{"id":"https://openalex.org/W4388721914","doi":"https://doi.org/10.1038/s43588-023-00544-w","title":"Predictive analyses of regulatory sequences with EUGENe","display_name":"Predictive analyses of regulatory sequences with EUGENe","publication_year":2023,"publication_date":"2023-11-16","ids":{"openalex":"https://openalex.org/W4388721914","doi":"https://doi.org/10.1038/s43588-023-00544-w","pmid":"https://pubmed.ncbi.nlm.nih.gov/38177592"},"language":"en","primary_location":{"id":"doi:10.1038/s43588-023-00544-w","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s43588-023-00544-w","pdf_url":"https://www.nature.com/articles/s43588-023-00544-w.pdf","source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","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":"Nature Computational Science","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://www.nature.com/articles/s43588-023-00544-w.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5035688269","display_name":"Adam Klie","orcid":"https://orcid.org/0000-0002-7600-3086"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Adam Klie","raw_affiliation_strings":["Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA","Department of Medicine, University of California San Diego, La Jolla, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-7600-3086","affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069837247","display_name":"David Laub","orcid":"https://orcid.org/0000-0001-5912-6458"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David Laub","raw_affiliation_strings":["Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA","Department of Medicine, University of California San Diego, La Jolla, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029735169","display_name":"James V. Talwar","orcid":"https://orcid.org/0000-0002-9520-1950"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James V. Talwar","raw_affiliation_strings":["Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA","Department of Medicine, University of California San Diego, La Jolla, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006657953","display_name":"Hayden Stites","orcid":"https://orcid.org/0000-0002-3448-2613"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hayden Stites","raw_affiliation_strings":["Daniel Hand High School, Madison, CT, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Daniel Hand High School, Madison, CT, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080279154","display_name":"Tobias Jores","orcid":"https://orcid.org/0000-0002-1804-7187"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tobias Jores","raw_affiliation_strings":["Department of Genome Sciences, University of Washington, Seattle, WA, USA"],"raw_orcid":"https://orcid.org/0000-0002-1804-7187","affiliations":[{"raw_affiliation_string":"Department of Genome Sciences, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081167889","display_name":"Joe J. Solvason","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joe J. Solvason","raw_affiliation_strings":["Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA","Department of Medicine, University of California San Diego, La Jolla, CA, USA","Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031598839","display_name":"Emma K. Farley","orcid":"https://orcid.org/0000-0002-9241-247X"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Emma K. Farley","raw_affiliation_strings":["Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA","Department of Medicine, University of California San Diego, La Jolla, CA, USA","Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101461760","display_name":"Hannah Carter","orcid":"https://orcid.org/0000-0002-1729-2463"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hannah Carter","raw_affiliation_strings":["Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA. hkcarter@ucsd.edu","Department of Medicine, University of California San Diego, La Jolla, CA, USA. hkcarter@ucsd.edu","Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-1729-2463","affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA. hkcarter@ucsd.edu","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, CA, USA. hkcarter@ucsd.edu","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5035688269"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":{"value":9750,"currency":"EUR","value_usd":11690},"apc_paid":{"value":9750,"currency":"EUR","value_usd":11690},"fwci":3.0527,"has_fulltext":true,"cited_by_count":21,"citation_normalized_percentile":{"value":0.91857154,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"3","issue":"11","first_page":"946","last_page":"956"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9991999864578247,"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":0.9991999864578247,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9986000061035156,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9975000023841858,"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/deep-learning","display_name":"Deep learning","score":0.7697441577911377},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7570158243179321},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7371141910552979},{"id":"https://openalex.org/keywords/interoperability","display_name":"Interoperability","score":0.6570395827293396},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6366651058197021},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.5313159823417664},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5172291994094849},{"id":"https://openalex.org/keywords/deep-sequencing","display_name":"Deep sequencing","score":0.46603506803512573},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4259398281574249},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.384499728679657},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.33357489109039307},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.22484099864959717},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.15301907062530518},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1246548593044281},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10644379258155823},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.08338701725006104}],"concepts":[{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.7697441577911377},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7570158243179321},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7371141910552979},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.6570395827293396},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6366651058197021},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.5313159823417664},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5172291994094849},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.46603506803512573},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4259398281574249},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.384499728679657},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.33357489109039307},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.22484099864959717},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.15301907062530518},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1246548593044281},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10644379258155823},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.08338701725006104},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1038/s43588-023-00544-w","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s43588-023-00544-w","pdf_url":"https://www.nature.com/articles/s43588-023-00544-w.pdf","source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","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":"Nature Computational Science","raw_type":"journal-article"},{"id":"pmid:38177592","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38177592","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":"Nature computational science","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt6wv915r1","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/6wv915r1","pdf_url":"https://escholarship.org/content/qt6wv915r1/qt6wv915r1.