{"id":"https://openalex.org/W4293574472","doi":"https://doi.org/10.1089/omi.2022.0089","title":"Precision Oncology: An Ensembled Machine Learning Approach to Identify a Candidate mRNA Panel for Stratification of Patients with Breast Cancer","display_name":"Precision Oncology: An Ensembled Machine Learning Approach to Identify a Candidate mRNA Panel for Stratification of Patients with Breast Cancer","publication_year":2022,"publication_date":"2022-08-30","ids":{"openalex":"https://openalex.org/W4293574472","doi":"https://doi.org/10.1089/omi.2022.0089","pmid":"https://pubmed.ncbi.nlm.nih.gov/36040394"},"language":"en","primary_location":{"id":"doi:10.1089/omi.2022.0089","doi":"https://doi.org/10.1089/omi.2022.0089","is_oa":false,"landing_page_url":"https://doi.org/10.1089/omi.2022.0089","pdf_url":null,"source":{"id":"https://openalex.org/S116972989","display_name":"OMICS A Journal of Integrative Biology","issn_l":"1536-2310","issn":["1536-2310","1557-8100"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443","https://openalex.org/P4310320017"],"host_organization_lineage_names":["Mary Ann Liebert, Inc.","SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"OMICS: A Journal of Integrative Biology","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"F\u0131rat Kurt","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I74897591","display_name":"Marmara University","ror":"https://ror.org/02kswqa67","country_code":"TR","type":"education","lineage":["https://openalex.org/I74897591"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"F\u0131rat Kurt","raw_affiliation_strings":["Department of Computer Engineering and Faculty of Engineering, Marmara University, Istanbul, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering and Faculty of Engineering, Marmara University, Istanbul, Turkey","institution_ids":["https://openalex.org/I74897591"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047072808","display_name":"Mustafa Agao\u011flu","orcid":"https://orcid.org/0000-0002-7678-6316","observed_orcids":["https://orcid.org/0000-0002-7678-6316"]},"institutions":[{"id":"https://openalex.org/I74897591","display_name":"Marmara University","ror":"https://ror.org/02kswqa67","country_code":"TR","type":"education","lineage":["https://openalex.org/I74897591"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Mustafa Agaoglu","raw_affiliation_strings":["Department of Computer Engineering and Faculty of Engineering, Marmara University, Istanbul, Turkey"],"raw_orcid":"https://orcid.org/0000-0002-7678-6316","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering and Faculty of Engineering, Marmara University, Istanbul, Turkey","institution_ids":["https://openalex.org/I74897591"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023136939","display_name":"Kaz\u0131m Yal\u00e7\u0131n Ar\u011fa","orcid":"https://orcid.org/0000-0002-6036-1348","observed_orcids":["https://orcid.org/0000-0002-6036-1348"]},"institutions":[{"id":"https://openalex.org/I74897591","display_name":"Marmara University","ror":"https://ror.org/02kswqa67","country_code":"TR","type":"education","lineage":["https://openalex.org/I74897591"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Kaz\u0131m Yal\u00e7\u0131n Arga","raw_affiliation_strings":["Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey","Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Turkey"],"raw_orcid":"https://orcid.org/0000-0002-6036-1348","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey","institution_ids":["https://openalex.org/I74897591"]},{"raw_affiliation_string":"Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Turkey","institution_ids":["https://openalex.org/I74897591"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5047072808"],"corresponding_institution_ids":["https://openalex.org/I74897591"],"apc_list":null,"apc_paid":null,"fwci":0.2105,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.38428215,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"26","issue":"9","first_page":"504","last_page":"511"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10183","display_name":"Breast Cancer Treatment Studies","score":0.9423999786376953,"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/T10183","display_name":"Breast Cancer Treatment