{"id":"https://openalex.org/W2158806109","doi":"https://doi.org/10.1093/bioinformatics/btn626","title":"Identification of microRNA regulatory modules in<i>Arabidopsis</i>via a probabilistic graphical model","display_name":"Identification of microRNA regulatory modules in<i>Arabidopsis</i>via a probabilistic graphical model","publication_year":2008,"publication_date":"2008-12-04","ids":{"openalex":"https://openalex.org/W2158806109","doi":"https://doi.org/10.1093/bioinformatics/btn626","mag":"2158806109","pmid":"https://pubmed.ncbi.nlm.nih.gov/19056778"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn626","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn626","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/3/387/48982733/bioinformatics_25_3_387.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/25/3/387/48982733/bioinformatics_25_3_387.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060488559","display_name":"Je\u2010Gun Joung","orcid":"https://orcid.org/0000-0003-2859-1036"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I4210142299","display_name":"Robert W. Holley Center for Agriculture & Health","ror":"https://ror.org/050z40a57","country_code":"US","type":"facility","lineage":["https://openalex.org/I1312222531","https://openalex.org/I1336096307","https://openalex.org/I4210138094","https://openalex.org/I4210142299"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Je-Gun Joung","raw_affiliation_strings":["1 Boyce Thompson Institute for Plant Research, Cornell University and 2USDA Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA"],"affiliations":[{"raw_affiliation_string":"1 Boyce Thompson Institute for Plant Research, Cornell University and 2USDA Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA","institution_ids":["https://openalex.org/I4210142299","https://openalex.org/I205783295"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060776410","display_name":"Zhangjun Fei","orcid":"https://orcid.org/0000-0001-9684-1450"},"institutions":[{"id":"https://openalex.org/I4210142299","display_name":"Robert W. Holley Center for Agriculture & Health","ror":"https://ror.org/050z40a57","country_code":"US","type":"facility","lineage":["https://openalex.org/I1312222531","https://openalex.org/I1336096307","https://openalex.org/I4210138094","https://openalex.org/I4210142299"]},{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhangjun Fei","raw_affiliation_strings":["1 Boyce Thompson Institute for Plant Research, Cornell University and 2USDA Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA"],"affiliations":[{"raw_affiliation_string":"1 Boyce Thompson Institute for Plant Research, Cornell University and 2USDA Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA","institution_ids":["https://openalex.org/I4210142299","https://openalex.org/I205783295"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5060488559"],"corresponding_institution_ids":["https://openalex.org/I205783295","https://openalex.org/I4210142299"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.9123,"has_fulltext":true,"cited_by_count":45,"citation_normalized_percentile":{"value":0.93261921,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"25","issue":"3","first_page":"387","last_page":"393"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10184","display_name":"Plant Molecular Biology Research","score":0.9998999834060669,"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":0.9998999834060669,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9829999804496765,"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/T10062","display_name":"MicroRNA in disease regulation","score":0.9746000170707703,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/microrna","display_name":"microRNA","score":0.7772588729858398},{"id":"https://openalex.org/keywords/arabidopsis","display_name":"Arabidopsis","score":0.6887990236282349},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6845209002494812},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6207534074783325},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.5677407383918762},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5154012441635132},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4941761791706085},{"id":"https://openalex.org/keywords/regulatory-sequence","display_name":"Regulatory sequence","score":0.46327826380729675},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.41529086232185364},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.37667062878608704}],"concepts":[{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.7772588729858398},{"id":"https://openalex.org/C2779491563","wikidata":"https://www.wikidata.org/wiki/Q157892","display_name":"Arabidopsis","level":4,"score":0.6887990236282349},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6845209002494812},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6207534074783325},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.5677407383918762},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5154012441635132},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4941761791706085},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.46327826380729675},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.41529086232185364},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.37667062878608704},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btn626","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn626","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/3/387/48982733/bioinformatics_25_3_387.