{"id":"https://openalex.org/W2154175537","doi":"https://doi.org/10.1093/nar/gku315","title":"DMINDA: an integrated web server for DNA motif identification and analyses","display_name":"DMINDA: an integrated web server for DNA motif identification and analyses","publication_year":2014,"publication_date":"2014-04-21","ids":{"openalex":"https://openalex.org/W2154175537","doi":"https://doi.org/10.1093/nar/gku315","mag":"2154175537","pmid":"https://pubmed.ncbi.nlm.nih.gov/24753419"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gku315","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gku315","pdf_url":"https://academic.oup.com/nar/article-pdf/42/W1/W12/17422984/gku315.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/42/W1/W12/17422984/gku315.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022408570","display_name":"Qin Ma","orcid":"https://orcid.org/0000-0002-3264-8392"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]},{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qin Ma","raw_affiliation_strings":["Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia,\u00a0Athens\u00a0GA 30602, USA BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA","BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA","Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia,\u00a0Athens\u00a0GA 30602, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia,\u00a0Athens\u00a0GA 30602, USA BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA","institution_ids":[]},{"raw_affiliation_string":"BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA","institution_ids":["https://openalex.org/I1289243028"]},{"raw_affiliation_string":"Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia,\u00a0Athens\u00a0GA 30602, USA","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091716924","display_name":"Han-Yuan Zhang","orcid":"https://orcid.org/0000-0001-5699-9560"},"institutions":[{"id":"https://openalex.org/I4210134929","display_name":"Jilin Province Science and Technology Department","ror":"https://ror.org/049x38272","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210134929"]},{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]},{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Hanyuan Zhang","raw_affiliation_strings":["Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia,\u00a0Athens\u00a0GA 30602, USA College of Computer Science and Technology, Jilin University, Changchun, China","College of Computer Science and Technology, Jilin University, Changchun, China","Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia,\u00a0Athens\u00a0GA 30602, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia,\u00a0Athens\u00a0GA 30602, USA College of Computer Science and Technology, Jilin University, Changchun, China","institution_ids":[]},{"raw_affiliation_string":"College of Computer Science and Technology, Jilin University, Changchun, China","institution_ids":["https://openalex.org/I4210134929","https://openalex.org/I194450716"]},{"raw_affiliation_string":"Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia,\u00a0Athens\u00a0GA 30602, USA","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113706218","display_name":"Xizeng Mao","orcid":null},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]},{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xizeng Mao","raw_affiliation_strings":["Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia,\u00a0Athens\u00a0GA 30602, USA BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA","BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA","Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia,\u00a0Athens\u00a0GA 30602, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia,\u00a0Athens\u00a0GA 30602, USA BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA","institution_ids":[]},{"raw_affiliation_string":"BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA","institution_ids":["https://openalex.org/I1289243028"]},{"raw_affiliation_string":"Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia,\u00a0Athens\u00a0GA 30602, USA","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065428486","display_name":"Chuan\u2010Min Zhou","orcid":"https://orcid.org/0000-0002-5975-4603"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chuan Zhou","raw_affiliation_strings":["School of Mathematics, Shandong University, Jinan, Shandong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics, Shandong University, Jinan, Shandong, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017344694","display_name":"Bingqiang Liu","orcid":"https://orcid.org/0000-0002-5734-1135"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bingqiang Liu","raw_affiliation_strings":["School of Mathematics, Shandong University, Jinan, Shandong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics, Shandong University, Jinan, Shandong, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102829580","display_name":"Xin Chen","orcid":"https://orcid.org/0000-0003-3304-8943"},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]},{"id":"https://openalex.org/I4210134929","display_name":"Jilin Province Science and Technology Department","ror":"https://ror.org/049x38272","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210134929"]},{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Xin Chen","raw_affiliation_strings":["Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia,\u00a0Athens\u00a0GA 30602, USA College of Computer Science and Technology, Jilin University, Changchun, China","Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia,\u00a0Athens\u00a0GA 30602, USA","College of Computer Science and Technology, Jilin University, Changchun, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia,\u00a0Athens\u00a0GA 30602, USA College of Computer Science and Technology, Jilin University, Changchun, China","institution_ids":[]},{"raw_affiliation_string":"Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia,\u00a0Athens\u00a0GA 30602, USA","institution_ids":["https://openalex.org/I165733156"]},{"raw_affiliation_string":"College