{"id":"https://openalex.org/W2979947476","doi":"https://doi.org/10.1093/bioinformatics/btz772","title":"Cancer classification of single-cell gene expression data by neural network","display_name":"Cancer classification of single-cell gene expression data by neural network","publication_year":2019,"publication_date":"2019-10-08","ids":{"openalex":"https://openalex.org/W2979947476","doi":"https://doi.org/10.1093/bioinformatics/btz772","mag":"2979947476","pmid":"https://pubmed.ncbi.nlm.nih.gov/31603465"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz772","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz772","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102957633","display_name":"Bong\u2010Hyun Kim","orcid":"https://orcid.org/0000-0002-1539-0203"},"institutions":[{"id":"https://openalex.org/I116631150","display_name":"Ulsan College","ror":"https://ror.org/02tec3785","country_code":"KR","type":"education","lineage":["https://openalex.org/I116631150"]},{"id":"https://openalex.org/I40542001","display_name":"University of Ulsan","ror":"https://ror.org/02c2f8975","country_code":"KR","type":"education","lineage":["https://openalex.org/I40542001"]},{"id":"https://openalex.org/I4210130649","display_name":"Frederick National Laboratory for Cancer Research","ror":"https://ror.org/03v6m3209","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210130649","https://openalex.org/I4210140884"]}],"countries":["KR","US"],"is_corresponding":true,"raw_author_name":"Bong-Hyun Kim","raw_affiliation_strings":["Advanced Bio Computing Center, Frederick National Laboratory for Cancer Research , Frederick, MD 21702, USA","Department of Biomedical Sciences, University of Ulsan College of Medicine, ASAN Medical Center , Seoul 05505, Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Advanced Bio Computing Center, Frederick National Laboratory for Cancer Research , Frederick, MD 21702, USA","institution_ids":["https://openalex.org/I4210130649"]},{"raw_affiliation_string":"Department of Biomedical Sciences, University of Ulsan College of Medicine, ASAN Medical Center , Seoul 05505, Korea","institution_ids":["https://openalex.org/I116631150","https://openalex.org/I40542001"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067955626","display_name":"Kijin Yu","orcid":null},"institutions":[{"id":"https://openalex.org/I116631150","display_name":"Ulsan College","ror":"https://ror.org/02tec3785","country_code":"KR","type":"education","lineage":["https://openalex.org/I116631150"]},{"id":"https://openalex.org/I40542001","display_name":"University of Ulsan","ror":"https://ror.org/02c2f8975","country_code":"KR","type":"education","lineage":["https://openalex.org/I40542001"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Kijin Yu","raw_affiliation_strings":["Department of Biomedical Sciences, University of Ulsan College of Medicine, ASAN Medical Center , Seoul 05505, Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Sciences, University of Ulsan College of Medicine, ASAN Medical Center , Seoul 05505, Korea","institution_ids":["https://openalex.org/I116631150","https://openalex.org/I40542001"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076846521","display_name":"Peter Chang-Whan Lee","orcid":"https://orcid.org/0000-0002-2320-6365"},"institutions":[{"id":"https://openalex.org/I116631150","display_name":"Ulsan College","ror":"https://ror.org/02tec3785","country_code":"KR","type":"education","lineage":["https://openalex.org/I116631150"]},{"id":"https://openalex.org/I40542001","display_name":"University of Ulsan","ror":"https://ror.org/02c2f8975","country_code":"KR","type":"education","lineage":["https://openalex.org/I40542001"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Peter C W Lee","raw_affiliation_strings":["Department of Biomedical Sciences, University of Ulsan College of Medicine, ASAN Medical Center , Seoul 05505, Korea"],"raw_orcid":"https://orcid.org/0000-0002-2320-6365","affiliations":[{"raw_affiliation_string":"Department of Biomedical Sciences, University of Ulsan College of Medicine, ASAN Medical Center , Seoul 05505, Korea","institution_ids":["https://openalex.org/I116631150","https://openalex.org/I40542001"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5076846521","https://openalex.org/A5102957633"],"corresponding_institution_ids":["https://openalex.org/I116631150","https://openalex.org/I40542001","https://openalex.org/I4210130649"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.4269,"has_fulltext":false,"cited_by_count":64,"citation_normalized_percentile":{"value":0.90197689,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"36","issue":"5","first_page":"1360","last_page":"1366"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9516000151634216,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9516000151634216,"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/T10885","display_name":"Gene expression and cancer classification","score":0.009800000116229057,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.009499999694526196,"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/support-vector-machine","display_name":"Support vector machine","score":0.7416592240333557},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.6977324485778809},{"id":"https://openalex.org/keywords/random-forest","display_name":"Random forest","score":0.666183590888977},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.6435675621032715},{"id":"https://openalex.org/keywords/smoothing","display_name":"Smoothing","score":0.5247419476509094},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5201685428619385},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5177285075187683},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5075408220291138},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.48327237367630005},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.4152109622955322},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.38618820905685425},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3792712688446045},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.36344122886657715},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3296544849872589},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1587858498096466},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.15118280053138733}],"concepts":[{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.7416592240333557},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.6977324485778809},{"id":"https://openalex.org/C169258074","wikidata":"https://www.wikidata.org/wiki/Q245748","display_name":"Random