{"id":"https://openalex.org/W4391964957","doi":"https://doi.org/10.1186/s12859-024-05645-5","title":"Proformer: a hybrid macaron transformer model predicts expression values from promoter sequences","display_name":"Proformer: a hybrid macaron transformer model predicts expression values from promoter sequences","publication_year":2024,"publication_date":"2024-02-20","ids":{"openalex":"https://openalex.org/W4391964957","doi":"https://doi.org/10.1186/s12859-024-05645-5","pmid":"https://pubmed.ncbi.nlm.nih.gov/38378442"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-024-05645-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05645-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05645-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05645-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014457836","display_name":"Il\u2010Youp Kwak","orcid":"https://orcid.org/0000-0002-7117-7669"},"institutions":[{"id":"https://openalex.org/I67900169","display_name":"Chung-Ang University","ror":"https://ror.org/01r024a98","country_code":"KR","type":"education","lineage":["https://openalex.org/I67900169"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Il-Youp Kwak","raw_affiliation_strings":["Department of Applied Statistics, Chung\u2011Ang University, Seoul, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Statistics, Chung\u2011Ang University, Seoul, Republic of Korea","institution_ids":["https://openalex.org/I67900169"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079661784","display_name":"Byeongchan Kim","orcid":"https://orcid.org/0009-0007-7113-9906"},"institutions":[{"id":"https://openalex.org/I67900169","display_name":"Chung-Ang University","ror":"https://ror.org/01r024a98","country_code":"KR","type":"education","lineage":["https://openalex.org/I67900169"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Byeong-Chan Kim","raw_affiliation_strings":["Department of Applied Statistics, Chung\u2011Ang University, Seoul, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Statistics, Chung\u2011Ang University, Seoul, Republic of Korea","institution_ids":["https://openalex.org/I67900169"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100396195","display_name":"Juhyun Lee","orcid":"https://orcid.org/0000-0002-9609-4376"},"institutions":[{"id":"https://openalex.org/I67900169","display_name":"Chung-Ang University","ror":"https://ror.org/01r024a98","country_code":"KR","type":"education","lineage":["https://openalex.org/I67900169"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Juhyun Lee","raw_affiliation_strings":["Department of Applied Statistics, Chung\u2011Ang University, Seoul, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Statistics, Chung\u2011Ang University, Seoul, Republic of Korea","institution_ids":["https://openalex.org/I67900169"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074333458","display_name":"Taein Kang","orcid":null},"institutions":[{"id":"https://openalex.org/I67900169","display_name":"Chung-Ang University","ror":"https://ror.org/01r024a98","country_code":"KR","type":"education","lineage":["https://openalex.org/I67900169"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Taein Kang","raw_affiliation_strings":["Department of Applied Statistics, Chung\u2011Ang University, Seoul, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Statistics, Chung\u2011Ang University, Seoul, Republic of Korea","institution_ids":["https://openalex.org/I67900169"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036817888","display_name":"Daniel J. Garry","orcid":"https://orcid.org/0000-0002-8970-7365"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]},{"id":"https://openalex.org/I4210134111","display_name":"Minneapolis Heart Institute Foundation","ror":"https://ror.org/03mhcky17","country_code":"US","type":"funder","lineage":["https://openalex.org/I4210134111"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Daniel J. Garry","raw_affiliation_strings":["Cardiovascular Division, Department of Medicine, Lillehei Heart Institute, University of Minnesota, 2231 6th St SE, Minneapolis, MN, 55455, USA. garry@umn.edu","Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, 55455, USA. garry@umn.edu","Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA. garry@umn.edu","Cardiovascular Division, Department of Medicine, Lillehei Heart Institute, University of Minnesota, 2231 6th St SE, Minneapolis, MN, 55455, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cardiovascular Division, Department of Medicine, Lillehei Heart Institute, University of Minnesota, 2231 6th St SE, Minneapolis, MN, 55455, USA. garry@umn.edu","institution_ids":["https://openalex.org/I4210134111"]},{"raw_affiliation_string":"Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, 55455, USA. garry@umn.edu","institution_ids":["https://openalex.org/I130238516"]},{"raw_affiliation_string":"Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA. garry@umn.edu","institution_ids":["https://openalex.org/I130238516"]},{"raw_affiliation_string":"Cardiovascular Division, Department of Medicine, Lillehei Heart Institute, University of Minnesota, 2231 6th St SE, Minneapolis, MN, 55455, USA","institution_ids":["https://openalex.org/I130238516","https://openalex.org/I4210134111"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030985040","display_name":"Jianyi Zhang","orcid":"https://orcid.org/0000-0002-3955-6554"},"institutions":[{"id":"https://openalex.org/I32389192","display_name":"University of Alabama at Birmingham","ror":"https://ror.org/008s83205","country_code":"US","type":"education","lineage":["https://openalex.org/I32389192"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jianyi Zhang","raw_affiliation_strings":["Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, AL, 35233, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, AL, 35233, USA","institution_ids":["https://openalex.org/I32389192"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066838536","display_name":"Wuming