{"id":"https://openalex.org/W2575256161","doi":"https://doi.org/10.1109/bibm.2016.7822581","title":"Unsupervised single-cell analysis in triple-negative breast cancer: A case study","display_name":"Unsupervised single-cell analysis in triple-negative breast cancer: A case study","publication_year":2016,"publication_date":"2016-12-01","ids":{"openalex":"https://openalex.org/W2575256161","doi":"https://doi.org/10.1109/bibm.2016.7822581","mag":"2575256161"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2016.7822581","doi":"https://doi.org/10.1109/bibm.2016.7822581","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2016.7822581","pdf_url":null,"source":{"id":"https://openalex.org/S4363607730","display_name":"IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"volume":null,"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017994099","display_name":"Arjun P. Athreya","orcid":"https://orcid.org/0000-0001-9764-1768","observed_orcids":["https://orcid.org/0000-0001-9764-1768","https://orcid.org/0000-0002-4172-9055"]},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arjun P. Athreya","raw_affiliation_strings":["University of Illinois at Urbana-Champaign, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Illinois at Urbana-Champaign, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009631883","display_name":"Alan J. Gaglio","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alan J. Gaglio","raw_affiliation_strings":["University of Illinois at Urbana-Champaign, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Illinois at Urbana-Champaign, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043860236","display_name":"Zbigniew Kalbarczyk","orcid":"https://orcid.org/0009-0002-6040-6865","observed_orcids":["https://orcid.org/0009-0002-6040-6865"]},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zbigniew T. Kalbarczyk","raw_affiliation_strings":["University of Illinois at Urbana-Champaign, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Illinois at Urbana-Champaign, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067802693","display_name":"Ravishankar K. Iyer","orcid":"https://orcid.org/0000-0003-2245-3038","observed_orcids":["https://orcid.org/0000-0003-2245-3038","https://orcid.org/0000-0002-2895-1065","https://orcid.org/0000-0001-5383-9561"]},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ravishankar K. Iyer","raw_affiliation_strings":["University of Illinois at Urbana-Champaign, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Illinois at Urbana-Champaign, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041627937","display_name":"Junmei Cairns","orcid":"https://orcid.org/0000-0002-3941-4564","observed_orcids":["https://orcid.org/0000-0002-3941-4564"]},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Junmei Cairns","raw_affiliation_strings":["Mayo Clinic, Rochester, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mayo Clinic, Rochester, MN, USA","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085014608","display_name":"Krishna R. Kalari","orcid":"https://orcid.org/0000-0001-8944-8378","observed_orcids":["https://orcid.org/0000-0001-8944-8378"]},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Krishna R. Kalari","raw_affiliation_strings":["Mayo Clinic, Rochester, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mayo Clinic, Rochester, MN, USA","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056312367","display_name":"Richard M. Weinshilboum","orcid":"https://orcid.org/0000-0002-4911-7985","observed_orcids":["https://orcid.org/0000-0002-4911-7985"]},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard M. Weinshilboum","raw_affiliation_strings":["Mayo Clinic, Rochester, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mayo Clinic, Rochester, MN, USA","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069578729","display_name":"Liewei Wang","orcid":"https://orcid.org/0000-0003-3818-8531","observed_orcids":["https://orcid.org/0000-0003-3818-8531"]},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Liewei Wang","raw_affiliation_strings":["Mayo Clinic, Rochester, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mayo Clinic, Rochester, MN, USA","institution_ids":["https://openalex.org/I1330342723"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":5.2069,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.95556502,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"764","issue":null,"first_page":"556","last_page":"563"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.6973000168800354,"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":0.6973000168800354,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.2281000018119812,"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/T10183","display_name":"Breast Cancer Treatment Studies","score":0.029999999329447746,"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/triple-negative-breast-cancer","display_name":"triple-negative breast cancer","score":0.9850000143051147},{"id":"https://openalex.org/keywords/single-cell-transcriptomics","display_name":"single-cell transcriptomics","score":0.6809999942779541},{"id":"https://openalex.org/keywords/unsupervised-learning","display_name":"unsupervised learning","score":0.8610000014305115},{"id":"https://openalex.org/keywords/differential-gene-expression","display_name":"differential gene expression","score":0.9300000071525574},{"id":"https://openalex.org/keywords/pathway-analysis","display_name":"pathway analysis","score":0.5860000252723694},{"id":"https://openalex.org/keywords/metformin","display_name":"metformin","score":0.9879999756813049},{"id":"https://openalex.org/keywords/anticancer-mechanism","display_name":"anticancer mechanism","score":0.7799999713897705},{"id":"https://openalex.org/keywords/drug-repurposing","display_name":"drug