{"id":"https://openalex.org/W2155383296","doi":"https://doi.org/10.1093/nar/gkt518","title":"PromoterCAD: data-driven design of plant regulatory DNA","display_name":"PromoterCAD: data-driven design of plant regulatory DNA","publication_year":2013,"publication_date":"2013-06-12","ids":{"openalex":"https://openalex.org/W2155383296","doi":"https://doi.org/10.1093/nar/gkt518","mag":"2155383296","pmid":"https://pubmed.ncbi.nlm.nih.gov/23766287"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkt518","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkt518","pdf_url":"https://academic.oup.com/nar/article-pdf/41/W1/W569/16944755/gkt518.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/41/W1/W569/16944755/gkt518.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042765353","display_name":"Robert Sidney Cox","orcid":"https://orcid.org/0000-0002-2009-6236"},"institutions":[{"id":"https://openalex.org/I4210100240","display_name":"RIKEN Center for Sustainable Resource Science","ror":"https://ror.org/010rf2m76","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210100240","https://openalex.org/I4210110652"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Robert Sidney Cox","raw_affiliation_strings":["Bioinformatics and Systems Engineering Division, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan","Bioinformatics and Systems Engineering Division (BASE), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan, 2Integrated Database Unit, Advanced Center for Computing and Communication (ACCC), RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and 3Synthetic Genomics Research Team, Biomass Engineering Program (BMEP), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Engineering Division, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan","institution_ids":[]},{"raw_affiliation_string":"Bioinformatics and Systems Engineering Division (BASE), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan, 2Integrated Database Unit, Advanced Center for Computing and Communication (ACCC), RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and 3Synthetic Genomics Research Team, Biomass Engineering Program (BMEP), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan","institution_ids":["https://openalex.org/I4210100240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005723484","display_name":"Koro Nishikata","orcid":null},"institutions":[{"id":"https://openalex.org/I4210100240","display_name":"RIKEN Center for Sustainable Resource Science","ror":"https://ror.org/010rf2m76","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210100240","https://openalex.org/I4210110652"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Koro Nishikata","raw_affiliation_strings":["Bioinformatics and Systems Engineering Division (BASE), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan, 2Integrated Database Unit, Advanced Center for Computing and Communication (ACCC), RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and 3Synthetic Genomics Research Team, Biomass Engineering Program (BMEP), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Engineering Division (BASE), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan, 2Integrated Database Unit, Advanced Center for Computing and Communication (ACCC), RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and 3Synthetic Genomics Research Team, Biomass Engineering Program (BMEP), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan","institution_ids":["https://openalex.org/I4210100240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079619879","display_name":"Sayoko Shimoyama","orcid":null},"institutions":[{"id":"https://openalex.org/I4210100240","display_name":"RIKEN Center for Sustainable Resource Science","ror":"https://ror.org/010rf2m76","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210100240","https://openalex.org/I4210110652"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Sayoko Shimoyama","raw_affiliation_strings":["Bioinformatics and Systems Engineering Division (BASE), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan, 2Integrated Database Unit, Advanced Center for Computing and Communication (ACCC), RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and 3Synthetic Genomics Research Team, Biomass Engineering Program (BMEP), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Engineering Division (BASE), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan, 2Integrated Database Unit, Advanced Center for Computing and Communication (ACCC), RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and 3Synthetic Genomics Research Team, Biomass Engineering Program (BMEP), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan","institution_ids":["https://openalex.org/I4210100240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029250115","display_name":"Yuko Yoshida","orcid":"https://orcid.org/0000-0001-7494-888X"},"institutions":[{"id":"https://openalex.org/I4210100240","display_name":"RIKEN Center for Sustainable Resource Science","ror":"https://ror.org/010rf2m76","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210100240","https://openalex.org/I4210110652"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yuko Yoshida","raw_affiliation_strings":["Bioinformatics and Systems Engineering Division (BASE), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan, 2Integrated Database Unit, Advanced Center for Computing and Communication (ACCC), RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and 3Synthetic Genomics Research Team, Biomass Engineering Program (BMEP), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Engineering Division (BASE), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan, 2Integrated Database Unit, Advanced Center for Computing and Communication (ACCC), RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and 3Synthetic Genomics Research Team, Biomass Engineering Program (BMEP), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan","institution_ids":["https://openalex.org/I4210100240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059614146","display_name":"Minami