{"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":false,"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":true,"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":2,"corresponding_author_ids":["https://openalex.org/A5101461760"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":{"value":11690,"currency":"USD","value_usd":11690},"apc_paid":{"value":11690,"currency":"USD","value_usd":11690},"fwci":2.133,"has_fulltext":true,"cited_by_count":23,"citation_normalized_percentile":{"value":0.88373246,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"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/G1658734105","display_name":null,"funder_award_id":"OT2 OD036440","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G16900677","display_name":null,"funder_award_id":"DP2HG010013","funder_id":"https://openalex.org/F4320306085","funder_display_name":"U.S. Department of Health and Human Services"},{"id":"https://openalex.org/G3316149902","display_name":null,"funder_award_id":"P41-GM103504","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G403864660","display_name":null,"funder_award_id":"T15 LM011271","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G4686268943","display_name":null,"funder_award_id":"DP2HG010013","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G507102813","display_name":"Identifikation von Enhancern im Pflanzengenom unter Verwendung eines in vitro Transkriptionssystems","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"},{"id":"https://openalex.org/G7955524994","display_name":null,"funder_award_id":"U01 HG012059","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320306085","display_name":"U.S. Department of Health and Human Services","ror":"https://ror.org/033jnv181"},{"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"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":false,"pdf":true},"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":7},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