Gong","orcid":"https://orcid.org/0000-0002-3147-4028"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]},{"id":"https://openalex.org/I4210134111","display_name":"Minneapolis Heart Institute Foundation","ror":"https://ror.org/03mhcky17","country_code":"US","type":"funder","lineage":["https://openalex.org/I4210134111"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Wuming Gong","raw_affiliation_strings":["Cardiovascular Division, Department of Medicine, Lillehei Heart Institute, University of Minnesota, 2231 6th St SE, Minneapolis, MN, 55455, USA. gongx030@umn.edu","Cardiovascular Division, Department of Medicine, Lillehei Heart Institute, University of Minnesota, 2231 6th St SE, Minneapolis, MN, 55455, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cardiovascular Division, Department of Medicine, Lillehei Heart Institute, University of Minnesota, 2231 6th St SE, Minneapolis, MN, 55455, USA. gongx030@umn.edu","institution_ids":["https://openalex.org/I4210134111"]},{"raw_affiliation_string":"Cardiovascular Division, Department of Medicine, Lillehei Heart Institute, University of Minnesota, 2231 6th St SE, Minneapolis, MN, 55455, USA","institution_ids":["https://openalex.org/I130238516","https://openalex.org/I4210134111"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5036817888","https://openalex.org/A5066838536"],"corresponding_institution_ids":["https://openalex.org/I130238516","https://openalex.org/I4210134111"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.8072,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.8445771,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"25","issue":"1","first_page":"81","last_page":"81"},"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/T11482","display_name":"RNA modifications and cancer","score":0.9955999851226807,"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":0.9944999814033508,"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/dna-microarray","display_name":"DNA microarray","score":0.5600425601005554},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.555856466293335},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.465717077255249},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.43276721239089966},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3720042109489441},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.35559898614883423},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.32576096057891846},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2397235631942749},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.17355161905288696},{"id":"https://openalex.org/keywords/electrical-engineering","display_name":"Electrical engineering","score":0.07721516489982605}],"concepts":[{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5600425601005554},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.555856466293335},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.465717077255249},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.43276721239089966},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3720042109489441},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.35559898614883423},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.32576096057891846},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2397235631942749},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.17355161905288696},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.07721516489982605},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011211","descriptor_name":"Electric Power Supplies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011211","descriptor_name":"Electric Power Supplies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011211","descriptor_name":"Electric Power Supplies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011211","descriptor_name":"Electric Power Supplies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011211","descriptor_name":"Electric Power Supplies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011211","descriptor_name":"Electric Power Supplies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011211","descriptor_name":"Electric Power Supplies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011211","descriptor_name":"Electric Power Supplies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011211","descriptor_name":"Electric Power Supplies","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":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":"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}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-024-05645-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05645-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05645-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38378442","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38378442","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10877777","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10877777","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10877777/pdf/12859_2024_Article_5645.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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:0af5c93b8a9a47479bfdcf64431a6871","is_oa":false,"landing_page_url":"https://doaj.org/article/0af5c93b8a9a47479bfdcf64431a6871","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 25, Iss 1, Pp 1-13 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-024-05645-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05645-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05645-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1288928909","display_name":null,"funder_award_id":"W81XWH2110606","funder_id":"https://openalex.org/F4320306078","funder_display_name":"U.S. Department of Defense"},{"id":"https://openalex.org/G2117164272","display_name":null,"funder_award_id":"P01 HL160476","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G2322737288","display_name":null,"funder_award_id":"R01 