{"id":"https://openalex.org/W2953976443","doi":"https://doi.org/10.1186/s12859-019-2893-3","title":"JCD-DEA: a joint covariate detection tool for differential expression analysis on tumor expression profiles","display_name":"JCD-DEA: a joint covariate detection tool for differential expression analysis on tumor expression profiles","publication_year":2019,"publication_date":"2019-06-28","ids":{"openalex":"https://openalex.org/W2953976443","doi":"https://doi.org/10.1186/s12859-019-2893-3","mag":"2953976443","pmid":"https://pubmed.ncbi.nlm.nih.gov/31253075"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-2893-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2893-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-019-2893-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-019-2893-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075872658","display_name":"Yi Li","orcid":"https://orcid.org/0000-0002-2580-7500"},"institutions":[{"id":"https://openalex.org/I47689461","display_name":"Northeast Forestry University","ror":"https://ror.org/02yxnh564","country_code":"CN","type":"education","lineage":["https://openalex.org/I47689461"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yi Li","raw_affiliation_strings":["College of Information and Computer Engineering, Northeast Forestry University, No.26 Hexing Road, Harbin, 150040, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information and Computer Engineering, Northeast Forestry University, No.26 Hexing Road, Harbin, 150040, China","institution_ids":["https://openalex.org/I47689461"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100387399","display_name":"Yanan Liu","orcid":"https://orcid.org/0000-0002-0091-7068"},"institutions":[{"id":"https://openalex.org/I47689461","display_name":"Northeast Forestry University","ror":"https://ror.org/02yxnh564","country_code":"CN","type":"education","lineage":["https://openalex.org/I47689461"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanan Liu","raw_affiliation_strings":["College of Information and Computer Engineering, Northeast Forestry University, No.26 Hexing Road, Harbin, 150040, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information and Computer Engineering, Northeast Forestry University, No.26 Hexing Road, Harbin, 150040, China","institution_ids":["https://openalex.org/I47689461"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101463861","display_name":"Yiming Wu","orcid":"https://orcid.org/0000-0002-2571-8065"},"institutions":[{"id":"https://openalex.org/I47689461","display_name":"Northeast Forestry University","ror":"https://ror.org/02yxnh564","country_code":"CN","type":"education","lineage":["https://openalex.org/I47689461"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yiming Wu","raw_affiliation_strings":["College of Information and Computer Engineering, Northeast Forestry University, No.26 Hexing Road, Harbin, 150040, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information and Computer Engineering, Northeast Forestry University, No.26 Hexing Road, Harbin, 150040, China","institution_ids":["https://openalex.org/I47689461"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054894664","display_name":"Xudong Zhao","orcid":"https://orcid.org/0000-0003-2272-6278"},"institutions":[{"id":"https://openalex.org/I47689461","display_name":"Northeast Forestry University","ror":"https://ror.org/02yxnh564","country_code":"CN","type":"education","lineage":["https://openalex.org/I47689461"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xudong Zhao","raw_affiliation_strings":["College of Information and Computer Engineering, Northeast Forestry University, No.26 Hexing Road, Harbin, 150040, China. zhaoxudong@nefu.edu.cn","College of Information and Computer Engineering, Northeast Forestry University, No.26 Hexing Road, Harbin, 150040, China"],"raw_orcid":"https://orcid.org/0000-0003-2272-6278","affiliations":[{"raw_affiliation_string":"College of Information and Computer Engineering, Northeast Forestry University, No.26 Hexing Road, Harbin, 150040, China. zhaoxudong@nefu.edu.cn","institution_ids":["https://openalex.org/I47689461"]},{"raw_affiliation_string":"College of Information and Computer Engineering, Northeast Forestry University, No.26 Hexing Road, Harbin, 150040, China","institution_ids":["https://openalex.org/I47689461"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5054894664"],"corresponding_institution_ids":["https://openalex.org/I47689461"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.2276,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.51017707,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"20","issue":"1","first_page":"365","last_page":"365"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.6395999789237976,"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/T10885","display_name":"Gene expression and cancer classification","score":0.6395999789237976,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.07249999791383743,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.020400000736117363,"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/covariate","display_name":"Covariate","score":0.8253348469734192},{"id":"https://openalex.org/keywords/feature-selection","display_name":"Feature selection","score":0.6692044138908386},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.6355788111686707},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5729654431343079},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5423797369003296},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.5204575061798096},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5198186635971069},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4546603858470917},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4345824420452118},{"id":"https://openalex.org/keywords/multivariate-statistics","display_name":"Multivariate statistics","score":0.43300649523735046},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3642100691795349},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.35363394021987915}],"concepts":[{"id":"https://openalex.org/C119043178","wikidata":"https://www.wikidata.org/wiki/Q320723","display_name":"Covariate","level":2,"score":0.8253348469734192},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.6692044138908386},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.6355788111686707},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5729654431343079},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5423797369003296},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.5204575061798096},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5198186635971069},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4546603858470917},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4345824420452118},{"id":"https://openalex.org/C161584116","wikidata":"https://www.wikidata.org/wiki/Q1952580","display_name":"Multivariate