{"id":"https://openalex.org/W2560125283","doi":"https://doi.org/10.1186/s12918-016-0373-1","title":"DMirNet: Inferring direct microRNA-mRNA association networks","display_name":"DMirNet: Inferring direct microRNA-mRNA association networks","publication_year":2016,"publication_date":"2016-12-01","ids":{"openalex":"https://openalex.org/W2560125283","doi":"https://doi.org/10.1186/s12918-016-0373-1","mag":"2560125283","pmid":"https://pubmed.ncbi.nlm.nih.gov/28105958"},"language":"en","primary_location":{"id":"doi:10.1186/s12918-016-0373-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-016-0373-1","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-016-0373-1","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-016-0373-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101411024","display_name":"Minsu Lee","orcid":"https://orcid.org/0000-0001-9017-6998"},"institutions":[{"id":"https://openalex.org/I138925566","display_name":"Ewha Womans University","ror":"https://ror.org/053fp5c05","country_code":"KR","type":"education","lineage":["https://openalex.org/I138925566"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Minsu Lee","raw_affiliation_strings":["Department of Computer Science and Engineering, Ewha Womans University, Seoul, South Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Ewha Womans University, Seoul, South Korea","institution_ids":["https://openalex.org/I138925566"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006920003","display_name":"HyungJune Lee","orcid":"https://orcid.org/0000-0003-4655-4298"},"institutions":[{"id":"https://openalex.org/I138925566","display_name":"Ewha Womans University","ror":"https://ror.org/053fp5c05","country_code":"KR","type":"education","lineage":["https://openalex.org/I138925566"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"HyungJune Lee","raw_affiliation_strings":["Department of Computer Science and Engineering, Ewha Womans University, Seoul, South Korea. hyungjune.lee@ewha.ac.kr","Department of Computer Science and Engineering, Ewha Womans University, Seoul, South Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Ewha Womans University, Seoul, South Korea. hyungjune.lee@ewha.ac.kr","institution_ids":["https://openalex.org/I138925566"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Ewha Womans University, Seoul, South Korea","institution_ids":["https://openalex.org/I138925566"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5006920003"],"corresponding_institution_ids":["https://openalex.org/I138925566"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":0.3539,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.62697371,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"10","issue":"S5","first_page":"125","last_page":"125"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":0.991100013256073,"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"}},"topics":[{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":0.991100013256073,"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"}},{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.002199999988079071,"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"}},{"id":"https://openalex.org/T11297","display_name":"Ferroptosis and cancer prognosis","score":0.0010000000474974513,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5622457265853882},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5600576400756836},{"id":"https://openalex.org/keywords/microrna","display_name":"microRNA","score":0.5418726801872253},{"id":"https://openalex.org/keywords/deconvolution","display_name":"Deconvolution","score":0.4178195595741272},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39862683415412903},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3933795690536499},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3380683660507202},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.240542471408844},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19061881303787231},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10322225093841553}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5622457265853882},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5600576400756836},{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.5418726801872253},{"id":"https://openalex.org/C174576160","wikidata":"https://www.wikidata.org/wiki/Q1183700","display_name":"Deconvolution","level":2,"score":0.4178195595741272},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39862683415412903},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3933795690536499},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3380683660507202},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.240542471408844},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19061881303787231},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10322225093841553}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","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":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/s12918-016-0373-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-016-0373-1","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-016-0373-1","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:28105958","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28105958","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":"BMC systems biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5249041","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5249041","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12918-016-0373-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-016-0373-1","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-016-0373-1","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.4399999976158142}],"awards":[{"id":"https://openalex.org/G4251555815","display_name":null,"funder_award_id":"2015H1C3A1064579","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"}],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320322030","display_name":"Ministry of Science, ICT and Future Planning","ror":"https://ror.org/032e49973"},{"id":"https://openalex.org/F4320322120","display_name":"National Research Foundation of Korea","ror":"https://ror.org/013aysd81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2560125283.pdf","grobid_xml":"https://content.openalex.org/works/W2560125283.