{"id":"https://openalex.org/W3165538067","doi":"https://doi.org/10.1093/nar/gkab383","title":"PlantDeepSEA, a deep learning-based web service to predict the regulatory effects of genomic variants in plants","display_name":"PlantDeepSEA, a deep learning-based web service to predict the regulatory effects of genomic variants in plants","publication_year":2021,"publication_date":"2021-04-28","ids":{"openalex":"https://openalex.org/W3165538067","doi":"https://doi.org/10.1093/nar/gkab383","mag":"3165538067","pmid":"https://pubmed.ncbi.nlm.nih.gov/34037796"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkab383","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkab383","pdf_url":"https://academic.oup.com/nar/article-pdf/49/W1/W523/38841926/gkab383.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/49/W1/W523/38841926/gkab383.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060891974","display_name":"Hu Zhao","orcid":"https://orcid.org/0000-0001-5046-6632"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hu Zhao","raw_affiliation_strings":["National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China"],"affiliations":[{"raw_affiliation_string":"National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010771420","display_name":"Zhuo Tu","orcid":null},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhuo Tu","raw_affiliation_strings":["National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China"],"affiliations":[{"raw_affiliation_string":"National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020373355","display_name":"Yinmeng Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yinmeng Liu","raw_affiliation_strings":["National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China"],"affiliations":[{"raw_affiliation_string":"National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007908515","display_name":"Zhanxiang Zong","orcid":"https://orcid.org/0000-0001-5287-420X"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhanxiang Zong","raw_affiliation_strings":["National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China"],"affiliations":[{"raw_affiliation_string":"National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100403785","display_name":"Jiacheng Li","orcid":"https://orcid.org/0000-0002-9681-7546"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiacheng Li","raw_affiliation_strings":["National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China"],"affiliations":[{"raw_affiliation_string":"National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100458790","display_name":"Hao Liu","orcid":"https://orcid.org/0000-0002-1979-8994"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hao Liu","raw_affiliation_strings":["National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China"],"affiliations":[{"raw_affiliation_string":"National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029095757","display_name":"Feng Xiong","orcid":"https://orcid.org/0000-0001-7051-6668"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Feng Xiong","raw_affiliation_strings":["National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China"],"affiliations":[{"raw_affiliation_string":"National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112899120","display_name":"Jinling Zhan","orcid":null},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jinling Zhan","raw_affiliation_strings":["National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China"],"affiliations":[{"raw_affiliation_string":"National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081798199","display_name":"Xuehai Hu","orcid":"https://orcid.org/0000-0001-6731-1602"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuehai Hu","raw_affiliation_strings":["Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China"],"affiliations":[{"raw_affiliation_string":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100458707","display_name":"Weibo Xie","orcid":"https://orcid.org/0000-0002-2768-3572"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Weibo Xie","raw_affiliation_strings":["Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China","National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China"],"affiliations":[{"raw_affiliation_string":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China","institution_ids":["https://openalex.org/I204823248"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5100458707"],"corresponding_institution_ids":["https://openalex.org/I204823248"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":2.6778,"has_fulltext":false,"cited_by_count":53,"citation_normalized_percentile":{"value":0.91283088,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"49","issue":"W1","first_page":"W523","last_page":"W529"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9987999796867371,"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/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.998199999332428,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/biology","display_name":"Biology","score":0.8326431512832642},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.66344153881073},{"id":"https://openalex.org/keywords/usability","display_name":"Usability","score":0.6345322132110596},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6340495347976685},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.6101372838020325},{"id":"https://openalex.org/keywords/web-service","display_name":"Web service","score":0.5342103242874146},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.46310943365097046},{"id":"https://openalex.org/keywords/service","display_name":"Service (business)","score":0.42476892471313477},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.41177552938461304},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.41033071279525757},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3780980110168457},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.370698481798172},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.35214632749557495},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.25704121589660645},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.21073362231254578},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1987406313419342}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8326431512832642},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.66344153881073},{"id":"https://openalex.org/C170130773","wikidata":"https://www.wikidata.org/wiki/Q216378","display_name":"Usability","level":2,"score":0.6345322132110596},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6340495347976685},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.6101372838020325},{"id":"https://openalex.org/C35578498","wikidata":"https://www.wikidata.org/wiki/Q193424","display_name":"Web service","level":2,"score":0.5342103242874146},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.46310943365097046},{"id":"https://openalex.org/C2780378061","wikidata":"https://www.wikidata.org/wiki/Q25351891","display_name":"Service (business)","level":2,"score":0.42476892471313477},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.41177552938461304},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.41033071279525757},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3780980110168457},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.370698481798172},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.35214632749557495},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.25704121589660645},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.21073362231254578},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1987406313419342},{"id":"https://openalex.org/C136264566","wikidata":"https://www.wikidata.org/wiki/Q159810","display_name":"Economy","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003313","descriptor_name":"Zea mays","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003313","descriptor_name":"Zea mays","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003313","descriptor_name":"Zea mays","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011110","descriptor_name":"Polymorphism, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011110","descriptor_name":"Polymorphism, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011110","descriptor_name":"Polymorphism, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012275","descriptor_name":"Oryza","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012275","descriptor_name":"Oryza","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012275","descriptor_name":"Oryza","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017343","descriptor_name":"Genes, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017343","descriptor_name":"Genes, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017343","descriptor_name":"Genes, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkab383","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkab383","pdf_url":"https://academic.oup.com/nar/article-pdf/49/W1/W523/38841926/gkab383.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:34037796","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34037796","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:8262748","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8262748","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkab383","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkab383","pdf_url":"https://academic.oup.com/nar/article-pdf/49/W1/W523/38841926/gkab383.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1996036885","display_name":null,"funder_award_id":"2016YFD0100803","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G3532615355","display_name":null,"funder_award_id":"31922065","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8693807041","display_name":null,"funder_award_id":"31771755","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3165538067.pdf","grobid_xml":"https://content.openalex.org/works/W3165538067.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1998000745","https://openalex.org/W2006066143","https://openalex.org/W2032700288","https://openalex.org/W2055494779","https://openalex.org/W2056198580","https://openalex.org/W2078059415","https://openalex.org/W2108234281","https://openalex.org/W2117757143","https://openalex.org/W2130774313","https://openalex.org/W2131271579","https://openalex.org/W2133301154","https://openalex.org/W2140952049","https://openalex.org/W2143295722","https://openalex.org/W2146849272","https://openalex.org/W2171808845","https://openalex.org/W2198606573","https://openalex.org/W2345512687","https://openalex.org/W2405567513","https://openalex.org/W2419574648","https://openalex.org/W2485985069","https://openalex.org/W2533355719","https://openalex.org/W2558928133","https://openalex.org/W2605409611","https://openalex.org/W2737673717","https://openalex.org/W2795927426","https://openalex.org/W2914241561","https://openalex.org/W2922979017","https://openalex.org/W2935703330","https://openalex.org/W2952239877","https://openalex.org/W2967866078","https://openalex.org/W2982979721","https://openalex.org/W2983958512","https://openalex.org/W2988716798","https://openalex.org/W3016695829","https://openalex.org/W3033871487","https://openalex.org/W3094864623","https://openalex.org/W3097994730","https://openalex.org/W3123776742","https://openalex.org/W4394666350","https://openalex.org/W6674561012","https://openalex.org/W6736518430","https://openalex.org/W6769944288"],"related_works":["https://openalex.org/W3129816939","https://openalex.org/W2912862995","https://openalex.org/W2985427592","https://openalex.org/W2101501829","https://openalex.org/W2400569965","https://openalex.org/W2060263731","https://openalex.org/W2003194288","https://openalex.org/W391093122","https://openalex.org/W1521239975","https://openalex.org/W4361305867"],"abstract_inverted_index":{"Characterizing":[0],"regulatory":[1,27,55,155],"effects":[2,56,85],"of":[3,57,63,86,128,143,163,166],"genomic":[4,58],"variants":[5,59,88,157],"in":[6,41,60,132,168,171],"plants":[7],"remains":[8],"a":[9,48,96,113],"challenge.":[10],"Although":[11],"several":[12],"tools":[13,34],"based":[14],"on":[15,89,117],"deep-learning":[16],"models":[17,131],"and":[18,29,158],"large-scale":[19],"chromatin-profiling":[20],"data":[21],"have":[22,38],"been":[23,39],"available":[24,175],"to":[25,53,82,105,137,153],"predict":[26,54,83],"elements":[28],"variant":[30],"effects,":[31],"no":[32],"dedicated":[33],"or":[35],"web":[36,51,145],"services":[37],"reported":[40],"plants.":[42,172],"Here,":[43],"we":[44],"present":[45],"PlantDeepSEA":[46,70,133,150,173],"as":[47],"deep":[49,129],"learning-based":[50],"service":[52,146],"multiple":[61],"tissues":[62,170],"six":[64],"plant":[65],"species":[66],"(including":[67],"four":[68],"crops).":[69],"provides":[71],"two":[72,148],"main":[73],"functions.":[74],"One":[75],"is":[76,93,174],"called":[77],"Variant":[78],"Effector,":[79],"which":[80],"aims":[81],"the":[84,121,141,144],"sequence":[87],"chromatin":[90],"accessibility.":[91],"Another":[92],"Sequence":[94],"Profiler,":[95],"utility":[97],"that":[98],"performs":[99],"'in":[100],"silico":[101],"saturated":[102],"mutagenesis'":[103],"analysis":[104],"discover":[106],"high-impact":[107],"sites":[108],"(e.g.,":[109],"cis-regulatory":[110],"elements)":[111],"within":[112],"sequence.":[114],"When":[115],"validated":[116],"independent":[118],"test":[119],"sets,":[120],"area":[122],"under":[123],"receiver":[124],"operating":[125],"characteristic":[126],"curve":[127],"learning":[130],"ranges":[134],"from":[135],"0.93":[136],"0.99.":[138],"We":[139],"demonstrate":[140],"usability":[142],"with":[147],"examples.":[149],"could":[151],"help":[152],"prioritize":[154],"causal":[156],"might":[159],"improve":[160],"our":[161],"understanding":[162],"their":[164],"mechanisms":[165],"action":[167],"different":[169],"at":[176],"http://plantdeepsea.ncpgr.cn/.":[177]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":16},{"year":2024,"cited_by_count":16},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":1}],"updated_date":"2026-03-30T08:08:38.191290","created_date":"2025-10-10T00:00:00"}