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"Nature Computational Science, vol 3, iss 11","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10768637","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10768637","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10768637/pdf/43588_2023_Article_544.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":"Nat Comput Sci","raw_type":"Text"},{"id":"pmh:ark:/13030/qt6wv915r1","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.1038/s43588-023-00544-w","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s43588-023-00544-w","pdf_url":"https://www.nature.com/articles/s43588-023-00544-w.pdf","source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","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":"Nature Computational Science","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1572119481","display_name":null,"funder_award_id":"1U01HG012059","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G507102813","display_name":null,"funder_award_id":"441540116","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G5289894485","display_name":null,"funder_award_id":"FL-000655","funder_id":"https://openalex.org/F4320309949","funder_display_name":"Canadian Institute for Advanced Research"},{"id":"https://openalex.org/G5564152542","display_name":null,"funder_award_id":"DP2HG010013","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320309949","display_name":"Canadian Institute for Advanced Research","ror":"https://ror.org/01sdtdd95"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4388721914.pdf"},"referenced_works_count":83,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1677182931","https://openalex.org/W1972978214","https://openalex.org/W2011301426","https://openalex.org/W2058832897","https://openalex.org/W2061834804","https://openalex.org/W2102619694","https://openalex.org/W2103777723","https://openalex.org/W2105694586","https://openalex.org/W2110065044","https://openalex.org/W2198606573","https://openalex.org/W2245493112","https://openalex.org/W2259938310","https://openalex.org/W2336509392","https://openalex.org/W2345512687","https://openalex.org/W2346578521","https://openalex.org/W2604239613","https://openalex.org/W2767749844","https://openalex.org/W2795735651","https://openalex.org/W2883945062","https://openalex.org/W2890028650","https://openalex.org/W2893045341","https://openalex.org/W2922979017","https://openalex.org/W2934716754","https://openalex.org/W2947187332","https://openalex.org/W2948532335","https://openalex.org/W2951410692","https://openalex.org/W2951748044","https://openalex.org/W2952239877","https://openalex.org/W2953306855","https://openalex.org/W2953384591","https://openalex.org/W2960370523","https://openalex.org/W2995175313","https://openalex.org/W2997580108","https://openalex.org/W3024755225","https://openalex.org/W3026475692","https://openalex.org/W3035587935","https://openalex.org/W3041325230","https://openalex.org/W3044478077","https://openalex.org/W3046345618","https://openalex.org/W3048429615","https://openalex.org/W3081278968","https://openalex.org/W3082810966","https://openalex.org/W3085380432","https://openalex.org/W3092624702","https://openalex.org/W3119817859","https://openalex.org/W3126464728","https://openalex.org/W3127238141","https://openalex.org/W3130819465","https://openalex.org/W3146159774","https://openalex.org/W3150635270","https://openalex.org/W3157449380","https://openalex.org/W3163257742","https://openalex.org/W3164328317","https://openalex.org/W3203588026","https://openalex.org/W3203959602","https://openalex.org/W3215596355","https://openalex.org/W3217314753","https://openalex.org/W4205345182","https://openalex.org/W4220711046","https://openalex.org/W4225256479","https://openalex.org/W4280512834","https://openalex.org/W4280563114","https://openalex.org/W4282024528","https://openalex.org/W4285006295","https://openalex.org/W4288077839","https://openalex.org/W4290672942","https://openalex.org/W4295312788","https://openalex.org/W4295830359","https://openalex.org/W4300862723","https://openalex.org/W4306173528","https://openalex.org/W4313893501","https://openalex.org/W4375852635","https://openalex.org/W4376132682","https://openalex.org/W4379536676","https://openalex.org/W4380153720","https://openalex.org/W4384920643","https://openalex.org/W4387687322","https://openalex.org/W4393004135","https://openalex.org/W6912515347","https://openalex.org/W6950047652","https://openalex.org/W6950566464","https://openalex.org/W6950657160"],"related_works":["https://openalex.org/W2093262417","https://openalex.org/W2123131699","https://openalex.org/W913131694","https://openalex.org/W650116260","https://openalex.org/W2378329187","https://openalex.org/W4390790060","https://openalex.org/W1603423477","https://openalex.org/W3209454962","https://openalex.org/W79697243","https://openalex.org/W2314257840"],"abstract_inverted_index":{"Deep":[0],"learning":[1,81],"has":[2],"become":[3],"a":[4,51,66,78,114,147,150],"popular":[5],"tool":[6],"to":[7,13,137],"study":[8],"cis-regulatory":[9],"function.":[10],"Yet":[11],"efforts":[12],"design":[14],"software":[15],"for":[16,54,72,120,153],"deep-learning":[17,125,154],"analyses":[18],"in":[19,156],"regulatory":[20],"genomics":[21,79,157],"that":[22,144],"are":[23],"findable,":[24],"accessible,":[25],"interoperable":[26],"and":[27,70,86,98,103,106,117,122,128],"reusable":[28],"(FAIR)":[29],"have":[30],"fallen":[31],"short":[32],"of":[33,44,57,65,68,77,134],"fully":[34],"meeting":[35],"these":[36,130],"criteria.":[37],"Here":[38],"we":[39],"present":[40],"elucidating":[41],"the":[42,55,74,135],"utility":[43],"genomic":[45,58],"elements":[46],"with":[47,60],"neural":[48],"nets":[49],"(EUGENe),":[50],"FAIR":[52],"toolkit":[53,136],"analysis":[56],"sequences":[59],"deep":[61,80],"learning.":[62],"EUGENe":[63,112,145],"consists":[64],"set":[67],"modules":[69],"subpackages":[71],"executing":[73],"key":[75],"functionality":[76],"workflow:":[82],"(1)":[83],"extracting,":[84],"transforming":[85],"loading":[87],"sequence":[88,126],"data":[89],"from":[90],"many":[91],"common":[92],"file":[93],"formats;":[94],"(2)":[95],"instantiating,":[96],"initializing":[97],"training":[99],"diverse":[100],"model":[101,108],"architectures;":[102],"(3)":[104],"evaluating":[105],"interpreting":[107],"behavior.":[109],"We":[110,142],"designed":[111],"as":[113],"simple,":[115],"flexible":[116],"extensible":[118],"interface":[119],"streamlining":[121],"customizing":[123],"end-to-end":[124],"analyses,":[127],"illustrate":[129],"principles":[131],"through":[132],"application":[133],"three":[138],"predictive":[139],"modeling":[140],"tasks.":[141],"hope":[143],"represents":[146],"springboard":[148],"towards":[149],"collaborative":[151],"ecosystem":[152],"applications":[155],"research.":[158]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}