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W144423133","https://openalex.org/W1648301895","https://openalex.org/W1794091547","https://openalex.org/W1877170500","https://openalex.org/W1890374229","https://openalex.org/W1944858750","https://openalex.org/W1974352012","https://openalex.org/W1990512452","https://openalex.org/W1995082021","https://openalex.org/W1996361117","https://openalex.org/W1997639391","https://openalex.org/W2001334414","https://openalex.org/W2007368465","https://openalex.org/W2009326616","https://openalex.org/W2011463435","https://openalex.org/W2015208937","https://openalex.org/W2016106370","https://openalex.org/W2021034217","https://openalex.org/W2024990640","https://openalex.org/W2053003053","https://openalex.org/W2065125559","https://openalex.org/W2069765376","https://openalex.org/W2083381199","https://openalex.org/W2084277087","https://openalex.org/W2095852413","https://openalex.org/W2096967557","https://openalex.org/W2101117089","https://openalex.org/W2109384743","https://openalex.org/W2119974836","https://openalex.org/W2120456037","https://openalex.org/W2122926097","https://openalex.org/W2134118500","https://openalex.org/W2135046866","https://openalex.org/W2135059404","https://openalex.org/W2136943892","https://openalex.org/W2140000393","https://openalex.org/W2153195747","https://openalex.org/W2157677823","https://openalex.org/W2159675211","https://openalex.org/W2162674813","https://openalex.org/W2165065179","https://openalex.org/W2169589032","https://openalex.org/W2197980526","https://openalex.org/W2229421811","https://openalex.org/W2912934387","https://openalex.org/W3103971085"],"related_works":["https://openalex.org/W2805745868","https://openalex.org/W3191462603","https://openalex.org/W3095610875","https://openalex.org/W1989319466","https://openalex.org/W2143341069","https://openalex.org/W3164586775","https://openalex.org/W2507286762","https://openalex.org/W2333231571","https://openalex.org/W2034768496","https://openalex.org/W2950221807"],"abstract_inverted_index":{"BACKGROUND:":[0],"MicroRNAs":[1],"(miRNAs)":[2],"play":[3],"important":[4],"regulatory":[5,340],"roles":[6],"in":[7,66,249],"the":[8,24,50,67,83,101,111,115,129,140,187,210,243,259,267,271,319,330,347],"wide":[9],"range":[10],"of":[11,29,128,135,246,278],"biological":[12],"processes":[13],"by":[14,48],"inducing":[15],"target":[16,34],"mRNA":[17,54],"degradation":[18],"or":[19,95,160],"translational":[20],"repression.":[21],"Based":[22],"on":[23,114,239],"correlation":[25,195],"between":[26,132],"expression":[27,55,77,85,136,218],"profiles":[28,86],"a":[30,153,176,222,228,276,307],"miRNA":[31,52],"and":[32,53,125,220,230,316],"its":[33],"mRNA,":[35],"various":[36,338],"computational":[37,143],"methods":[38,90,144,197],"have":[39],"previously":[40,141],"been":[41],"proposed":[42,142],"to":[43,63,100,110,121,203,213,226,280,310,317,336],"identify":[44,284,311],"miRNA-mRNA":[45,73,182,206,289,298,314,321,349],"association":[46,74,183,207,290,299,322,350],"networks":[47,75],"incorporating":[49],"matched":[51],"profiles.":[56,78,137],"However,":[57],"there":[58],"remain":[59],"three":[60,193,240,273],"major":[61],"issues":[62],"be":[64],"resolved":[65],"conventional":[68,88],"computation":[69],"approaches":[70],"for":[71,179],"inferring":[72],"from":[76,82,147,292,329],"1)":[79,192],"Inferred":[80],"correlations":[81,131],"observed":[84,331],"using":[87],"correlation-based":[89],"include":[91],"numerous":[92],"erroneous":[93],"links":[94],"over-estimated":[96],"edge":[97],"weight":[98],"due":[99],"transitive":[102],"information":[103],"flow":[104],"among":[105],"direct":[106,181,194,205,297,313,320,327,339,348],"associations.":[107],"2)":[108,209],"Due":[109],"high-dimension-low-sample-size":[112],"problem":[113],"microarray":[116],"dataset,":[117],"it":[118],"is":[119,166,306],"difficult":[120],"obtain":[122],"an":[123,293],"accurate":[124],"reliable":[126,155,229],"estimate":[127],"empirical":[130,237],"all":[133],"pairs":[134],"3)":[138,221],"Because":[139],"usually":[145],"suffer":[146],"varying":[148],"performance":[149,162,252,269],"across":[150,163,233,270],"different":[151,164,234],"datasets,":[152,274],"more":[154],"model":[156,232,262],"that":[157,256,304],"guarantees":[158],"optimal":[159],"suboptimal":[161],"datasets":[165,241],"highly":[167],"needed.":[168],"RESULTS:":[169],"In":[170],"this":[171],"paper,":[172],"we":[173,283],"present":[174],"DMirNet,":[175],"new":[177],"framework":[178],"identifying":[180],"networks.":[184,323,351],"To":[185],"tackle":[186],"aforementioned":[188],"issues,":[189],"DMirNet":[190,257,305,325,333],"incorporates":[191],"estimation":[196],"(namely":[198],"Corpcor,":[199],"SPACE,":[200],"Network":[201],"deconvolution)":[202],"infer":[204],"networks,":[208],"bootstrapping":[211],"method":[212,309],"fully":[214],"utilize":[215],"insufficient":[216],"training":[217],"profiles,":[219],"rank-based":[223],"Ensemble":[224],"aggregation":[225],"build":[227],"robust":[231],"datasets.":[235],"Our":[236],"experiments":[238,254],"demonstrate":[242],"combinatorial":[244],"effects":[245],"necessary":[247],"components":[248],"DMirNet.":[250],"Additional":[251],"comparison":[253],"show":[255],"outperforms":[258],"state-of-the-art":[260],"Ensemble-based":[261],"[1]":[263],"which":[264],"has":[265],"shown":[266],"best":[268],"same":[272],"with":[275],"factor":[277],"up":[279],"1.29.":[281],"Further,":[282],"43":[285],"putative":[286],"novel":[287,312],"multi-cancer-related":[288],"relationships":[291,328],"inferred":[294],"Top":[295],"1000":[296],"network.":[300],"CONCLUSIONS:":[301],"We":[302],"believe":[303],"promising":[308],"relations":[315],"elucidate":[318],"Since":[324],"infers":[326],"data,":[332],"can":[334],"contribute":[335],"reconstructing":[337],"pathways,":[341],"including,":[342],"but":[343],"not":[344],"limited":[345],"to,":[346]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
