award_id":"1750532","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4399676687.pdf"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1718129080","https://openalex.org/W1783978207","https://openalex.org/W1971615450","https://openalex.org/W1998306196","https://openalex.org/W2004966039","https://openalex.org/W2089894746","https://openalex.org/W2120628024","https://openalex.org/W2122205071","https://openalex.org/W2156665896","https://openalex.org/W2333286569","https://openalex.org/W2587454956","https://openalex.org/W2591130492","https://openalex.org/W2620165518","https://openalex.org/W2752211734","https://openalex.org/W2906884244","https://openalex.org/W2949213644","https://openalex.org/W2949423586","https://openalex.org/W2952276239","https://openalex.org/W2968818167","https://openalex.org/W2972483091","https://openalex.org/W2991283206","https://openalex.org/W3002964216","https://openalex.org/W3029730770","https://openalex.org/W3135152445","https://openalex.org/W3163548490","https://openalex.org/W3217314753","https://openalex.org/W4225797159","https://openalex.org/W4281254649","https://openalex.org/W4293692683","https://openalex.org/W4318393690"],"related_works":["https://openalex.org/W2113330652","https://openalex.org/W2061914098","https://openalex.org/W4393004084","https://openalex.org/W4309683845","https://openalex.org/W4303699336","https://openalex.org/W2152841149","https://openalex.org/W2586783543","https://openalex.org/W4387598842","https://openalex.org/W2973036402","https://openalex.org/W2053972265"],"abstract_inverted_index":{"The":[0],"trained":[1],"models,":[2],"data,":[3],"and":[4,12],"the":[5],"source":[6],"code":[7],"are":[8],"available":[9],"at":[10],"http://doi.org/10.5281/zenodo.11290386":[11],"https://github.com/HanLabUNLV/sleps.":[13]},"counts_by_year":[],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