HL168647","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G3984847229","display_name":null,"funder_award_id":"RS-2023-00208284","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"},{"id":"https://openalex.org/G4916494541","display_name":null,"funder_award_id":"RS-2023-00208284","funder_id":"https://openalex.org/F4320328359","funder_display_name":"Ministry of Science and ICT, South Korea"},{"id":"https://openalex.org/G6829747447","display_name":null,"funder_award_id":"P01HL160476","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G7124242785","display_name":null,"funder_award_id":"R01 HL144582","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"}],"funders":[{"id":"https://openalex.org/F4320306078","display_name":"U.S. Department of Defense","ror":"https://ror.org/0447fe631"},{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320322120","display_name":"National Research Foundation of Korea","ror":"https://ror.org/013aysd81"},{"id":"https://openalex.org/F4320328359","display_name":"Ministry of Science and ICT, South Korea","ror":"https://ror.org/01wpjm123"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4391964957.pdf"},"referenced_works_count":59,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1841597658","https://openalex.org/W1989004527","https://openalex.org/W2007694108","https://openalex.org/W2008047506","https://openalex.org/W2023386301","https://openalex.org/W2077874719","https://openalex.org/W2093146349","https://openalex.org/W2107596936","https://openalex.org/W2112500061","https://openalex.org/W2117757143","https://openalex.org/W2136518208","https://openalex.org/W2143855992","https://openalex.org/W2145674897","https://openalex.org/W2159664283","https://openalex.org/W2159933659","https://openalex.org/W2170551349","https://openalex.org/W2170739826","https://openalex.org/W2171808845","https://openalex.org/W2198606573","https://openalex.org/W2202976683","https://openalex.org/W2308616703","https://openalex.org/W2336509392","https://openalex.org/W2345512687","https://openalex.org/W2412481123","https://openalex.org/W2413629639","https://openalex.org/W2424483111","https://openalex.org/W2566958422","https://openalex.org/W2581468399","https://openalex.org/W2766421346","https://openalex.org/W2793714280","https://openalex.org/W2883945062","https://openalex.org/W2887466218","https://openalex.org/W2893045341","https://openalex.org/W2896262061","https://openalex.org/W2910487490","https://openalex.org/W2920892675","https://openalex.org/W2945999435","https://openalex.org/W2948981900","https://openalex.org/W2950235380","https://openalex.org/W2951195117","https://openalex.org/W2951748044","https://openalex.org/W2951760474","https://openalex.org/W2952239877","https://openalex.org/W2952935243","https://openalex.org/W2953622121","https://openalex.org/W2990395719","https://openalex.org/W3035691519","https://openalex.org/W3048429615","https://openalex.org/W3092421956","https://openalex.org/W3097777922","https://openalex.org/W4221128536","https://openalex.org/W4221161157","https://openalex.org/W4280499725","https://openalex.org/W4320726002","https://openalex.org/W4324145726","https://openalex.org/W4367301984","https://openalex.org/W4377293234","https://openalex.org/W4391964957"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2415545834","https://openalex.org/W2069695727","https://openalex.org/W106077234","https://openalex.org/W2041374557","https://openalex.org/W2081929287","https://openalex.org/W2132561013","https://openalex.org/W2144348650","https://openalex.org/W1994852842","https://openalex.org/W4246178523"],"abstract_inverted_index":{"The":[0,93],"breakthrough":[1],"high-throughput":[2],"measurement":[3],"of":[4,8,10,68,88,147,189,195],"the":[5,21,26,40,63,66,81,89,108,122,136,160,166,171,175,181,200],"cis-regulatory":[6,22,197],"activity":[7],"millions":[9],"randomly":[11],"generated":[12],"promoters":[13],"provides":[14,185],"an":[15,31],"unprecedented":[16],"opportunity":[17],"to":[18,38,134],"systematically":[19],"decode":[20],"logic":[23],"that":[24,152,183],"determines":[25],"expression":[27,41,129,201],"values.":[28,202],"We":[29,149],"developed":[30],"end-to-end":[32],"transformer":[33,137],"encoder":[34,51,70],"architecture":[35],"named":[36],"Proformer":[37,46,126,184],"predict":[39],"values":[42],"from":[43,96,139],"DNA":[44],"sequences.":[45],"used":[47],"a":[48,73,103,186],"Macaron-like":[49],"Transformer":[50],"architecture,":[52],"where":[53],"two":[54],"half-step":[55],"feed":[56],"forward":[57],"(FFN)":[58],"layers":[59],"were":[60,100],"placed":[61],"at":[62],"beginning":[64],"and":[65,72,85,112,191],"end":[67],"each":[69],"block,":[71],"separable":[74],"1D":[75],"convolution":[76],"layer":[77,84,169,173],"was":[78],"inserted":[79],"after":[80],"first":[82],"FFN":[83],"in":[86],"front":[87],"multi-head":[90],"attention":[91],"layer.":[92],"sliding":[94],"k-mers":[95],"one-hot":[97],"encoded":[98],"sequences":[99,198],"mapped":[101],"onto":[102],"continuous":[104],"embedding,":[105],"combined":[106],"with":[107,131],"learned":[109],"positional":[110],"embedding":[111,114],"strand":[113,116],"(forward":[115],"vs.":[117],"reverse":[118],"complemented":[119],"strand)":[120],"as":[121,164,170],"sequence":[123],"input.":[124],"Moreover,":[125],"introduced":[127],"multiple":[128],"heads":[130],"mask":[132],"filling":[133],"prevent":[135],"models":[138],"collapsing":[140],"when":[141],"training":[142],"on":[143],"relatively":[144],"small":[145],"amount":[146],"data.":[148],"empirically":[150],"determined":[151],"this":[153],"design":[154,162],"had":[155],"significantly":[156],"better":[157],"performance":[158],"than":[159],"conventional":[161],"such":[163],"using":[165],"global":[167],"pooling":[168],"output":[172],"for":[174],"regression":[176],"task.":[177],"These":[178],"analyses":[179],"support":[180],"notion":[182],"novel":[187],"method":[188],"learning":[190],"enhances":[192],"our":[193],"understanding":[194],"how":[196],"determine":[199]},"counts_by_year":[{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