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19056778","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19056778","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btn626","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn626","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/3/387/48982733/bioinformatics_25_3_387.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1923747540","display_name":"Functional Genomic Analysis of Fruit Flavor and Nutrition Pathways","funder_award_id":"0501778","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","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"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2158806109.pdf","grobid_xml":"https://content.openalex.org/works/W2158806109.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W144423133","https://openalex.org/W1967543716","https://openalex.org/W1973614663","https://openalex.org/W1975304818","https://openalex.org/W1979268646","https://openalex.org/W1994814273","https://openalex.org/W2001605136","https://openalex.org/W2002745689","https://openalex.org/W2005557141","https://openalex.org/W2007220556","https://openalex.org/W2011518477","https://openalex.org/W2017270642","https://openalex.org/W2018403717","https://openalex.org/W2018899540","https://openalex.org/W2030583245","https://openalex.org/W2032231928","https://openalex.org/W2038303173","https://openalex.org/W2038622868","https://openalex.org/W2053427298","https://openalex.org/W2057606871","https://openalex.org/W2057682468","https://openalex.org/W2067854876","https://openalex.org/W2070571588","https://openalex.org/W2079165446","https://openalex.org/W2084833542","https://openalex.org/W2087430129","https://openalex.org/W2090822981","https://openalex.org/W2096600985","https://openalex.org/W2097820884","https://openalex.org/W2099485284","https://openalex.org/W2100890297","https://openalex.org/W2109154616","https://openalex.org/W2111250074","https://openalex.org/W2111773716","https://openalex.org/W2125879257","https://openalex.org/W2128667600","https://openalex.org/W2129243798","https://openalex.org/W2131253190","https://openalex.org/W2131674459","https://openalex.org/W2134515324","https://openalex.org/W2137523780","https://openalex.org/W2137672602","https://openalex.org/W2140124448","https://openalex.org/W2140415861","https://openalex.org/W2142204601","https://openalex.org/W2143274936","https://openalex.org/W2153195747","https://openalex.org/W2156852055","https://openalex.org/W2157039533","https://openalex.org/W2158128075","https://openalex.org/W2158962723","https://openalex.org/W2160069833","https://openalex.org/W2162170048","https://openalex.org/W2166574880","https://openalex.org/W2167190345","https://openalex.org/W6680343917"],"related_works":["https://openalex.org/W2128583238","https://openalex.org/W2134405083","https://openalex.org/W2049907435","https://openalex.org/W2010571965","https://openalex.org/W2034377088","https://openalex.org/W3128451840","https://openalex.org/W2002709996","https://openalex.org/W4387092964","https://openalex.org/W2277277196","https://openalex.org/W2043274041"],"abstract_inverted_index":{"We":[0],"applied":[1],"our":[2,104],"method":[3,78,105],"to":[4,52,97],"datasets":[5],"of":[6,12,18,81,91,101,119],"different":[7],"sources":[8],"from":[9],"Arabidopsis":[10],"consisting":[11],"miRNA-target":[13],"pair":[14],"information,":[15],"upstream":[16],"sequences":[17],"miRNAs,":[19,82,92],"transcriptional":[20,70,117,122],"regulatory":[21,57,110,127],"motifs":[22],"and":[23,41,121],"gene":[24,126],"expression":[25,90],"profiles.":[26],"The":[27,76],"graphical":[28],"model":[29],"used":[30],"in":[31,60,125],"this":[32,65],"study":[33],"can":[34,67,106],"efficiently":[35],"capture":[36],"the":[37,89],"relationship":[38],"between":[39],"miRNAs":[40,120],"diverse":[42,98],"conditions":[43],"such":[44],"as":[45,83,85],"various":[46],"developmental":[47,99],"processes,":[48],"thus":[49],"allowing":[50],"us":[51],"detect":[53],"functionally":[54],"correlated":[55],"miRNA":[56,109],"modules":[58],"involved":[59,124],"specific":[61],"biological":[62],"processes.":[63],"Furthermore,":[64],"approach":[66],"reveal":[68],"core":[69],"elements":[71],"associated":[72],"with":[73],"their":[74],"miRNAs.":[75],"proposed":[77],"found":[79],"clusters":[80],"well":[84],"putative":[86],"regulators":[87],"controlling":[88],"which":[93],"were":[94],"highly":[95],"related":[96],"processes":[100],"Arabidopsis.":[102],"Consequently,":[103],"provide":[107],"hypothetical":[108],"circuits":[111],"for":[112],"functional":[113],"testing":[114],"that":[115],"represent":[116],"events":[118],"factors":[123],"pathways.":[128]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":5}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2016-06-24T00:00:00"}