Matsui","orcid":"https://orcid.org/0000-0001-5162-2668"},"institutions":[{"id":"https://openalex.org/I4210100240","display_name":"RIKEN Center for Sustainable Resource Science","ror":"https://ror.org/010rf2m76","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210100240","https://openalex.org/I4210110652"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Minami Matsui","raw_affiliation_strings":["Bioinformatics and Systems Engineering Division (BASE), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan, 2Integrated Database Unit, Advanced Center for Computing and Communication (ACCC), RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and 3Synthetic Genomics Research Team, Biomass Engineering Program (BMEP), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Engineering Division (BASE), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan, 2Integrated Database Unit, Advanced Center for Computing and Communication (ACCC), RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and 3Synthetic Genomics Research Team, Biomass Engineering Program (BMEP), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan","institution_ids":["https://openalex.org/I4210100240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066711822","display_name":"Yuko Makita","orcid":"https://orcid.org/0000-0001-5745-6007"},"institutions":[{"id":"https://openalex.org/I4210100240","display_name":"RIKEN Center for Sustainable Resource Science","ror":"https://ror.org/010rf2m76","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210100240","https://openalex.org/I4210110652"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yuko Makita","raw_affiliation_strings":["Bioinformatics and Systems Engineering Division (BASE), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan, 2Integrated Database Unit, Advanced Center for Computing and Communication (ACCC), RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and 3Synthetic Genomics Research Team, Biomass Engineering Program (BMEP), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Engineering Division (BASE), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan, 2Integrated Database Unit, Advanced Center for Computing and Communication (ACCC), RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and 3Synthetic Genomics Research Team, Biomass Engineering Program (BMEP), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan","institution_ids":["https://openalex.org/I4210100240"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071431815","display_name":"Tetsuro Toyoda","orcid":null},"institutions":[{"id":"https://openalex.org/I4210100240","display_name":"RIKEN Center for Sustainable Resource Science","ror":"https://ror.org/010rf2m76","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210100240","https://openalex.org/I4210110652"]},{"id":"https://openalex.org/I4210165842","display_name":"RIKEN Center for Advanced Photonics","ror":"https://ror.org/05vmjks78","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210165842"]},{"id":"https://openalex.org/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]},{"id":"https://openalex.org/I4210128938","display_name":"RIKEN Advanced Science Institute","ror":"https://ror.org/030vbmf58","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210128938"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Tetsuro Toyoda","raw_affiliation_strings":["Bioinformatics and Systems Engineering Division (BASE), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan,","Integrated Database Unit, Advanced Center for Computing and Communication (ACCC), RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and","Bioinformatics and Systems Engineering Division (BASE), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan, 2Integrated Database Unit, Advanced Center for Computing and Communication (ACCC), RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and 3Synthetic Genomics Research Team, Biomass Engineering Program (BMEP), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Engineering Division (BASE), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan,","institution_ids":["https://openalex.org/I4210150921"]},{"raw_affiliation_string":"Integrated Database Unit, Advanced Center for Computing and Communication (ACCC), RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and","institution_ids":["https://openalex.org/I4210165842","https://openalex.org/I4210128938"]},{"raw_affiliation_string":"Bioinformatics and Systems Engineering Division (BASE), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan, 2Integrated Database Unit, Advanced Center for Computing and Communication (ACCC), RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and 3Synthetic Genomics Research Team, Biomass Engineering Program (BMEP), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan","institution_ids":["https://openalex.org/I4210100240"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5071431815"],"corresponding_institution_ids":["https://openalex.org/I4210100240","https://openalex.org/I4210128938","https://openalex.org/I4210150921","https://openalex.org/I4210165842"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":2.3128,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.89416757,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"41","issue":"W1","first_page":"W569","last_page":"W574"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10184","display_name":"Plant Molecular Biology Research","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10184","display_name":"Plant Molecular Biology Research","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11927","display_name":"Plant Reproductive Biology","score":0.9988999962806702,"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/T10494","display_name":"Plant Virus Research Studies","score":0.9937999844551086,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.8928771018981934},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5969029664993286},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.579707145690918},{"id":"https://openalex.org/keywords/synthetic-biology","display_name":"Synthetic