repurposing","score":0.7570000290870667},{"id":"https://openalex.org/keywords/candidate-gene-identification","display_name":"candidate gene identification","score":0.5550000071525574},{"id":"https://openalex.org/keywords/model-based-clustering","display_name":"model-based clustering","score":0.5199999809265137}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6688435077667236},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5528570413589478},{"id":"https://openalex.org/C9927688","wikidata":"https://www.wikidata.org/wiki/Q4915012","display_name":"Biological pathway","level":4,"score":0.48250317573547363},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4412306845188141},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.43935948610305786},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.430422306060791},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4285426139831543},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4062221050262451},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3634703457355499},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2813188433647156},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18028780817985535},{"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/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2016.7822581","doi":"https://doi.org/10.1109/bibm.2016.7822581","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2016.7822581","pdf_url":null,"source":{"id":"https://openalex.org/S4363607730","display_name":"IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.7246000170707703,"id":"https://metadata.un.org/sdg/3"}],"sustainable_development_goals_aurora":[{"display_name":"Good health and well-being","score":0.6499999761581421,"id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306143","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03"},{"id":"https://openalex.org/F4320333659","display_name":"Center for Individualized Medicine, Mayo Clinic","ror":"https://ror.org/03zzw1w08"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1535020552","https://openalex.org/W1563425389","https://openalex.org/W1859313465","https://openalex.org/W1882541842","https://openalex.org/W1891956616","https://openalex.org/W1970073870","https://openalex.org/W1992294319","https://openalex.org/W2010653277","https://openalex.org/W2011832962","https://openalex.org/W2012420608","https://openalex.org/W2016728733","https://openalex.org/W2056780622","https://openalex.org/W2074847845","https://openalex.org/W2089468765","https://openalex.org/W2109890799","https://openalex.org/W2125094267","https://openalex.org/W2128120736","https://openalex.org/W2134513968","https://openalex.org/W2152561870","https://openalex.org/W2154285890","https://openalex.org/W2178888844","https://openalex.org/W2186118939","https://openalex.org/W2187089797","https://openalex.org/W2195022070"],"related_works":["https://openalex.org/W2086525401","https://openalex.org/W2006735166","https://openalex.org/W2079327011","https://openalex.org/W2053325634","https://openalex.org/W3178279768","https://openalex.org/W193851735","https://openalex.org/W2898732673","https://openalex.org/W2888097224","https://openalex.org/W2394308601","https://openalex.org/W4399552602"],"abstract_inverted_index":{"This":[0],"paper":[1],"demonstrates":[2],"an":[3,106],"unsupervised":[4,112],"learning":[5],"approach":[6],"to":[7,29,38,51,70,94,137,190,227],"identify":[8,115],"genes":[9,25,64,120,156,164,181],"with":[10,66,91,144],"significant":[11,103,127,213,224],"differential":[12,128],"expression":[13,129],"across":[14],"single-cell":[15],"subpopulations":[16],"induced":[17],"by":[18,148,176],"therapeutic":[19],"treatment.":[20],"Identifying":[21],"this":[22],"set":[23,118],"of":[24,63,74,119,122,155,179,195,210],"makes":[26],"it":[27],"possible":[28],"use":[30,47],"well-established":[31],"bioinformatics":[32],"approaches":[33],"such":[34,223],"as":[35],"pathway":[36,92],"analysis":[37,93,154],"establish":[39,191],"their":[40],"biological":[41,229],"relevance.":[42],"Then,":[43],"a":[44,56,101,116,202],"biologist":[45],"can":[46,114,182,221],"his/her":[48],"prior":[49,208],"knowledge":[50,209],"investigate":[52],"in":[53,80,130,167,171,197],"the":[54,61,71,75,123,149,192],"laboratory,":[55],"few":[57,102],"particular":[58],"candidates":[59],"among":[60],"subset":[62],"overlapping":[65],"relevant":[67,159],"pathways.":[68],"Due":[69],"large":[72],"size":[73],"human":[76],"genome":[77],"and":[78,82,132,185],"limitations":[79],"cost":[81],"skilled":[83],"resources,":[84],"biologists":[85,184],"benefit":[86],"from":[87],"analytical":[88],"methods":[89,113,220],"combined":[90],"design":[95,187],"laboratory":[96,188],"experiments":[97,189],"focusing":[98],"on":[99,157],"only":[100],"genes.":[104],"As":[105],"example,":[107],"we":[108,215],"show":[109],"how":[110],"model-based":[111],"small":[117,211,225],"(1%":[121],"genome)":[124],"that":[125,217],"have":[126],"single-cells":[131],"are":[133],"also":[134],"highly":[135],"correlated":[136],"pathways":[138,160],"(p-value":[139],"<":[140],"1E":[141],"\u2212":[142],"7)":[143],"anticancer":[145,169],"effects":[146],"driven":[147,175],"antidiabetic":[150],"drug":[151],"metformin.":[152,177],"Further":[153],"these":[158,180],"reveal":[161],"three":[162],"candidate":[163],"previously":[165],"implicated":[166],"several":[168],"mechanisms":[170,194],"other":[172],"cancers,":[173],"not":[174],"Identification":[178],"help":[183],"clinicians":[186],"molecular":[193],"metformin":[196],"triple-negative":[198],"breast":[199],"cancer.":[200],"In":[201],"domain":[203],"where":[204],"there":[205],"is":[206],"no":[207],"biologically":[212],"data,":[214],"demonstrate":[216],"careful":[218],"data-driven":[219],"infer":[222],"data":[226],"explain":[228],"mechanisms.":[230]},"counts_by_year":[{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2}],"updated_date":"2026-10-16T09:59:22.235173","created_date":"2025-10-10T00:00:00"}