statistics","level":2,"score":0.43300649523735046},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3642100691795349},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.35363394021987915},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015999","descriptor_name":"Multivariate Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015999","descriptor_name":"Multivariate Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015999","descriptor_name":"Multivariate Analysis","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":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-019-2893-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2893-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-019-2893-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31253075","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31253075","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 bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:65df488f69f244f590631c736fa018da","is_oa":false,"landing_page_url":"https://doaj.org/article/65df488f69f244f590631c736fa018da","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 20, Iss 1, Pp 1-13 (2019)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6599234","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6599234","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 Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-2893-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2893-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-019-2893-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Reduced inequalities","score":0.6899999976158142,"id":"https://metadata.un.org/sdg/10"}],"awards":[{"id":"https://openalex.org/G1896700244","display_name":null,"funder_award_id":"2572018BH01","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"}],"funders":[{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2953976443.pdf","grobid_xml":"https://content.openalex.org/works/W2953976443.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W138536204","https://openalex.org/W205781740","https://openalex.org/W563832787","https://openalex.org/W1533335653","https://openalex.org/W1663973292","https://openalex.org/W1937026393","https://openalex.org/W1964895626","https://openalex.org/W1997917263","https://openalex.org/W2007601283","https://openalex.org/W2023558395","https://openalex.org/W2056353125","https://openalex.org/W2062353821","https://openalex.org/W2099954091","https://openalex.org/W2110065044","https://openalex.org/W2120824812","https://openalex.org/W2121966150","https://openalex.org/W2138421578","https://openalex.org/W2146512944","https://openalex.org/W2147528194","https://openalex.org/W2288929640","https://openalex.org/W2497297917","https://openalex.org/W2580767461","https://openalex.org/W2594639291","https://openalex.org/W2601734289","https://openalex.org/W2728595591","https://openalex.org/W2756016415","https://openalex.org/W2797584152","https://openalex.org/W2904560543","https://openalex.org/W2911964244","https://openalex.org/W2951936974","https://openalex.org/W2962894282","https://openalex.org/W3099018540","https://openalex.org/W3121452939","https://openalex.org/W4205210034","https://openalex.org/W4206080774","https://openalex.org/W4210793115","https://openalex.org/W6649495440"],"related_works":["https://openalex.org/W2985746494","https://openalex.org/W4206042385","https://openalex.org/W2511384863","https://openalex.org/W2096089271","https://openalex.org/W2923628599","https://openalex.org/W2051519658","https://openalex.org/W2014100433","https://openalex.org/W2002304499","https://openalex.org/W4386564352","https://openalex.org/W2952668426"],"abstract_inverted_index":{"BACKGROUND:":[0],"Differential":[1],"expression":[2,6,100,104,186,190],"analysis":[3,39,101,187],"on":[4,47,51,69,84,102,122,164,188],"tumor":[5,103,189],"profiles":[7],"has":[8],"always":[9],"been":[10],"a":[11,75,93,135],"key":[12],"issue":[13],"for":[14,58,98,129,140,151,184],"subsequent":[15],"biological":[16],"experimental":[17],"validation.":[18],"It":[19],"is":[20,126,138,194],"important":[21],"how":[22],"to":[23,114],"select":[24],"features":[25],"which":[26,65,154,176],"best":[27],"discriminate":[28],"between":[29],"different":[30],"groups":[31],"of":[32,37,78,132,172,180],"patients.":[33],"Despite":[34],"the":[35,79,141,149,170,173,178],"emergence":[36],"multivariate":[38],"approaches,":[40],"prevailing":[41],"feature":[42,88],"selection":[43,89,119,131],"methods":[44],"primarily":[45],"focus":[46],"multiple":[48],"hypothesis":[49,70,109],"testing":[50,110,112],"individual":[52],"variables,":[53],"and":[54,166],"then":[55],"combine":[56],"them":[57],"an":[59],"explanatory":[60],"result.":[61],"Besides,":[62,134],"these":[63],"methods,":[64],"are":[66,155],"commonly":[67],"based":[68,121],"testing,":[71],"view":[72],"classification":[73,115],"as":[74],"posterior":[76],"validation":[77],"selected":[80],"variables.":[81],"RESULTS:":[82],"Based":[83],"previously":[85],"provided":[86],"A5":[87],"strategy,":[90],"we":[91],"develop":[92],"joint":[94,181],"covariate":[95,146,182],"detection":[96,147,183],"tool":[97],"differential":[99,185],"profiles.":[105,191],"This":[106],"software":[107,193],"combines":[108],"with":[111],"according":[113],"results.":[116],"A":[117],"model":[118,125],"approach":[120],"Gaussian":[123],"mixture":[124],"introduced":[127],"in":[128],"automatic":[130],"features.":[133],"projection":[136],"heatmap":[137],"proposed":[139],"first":[142],"time.":[143],"CONCLUSIONS:":[144],"Joint":[145],"strengthens":[148],"viewpoint":[150],"selecting":[152],"variables":[153],"not":[156],"only":[157],"individually":[158],"but":[159],"also":[160],"jointly":[161],"significant.":[162],"Experiments":[163],"simulation":[165],"realistic":[167],"data":[168],"show":[169],"effectiveness":[171],"developed":[174],"software,":[175],"enhances":[177],"reliability":[179],"The":[192],"available":[195],"at":[196],"http://bio-nefu.com/resource/jcd-dea":[197],".":[198]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":2}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