of Computer Science and Technology, Jilin University, Changchun, China","institution_ids":["https://openalex.org/I4210134929","https://openalex.org/I194450716"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5108133776","display_name":"Ying Xu","orcid":"https://orcid.org/0009-0004-8767-7635"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]},{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]},{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]},{"id":"https://openalex.org/I4210134929","display_name":"Jilin Province Science and Technology Department","ror":"https://ror.org/049x38272","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210134929"]}],"countries":["CN","US"],"is_corresponding":true,"raw_author_name":"Ying Xu","raw_affiliation_strings":["Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia,\u00a0Athens\u00a0GA 30602, USA BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA College of Computer Science and Technology, Jilin University, Changchun, China xyn@bmb.uga.edu","BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA","College of Computer Science and Technology, Jilin University, Changchun, China","Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia,\u00a0Athens\u00a0GA 30602, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia,\u00a0Athens\u00a0GA 30602, USA BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA College of Computer Science and Technology, Jilin University, Changchun, China xyn@bmb.uga.edu","institution_ids":[]},{"raw_affiliation_string":"BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA","institution_ids":["https://openalex.org/I1289243028"]},{"raw_affiliation_string":"College of Computer Science and Technology, Jilin University, Changchun, China","institution_ids":["https://openalex.org/I4210134929","https://openalex.org/I194450716"]},{"raw_affiliation_string":"Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia,\u00a0Athens\u00a0GA 30602, USA","institution_ids":["https://openalex.org/I165733156"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5108133776"],"corresponding_institution_ids":["https://openalex.org/I1289243028","https://openalex.org/I165733156","https://openalex.org/I194450716","https://openalex.org/I4210134929"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":3.49,"has_fulltext":true,"cited_by_count":47,"citation_normalized_percentile":{"value":0.93546216,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"42","issue":"W1","first_page":"W12","last_page":"W19"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998999834060669,"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":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987000226974487,"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/motif","display_name":"Motif (music)","score":0.7953041791915894},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7782621383666992},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.578139066696167},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5525814294815063},{"id":"https://openalex.org/keywords/login","display_name":"Login","score":0.49779629707336426},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.4954742193222046},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4680314362049103},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.44870391488075256},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.32936686277389526},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2838352918624878},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.20550382137298584},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.20005401968955994},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.13031455874443054}],"concepts":[{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.7953041791915894},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7782621383666992},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.578139066696167},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5525814294815063},{"id":"https://openalex.org/C113324615","wikidata":"https://www.wikidata.org/wiki/Q472302","display_name":"Login","level":2,"score":0.49779629707336426},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.4954742193222046},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4680314362049103},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.44870391488075256},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.32936686277389526},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2838352918624878},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.20550382137298584},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.20005401968955994},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.13031455874443054},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","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":"D020407","descriptor_name":"Internet","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":4,"locations":[{"id":"doi:10.1093/nar/gku315","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gku315","pdf_url":"https://academic.oup.com/nar/article-pdf/42/W1/W12/17422984/gku315.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:24753419","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24753419","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:osti.gov:1625537","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1625537","pdf_url":"https://www.osti.gov/servlets/purl/1625537","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:europepmc.org:3221339","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4086085","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/gku315","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gku315","pdf_url":"https://academic.oup.com/nar/article-pdf/42/W1/W12/17422984/gku315.