biology","score":0.49419453740119934},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4386788010597229},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.433165967464447},{"id":"https://openalex.org/keywords/arabidopsis-thaliana","display_name":"Arabidopsis thaliana","score":0.4230271279811859},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.41805410385131836},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4139314591884613},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.41029125452041626},{"id":"https://openalex.org/keywords/mutant","display_name":"Mutant","score":0.09137415885925293}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8928771018981934},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5969029664993286},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.579707145690918},{"id":"https://openalex.org/C191908910","wikidata":"https://www.wikidata.org/wiki/Q862838","display_name":"Synthetic biology","level":2,"score":0.49419453740119934},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4386788010597229},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.433165967464447},{"id":"https://openalex.org/C2775988993","wikidata":"https://www.wikidata.org/wiki/Q158695","display_name":"Arabidopsis thaliana","level":4,"score":0.4230271279811859},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.41805410385131836},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4139314591884613},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.41029125452041626},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.09137415885925293}],"mesh":[{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"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":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018506","descriptor_name":"Gene Expression Regulation, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018506","descriptor_name":"Gene Expression Regulation, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018506","descriptor_name":"Gene Expression Regulation, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018744","descriptor_name":"DNA, Plant","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018744","descriptor_name":"DNA, Plant","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018744","descriptor_name":"DNA, Plant","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkt518","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkt518","pdf_url":"https://academic.oup.com/nar/article-pdf/41/W1/W569/16944755/gkt518.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:23766287","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23766287","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:europepmc.org:2686106","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3692106","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkt518","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkt518","pdf_url":"https://academic.oup.com/nar/article-pdf/41/W1/W569/16944755/gkt518.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":[],"funders":[{"id":"https://openalex.org/F4320334789","display_name":"Japan Science and Technology Agency","ror":"https://ror.org/00097mb19"},{"id":"https://openalex.org/F4320335125","display_name":"RIKEN","ror":"https://ror.org/01sjwvz98"},{"id":"https://openalex.org/F4320338078","display_name":"National Bioscience Database Center","ror":"https://ror.org/00097mb19"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2155383296.pdf","grobid_xml":"https://content.openalex.org/works/W2155383296.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1605442704","https://openalex.org/W1760665500","https://openalex.org/W2002900187","https://openalex.org/W2017470450","https://openalex.org/W2025529750","https://openalex.org/W2029370898","https://openalex.org/W2029617325","https://openalex.org/W2036370503","https://openalex.org/W2050541807","https://openalex.org/W2051434262","https://openalex.org/W2053427298","https://openalex.org/W2057586591","https://openalex.org/W2057720426","https://openalex.org/W2063671508","https://openalex.org/W2065716803","https://openalex.org/W2088476626","https://openalex.org/W2091731123","https://openalex.org/W2101506009","https://openalex.org/W2102634667","https://openalex.org/W2104593368","https://openalex.org/W2109906206","https://openalex.org/W2109972881","https://openalex.org/W2113328169","https://openalex.org/W2121806138","https://openalex.org/W2135230723","https://openalex.org/W2145091349","https://openalex.org/W2160508925","https://openalex.org/W2160795956","https://openalex.org/W2321143980","https://openalex.org/W2610493035"],"related_works":["https://openalex.org/W2549283853","https://openalex.org/W2581702729","https://openalex.org/W2613929436","https://openalex.org/W2347793859","https://openalex.org/W3151254369","https://openalex.org/W46113340","https://openalex.org/W2093869340","https://openalex.org/W2016183850","https://openalex.org/W2175857012","https://openalex.org/W2056355047"],"abstract_inverted_index":{"Synthetic":[0],"promoters":[1,23],"can":[2],"control":[3],"the":[4,68,88],"timing,":[5],"location":[6],"and":[7,37,60,75,87],"amount":[8],"of":[9],"gene":[10],"expression":[11,36,62],"for":[12,20,41,53,72],"any":[13],"organism.":[14],"PromoterCAD":[15,64,96],"is":[16,65],"a":[17,30],"web":[18,77],"application":[19,78],"designing":[21],"synthetic":[22],"with":[24],"altered":[25],"transcriptional":[26],"regulation.":[27],"We":[28,48],"use":[29],"data-first":[31],"approach,":[32],"using":[33],"published":[34],"high-throughput":[35],"motif":[38],"data":[39,50,73,82],"from":[40],"Arabidopsis":[42],"thaliana":[43],"to":[44,57,83,92],"guide":[45],"DNA":[46],"design.":[47],"demonstrate":[49],"mining":[51],"tools":[52],"finding":[54],"motifs":[55],"related":[56],"circadian":[58],"oscillations":[59],"tissue-specific":[61],"patterns.":[63],"built":[66],"on":[67],"LinkData":[69,99],"open":[70],"platform":[71],"publication":[74],"rapid":[76],"development,":[79],"allowing":[80],"new":[81,94],"be":[84],"easily":[85],"added,":[86],"source":[89],"code":[90],"modified":[91],"add":[93],"functionality.":[95],"URL:":[97,100],"http://promotercad.org.":[98],"http://linkdata.org.":[101]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