Studies","score":0.9423999786376953,"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/T10885","display_name":"Gene expression and cancer classification","score":0.05480000004172325,"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/T10862","display_name":"AI in cancer detection","score":0.0010000000474974513,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/breast-cancer","display_name":"breast cancer","score":0.9089999794960022},{"id":"https://openalex.org/keywords/precision-oncology","display_name":"precision oncology","score":0.9480000138282776},{"id":"https://openalex.org/keywords/ensemble-learning","display_name":"ensemble learning","score":0.8769999742507935},{"id":"https://openalex.org/keywords/basal-like-breast-cancer","display_name":"basal-like breast cancer","score":0.6660000085830688},{"id":"https://openalex.org/keywords/luminal-b","display_name":"luminal B","score":0.8370000123977661},{"id":"https://openalex.org/keywords/her2-positive-breast-cancer","display_name":"HER2-positive breast cancer","score":0.972000002861023},{"id":"https://openalex.org/keywords/overall-survival","display_name":"overall survival","score":0.6899999976158142},{"id":"https://openalex.org/keywords/carcinogenesis-pathways","display_name":"carcinogenesis pathways","score":0.7870000004768372},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-seq","score":0.5799999833106995},{"id":"https://openalex.org/keywords/the-cancer-genome-atlas","display_name":"TCGA","score":0.800000011920929},{"id":"https://openalex.org/keywords/metabric","display_name":"METABRIC","score":0.9980000257492065}],"concepts":[{"id":"https://openalex.org/C530470458","wikidata":"https://www.wikidata.org/wiki/Q128581","display_name":"Breast cancer","level":3,"score":0.8376885652542114},{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.6533042788505554},{"id":"https://openalex.org/C143998085","wikidata":"https://www.wikidata.org/wiki/Q162555","display_name":"Oncology","level":1,"score":0.6441195011138916},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.6241230368614197},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.5719223618507385},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.5408459305763245},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4560633897781372},{"id":"https://openalex.org/C207103383","wikidata":"https://www.wikidata.org/wiki/Q3930246","display_name":"Hazard ratio","level":3,"score":0.4424591064453125},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.37028345465660095},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.2339971661567688},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20332705974578857},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C44249647","wikidata":"https://www.wikidata.org/wiki/Q208498","display_name":"Confidence interval","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D005260","descriptor_name":"Female","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":"D011446","descriptor_name":"Prospective Studies","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":"D057285","descriptor_name":"Precision Medicine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1089/omi.2022.0089","doi":"https://doi.org/10.1089/omi.2022.0089","is_oa":false,"landing_page_url":"https://doi.org/10.1089/omi.2022.0089","pdf_url":null,"source":{"id":"https://openalex.org/S116972989","display_name":"OMICS A Journal of Integrative Biology","issn_l":"1536-2310","issn":["1536-2310","1557-8100"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443","https://openalex.org/P4310320017"],"host_organization_lineage_names":["Mary Ann Liebert, Inc.","SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"OMICS: A Journal of Integrative Biology","raw_type":"journal-article"},{"id":"pmid:36040394","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36040394","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,"listed_in":[],"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":"Omics : a journal of integrative biology","raw_type":"Journal Article"},{"id":"pmh:oai:openaccess.marmara.edu.tr:11424/281746","doi":null,"is_oa":false,"landing_page_url":"https://hdl.handle.net/11424/281746","pdf_url":null,"source":{"id":"https://openalex.org/S4306401380","display_name":"Dspace Repository (Marmara \u00dcniversitesi)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I74897591","host_organization_name":"Marmara University","host_organization_lineage":["https://openalex.org/I74897591"],"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":"article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.9476000070571899,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1606544556","https://openalex.org/W1908864745","https://openalex.org/W1915129189","https://openalex.org/W2005895632","https://openalex.org/W2053183259","https://openalex.org/W2103017472","https://openalex.org/W2136132422","https://openalex.org/W2143426320","https://openalex.org/W2150420891","https://openalex.org/W2158485828","https://openalex.org/W2295598076","https://openalex.org/W2481801577","https://openalex.org/W2559588208","https://openalex.org/W2911964244","https://openalex.org/W2945574311","https://openalex.org/W2949676527","https://openalex.org/W3014006479","https://openalex.org/W3116143478","https://openalex.org/W3121563664","https://openalex.org/W3213614727","https://openalex.org/W4206841660","https://openalex.org/W4280602307"],"related_works":["https://openalex.org/W2912300303","https://openalex.org/W3033164081","https://openalex.org/W3080717832","https://openalex.org/W4312914483","https://openalex.org/W7125014716","https://openalex.org/W4308784357","https://openalex.org/W7131069385","https://openalex.org/W7214158802","https://openalex.org/W4410361725","https://openalex.org/W7217795609"],"abstract_inverted_index":{"The":[0,51,115],"rise":[1],"of":[2,30,39,69,91,169],"machine":[3],"learning":[4,242],"(ML)":[5],"has":[6],"recently":[7],"buttressed":[8],"the":[9,31,40,66,89,147,162,229,247],"efforts":[10],"for":[11,21,179],"big":[12],"data-driven":[13],"precision":[14,22,248],"oncology.":[15],"This":[16],"study":[17],"used":[18],"ensemble":[19,92,116,195,230,241],"ML":[20,196,231,237],"oncology":[23,249],"in":[24,88,130,136,145,220,233],"breast":[25,59,78,110,152,180,208,234],"cancer,":[26],"which":[27],"is":[28],"one":[29],"most":[32],"common":[33],"malignancies":[34],"worldwide":[35],"with":[36,58,77,186,206,223],"marked":[37],"heterogeneity":[38],"underlying":[41],"molecular":[42,113,134,187],"mechanisms.":[43],"We":[44,84],"analyzed":[45],"clinical":[46],"and":[47,61,65,80,94,108,121,127,150,182,211],"RNA-seq":[48],"data":[49],"from":[50,105,155,214],"Cancer":[52,71],"Genome":[53],"Atlas":[54],"(TCGA)":[55],"(844":[56],"patients":[57,76,104,132,205],"cancer":[60,79,111,153,181,209],"113":[62],"healthy":[63,82,106,156,215],"individuals)":[64],"Molecular":[67],"Taxonomy":[68],"Breast":[70],"International":[72],"Consortium":[73],"(METABRIC)":[74],"(1784":[75],"202":[81],"individuals).":[83],"evaluated":[85],"six":[86],"algorithms":[87],"context":[90],"modeling":[93],"identified":[95],"a":[96,166],"candidate":[97],"mRNA":[98,163],"diagnostic":[99],"panel":[100,164],"that":[101],"can":[102,226],"differentiate":[103,212],"controls,":[107],"stratify":[109,204],"into":[112,133],"subtypes.":[114],"model":[117],"included":[118],"50":[119,199],"mRNAs":[120],"displayed":[122],"82.55%":[123],"accuracy,":[124],"79.22%":[125],"specificity,":[126],"84.55%":[128],"sensitivity":[129],"stratifying":[131],"subtypes":[135,154,210],"TCGA":[137],"cohort.":[138],"Its":[139],"performance":[140],"was":[141,183,201],"markedly":[142],"higher,":[143],"however,":[144],"distinguishing":[146],"basal,":[148],"LumB,":[149],"Her2+":[151],"individuals.":[157,216],"In":[158,192],"overall":[159],"survival":[160],"analysis,":[161],"showed":[165],"hazard":[167],"ratio":[168],"2.25":[170],"(":[171],"p":[172],"=":[173],"5":[174],"\u00d7":[175],"10":[176],"\u22127":[177],")":[178],"significantly":[184],"associated":[185],"pathways":[188],"related":[189],"to":[190,203,246],"carcinogenesis.":[191],"conclusion,":[193],"an":[194],"approach,":[197],"including":[198],"mRNAs,":[200],"able":[202],"different":[207],"them":[213],"Future":[217],"prospective":[218],"studies":[219],"large":[221],"samples":[222],"deep":[224],"phenotyping":[225],"help":[227],"advance":[228],"approaches":[232],"cancer.":[235],"Advanced":[236],"methods":[238],"such":[239],"as":[240],"are":[243],"timely":[244],"additions":[245],"research":[250],"toolbox.":[251]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2022-08-30T00:00:00"}