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/G2225572173","display_name":null,"funder_award_id":"0830024","funder_id":"https://openalex.org/F4320337400","funder_display_name":"Division of Environmental Biology"},{"id":"https://openalex.org/G2236177641","display_name":"Horizontal gene transfer and among phyla relationships","funder_award_id":"0830024","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2377916143","display_name":"Experimental and Computational Systems Analysis of Stress Responses in Lactococcus","funder_award_id":"0958172","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2529231737","display_name":null,"funder_award_id":"NSF MCB-0958172","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2960156542","display_name":null,"funder_award_id":"MCB-0958172","funder_id":"https://openalex.org/F4320337397","funder_display_name":"Division of Molecular and Cellular Biosciences"},{"id":"https://openalex.org/G4232076736","display_name":null,"funder_award_id":"61303084","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4493873119","display_name":null,"funder_award_id":"DE-PS02-06ER64304","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G5200835839","display_name":null,"funder_award_id":"ZR2011FQ010","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6328578889","display_name":null,"funder_award_id":"DE-PS02-06ER64304","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G7076439875","display_name":null,"funder_award_id":"NSF DEB-0830024","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7892530385","display_name":null,"funder_award_id":"DEB-0830024","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G822646400","display_name":null,"funder_award_id":"DE-PS02-06ER64304","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G8838764843","display_name":null,"funder_award_id":"MCB-0958172","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"},{"id":"https://openalex.org/F4320337397","display_name":"Division of Molecular and Cellular Biosciences","ror":"https://ror.org/002jdaq33"},{"id":"https://openalex.org/F4320337400","display_name":"Division of Environmental Biology","ror":"https://ror.org/03g87he71"},{"id":"https://openalex.org/F4320337509","display_name":"Biological and Environmental Research","ror":"https://ror.org/0114b2m14"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2154175537.pdf","grobid_xml":"https://content.openalex.org/works/W2154175537.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1263422348","https://openalex.org/W1644724366","https://openalex.org/W1964733653","https://openalex.org/W1975992663","https://openalex.org/W1988294855","https://openalex.org/W1998040815","https://openalex.org/W2011457803","https://openalex.org/W2036131961","https://openalex.org/W2036771037","https://openalex.org/W2055016234","https://openalex.org/W2055109879","https://openalex.org/W2067524083","https://openalex.org/W2073661767","https://openalex.org/W2074584798","https://openalex.org/W2080152736","https://openalex.org/W2089783852","https://openalex.org/W2100945610","https://openalex.org/W2101292724","https://openalex.org/W2108478344","https://openalex.org/W2121365413","https://openalex.org/W2123732476","https://openalex.org/W2124201730","https://openalex.org/W2135861471","https://openalex.org/W2140952049","https://openalex.org/W2145010689","https://openalex.org/W2145921127","https://openalex.org/W2148032724","https://openalex.org/W2152071686","https://openalex.org/W2152121035","https://openalex.org/W2152269861","https://openalex.org/W2156553342","https://openalex.org/W2156627746","https://openalex.org/W2157009395","https://openalex.org/W2168249156","https://openalex.org/W2169056802","https://openalex.org/W2795830831","https://openalex.org/W6628043643","https://openalex.org/W6641349891","https://openalex.org/W6678841368"],"related_works":["https://openalex.org/W4256170434","https://openalex.org/W4233948907","https://openalex.org/W2073661767","https://openalex.org/W2380185347","https://openalex.org/W2370034659","https://openalex.org/W2159636084","https://openalex.org/W2117168988","https://openalex.org/W2103777723","https://openalex.org/W2610941444","https://openalex.org/W1998040815"],"abstract_inverted_index":{"DMINDA":[0],"(DNA":[1],"motif":[2,13,44,64,92,97,103,140,160],"identification":[3,14],"and":[4,15,31,105,110,135,142,154,162,172],"analyses)":[5],"is":[6,18,25,33,123,136],"an":[7],"integrated":[8],"web":[9,23,156],"server":[10,38,122,157],"for":[11,66,77,139,158],"DNA":[12,48],"analyses,":[16,163],"which":[17,50],"accessible":[19],"at":[20],"http://csbl.bmb.uga.edu/DMINDA/.":[21],"This":[22,37],"site":[24],"freely":[26],"available":[27],"to":[28,53],"all":[29],"users":[30],"there":[32],"no":[34],"login":[35],"requirement.":[36],"provides":[39],"a":[40,67,87,95,126,152],"suite":[41],"of":[42,55,58,70,94,107,114],"cis-regulatory":[43,159],"analysis":[45],"functions":[46],"on":[47,83],"sequences,":[49,101],"are":[51],"important":[52],"elucidation":[54],"the":[56,78,166],"mechanisms":[57],"transcriptional":[59],"regulation:":[60],"(i)":[61],"de":[62],"novo":[63],"finding":[65,161],"given":[68,118],"set":[69],"promoter":[71,119],"sequences":[72],"along":[73],"with":[74,130],"statistical":[75],"scores":[76],"predicted":[79],"motifs":[80,116],"derived":[81],"based":[82],"information":[84],"extracted":[85],"from":[86],"control":[88],"set,":[89],"(ii)":[90],"scanning":[91],"instances":[93],"query":[96,115],"in":[98,117,144,170,176],"provided":[99],"genomic":[100,167],"(iii)":[102],"comparison":[104],"clustering":[106],"identified":[108],"motifs,":[109],"(iv)":[111],"co-occurrence":[112],"analyses":[113,143],"sequences.":[120],"The":[121],"powered":[124],"by":[125],"backend":[127],"computer":[128],"cluster":[129],"over":[131],"150":[132],"computing":[133],"nodes,":[134],"particularly":[137],"useful":[138],"prediction":[141],"prokaryotic":[145,173],"genomes.":[146],"We":[147],"believe":[148],"that":[149],"DMINDA,":[150],"as":[151],"new":[153],"comprehensive":[155],"will":[164],"benefit":[165],"research":[168],"community":[169],"general":[171],"genome":[174],"researchers":[175],"particular.":[177]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":10},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":2}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