forest","level":2,"score":0.666183590888977},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.6435675621032715},{"id":"https://openalex.org/C3770464","wikidata":"https://www.wikidata.org/wiki/Q775963","display_name":"Smoothing","level":2,"score":0.5247419476509094},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5201685428619385},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5177285075187683},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5075408220291138},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48327237367630005},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.4152109622955322},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.38618820905685425},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3792712688446045},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.36344122886657715},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3296544849872589},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1587858498096466},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.15118280053138733},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btz772","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz772","pdf_url":null,"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:31603465","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31603465","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":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.4300000071525574}],"awards":[{"id":"https://openalex.org/G5419688476","display_name":null,"funder_award_id":"NRF-2019R1A2C2084181","funder_id":"https://openalex.org/F4320328359","funder_display_name":"Ministry of Science and ICT, South Korea"}],"funders":[{"id":"https://openalex.org/F4320322120","display_name":"National Research Foundation of Korea","ror":"https://ror.org/013aysd81"},{"id":"https://openalex.org/F4320328359","display_name":"Ministry of Science and ICT, South Korea","ror":"https://ror.org/01wpjm123"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":55,"referenced_works":["https://openalex.org/W1965856472","https://openalex.org/W1967220865","https://openalex.org/W1985258161","https://openalex.org/W1995232318","https://openalex.org/W1999574084","https://openalex.org/W2003372603","https://openalex.org/W2016661249","https://openalex.org/W2016884187","https://openalex.org/W2025183726","https://openalex.org/W2042933379","https://openalex.org/W2070124744","https://openalex.org/W2084147994","https://openalex.org/W2096283457","https://openalex.org/W2101234009","https://openalex.org/W2103017472","https://openalex.org/W2109553965","https://openalex.org/W2111547563","https://openalex.org/W2119821739","https://openalex.org/W2123696077","https://openalex.org/W2128084896","https://openalex.org/W2130410032","https://openalex.org/W2140258573","https://openalex.org/W2150078499","https://openalex.org/W2158485828","https://openalex.org/W2159084616","https://openalex.org/W2159482845","https://openalex.org/W2162116127","https://openalex.org/W2185207072","https://openalex.org/W2245213139","https://openalex.org/W2262414037","https://openalex.org/W2329659234","https://openalex.org/W2332292689","https://openalex.org/W2412681020","https://openalex.org/W2502949459","https://openalex.org/W2522775671","https://openalex.org/W2568642260","https://openalex.org/W2594016532","https://openalex.org/W2605449204","https://openalex.org/W2610509384","https://openalex.org/W2724430069","https://openalex.org/W2753432109","https://openalex.org/W2775443868","https://openalex.org/W2782146634","https://openalex.org/W2785148091","https://openalex.org/W2796153844","https://openalex.org/W2796366554","https://openalex.org/W2799274909","https://openalex.org/W2951381561","https://openalex.org/W3101634756","https://openalex.org/W3142517368","https://openalex.org/W4239510810","https://openalex.org/W4242404314","https://openalex.org/W4294216483","https://openalex.org/W6654828700","https://openalex.org/W6675354045"],"related_works":["https://openalex.org/W1978572805","https://openalex.org/W2383807498","https://openalex.org/W1997992934","https://openalex.org/W1987225439","https://openalex.org/W4238188170","https://openalex.org/W3193043704","https://openalex.org/W4396689146","https://openalex.org/W4200112873","https://openalex.org/W2955796858","https://openalex.org/W2004826645"],"abstract_inverted_index":{"MOTIVATION:":[0],"Cancer":[1,152],"classification":[2,153],"based":[3,61,89],"on":[4,11,62,90],"gene":[5,36],"expression":[6,37],"profiles":[7],"has":[8],"provided":[9],"insight":[10],"the":[12,32,91],"causes":[13],"of":[14,56],"cancer":[15,17,28,49,75,144],"and":[16,58,77,84,113,137,146],"treatment.":[18],"Recently,":[19],"machine":[20,108],"learning-based":[21],"approaches":[22],"have":[23],"been":[24],"attempted":[25],"in":[26,35,87,97],"downstream":[27],"analysis":[29],"to":[30,131],"address":[31],"large":[33],"differences":[34],"values,":[38],"as":[39,65,67],"determined":[40],"by":[41,134,154],"single-cell":[42],"RNA":[43],"sequencing":[44],"(scRNA-seq).":[45],"RESULTS:":[46],"We":[47,126],"designed":[48],"classifiers":[50],"that":[51,139],"can":[52],"identify":[53],"21":[54,82],"types":[55,145],"cancers":[57],"normal":[59,79,85,147],"tissues":[60,86],"bulk":[63],"RNA-seq":[64],"well":[66],"scRNA-seq":[68,132],"data.":[69],"Training":[70],"was":[71],"performed":[72,120],"with":[73],"7398":[74],"samples":[76,80],"640":[78],"from":[81],"tumors":[83],"TCGA":[88],"300":[92],"most":[93],"significant":[94],"genes":[95],"expressed":[96],"each":[98],"cancer.":[99],"Then,":[100],"we":[101],"compared":[102],"neural":[103,155],"network":[104],"(NN),":[105],"support":[106],"vector":[107],"(SVM),":[109],"k-nearest":[110],"neighbors":[111],"(kNN)":[112],"random":[114],"forest":[115],"(RF)":[116],"methods.":[117,125],"The":[118],"NN":[119],"consistently":[121],"better":[122],"than":[123],"other":[124],"further":[127],"applied":[128],"our":[129,140],"approach":[130],"transformed":[133],"kNN":[135],"smoothing":[136],"found":[138],"model":[141],"successfully":[142],"classified":[143],"samples.":[148],"AVAILABILITY":[149],"AND":[150],"IMPLEMENTATION:":[151],"network.":[156],"SUPPLEMENTARY":[157],"INFORMATION:":[158],"Supplementary":[159],"data":[160],"are":[161],"available":[162],"at":[163],"Bioinformatics":[164],"online.":[165]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":13},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":6}],"updated_date":"2026-08-13T07:04:57.449891","created_date":"2025-10-10T00:00:00"}
