{"id":"https://openalex.org/W4310947643","doi":"https://doi.org/10.1093/bioinformatics/btac790","title":"bmVAE: a variational autoencoder method for clustering single-cell mutation data","display_name":"bmVAE: a variational autoencoder method for clustering single-cell mutation data","publication_year":2022,"publication_date":"2022-12-07","ids":{"openalex":"https://openalex.org/W4310947643","doi":"https://doi.org/10.1093/bioinformatics/btac790","pmid":"https://pubmed.ncbi.nlm.nih.gov/36478203"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac790","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac790","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac790/48520788/btac790.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac790/48520788/btac790.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048809041","display_name":"Jiaqian Yan","orcid":null},"institutions":[{"id":"https://openalex.org/I21642278","display_name":"Ningxia University","ror":"https://ror.org/04j7b2v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I21642278"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiaqian Yan","raw_affiliation_strings":["School of Information Engineering, Ningxia University , Yinchuan 750021, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Engineering, Ningxia University , Yinchuan 750021, China","institution_ids":["https://openalex.org/I21642278"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088025180","display_name":"Ming Ma","orcid":"https://orcid.org/0000-0001-8045-0471"},"institutions":[{"id":"https://openalex.org/I21642278","display_name":"Ningxia University","ror":"https://ror.org/04j7b2v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I21642278"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ming Ma","raw_affiliation_strings":["School of Information Engineering, Ningxia University , Yinchuan 750021, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Engineering, Ningxia University , Yinchuan 750021, China","institution_ids":["https://openalex.org/I21642278"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000095054","display_name":"Zhenhua Yu","orcid":"https://orcid.org/0000-0001-6526-6991"},"institutions":[{"id":"https://openalex.org/I21642278","display_name":"Ningxia University","ror":"https://ror.org/04j7b2v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I21642278"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhenhua Yu","raw_affiliation_strings":["Collaborative Innovation Center for Ningxia Big Data and Artificial Intelligence Co-founded by Ningxia Municipality and Ministry of Education, Ningxia University , Yinchuan 750021, China","School of Information Engineering, Ningxia University , Yinchuan 750021, China"],"raw_orcid":"https://orcid.org/0000-0001-6526-6991","affiliations":[{"raw_affiliation_string":"Collaborative Innovation Center for Ningxia Big Data and Artificial Intelligence Co-founded by Ningxia Municipality and Ministry of Education, Ningxia University , Yinchuan 750021, China","institution_ids":["https://openalex.org/I21642278"]},{"raw_affiliation_string":"School of Information Engineering, Ningxia University , Yinchuan 750021, China","institution_ids":["https://openalex.org/I21642278"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5000095054"],"corresponding_institution_ids":["https://openalex.org/I21642278"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.9336,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.88189591,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"39","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.504800021648407,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.504800021648407,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.4413999915122986,"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/T10336","display_name":"Cancer Cells and Metastasis","score":0.012400000356137753,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"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/autoencoder","display_name":"Autoencoder","score":0.8562346696853638},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.7801111936569214},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.653952419757843},{"id":"https://openalex.org/keywords/dimensionality-reduction","display_name":"Dimensionality reduction","score":0.5306462645530701},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.459972620010376},{"id":"https://openalex.org/keywords/binary-number","display_name":"Binary number","score":0.4436795115470886},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4364510476589203},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38936829566955566},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.366941899061203},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2556954324245453},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.20449358224868774},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15503749251365662},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.12430992722511292},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07552814483642578}],"concepts":[{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.8562346696853638},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.7801111936569214},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.653952419757843},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.5306462645530701},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.459972620010376},{"id":"https://openalex.org/C48372109","wikidata":"https://www.wikidata.org/wiki/Q3913","display_name":"Binary number","level":2,"score":0.4436795115470886},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4364510476589203},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38936829566955566},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.366941899061203},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2556954324245453},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.20449358224868774},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15503749251365662},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.12430992722511292},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07552814483642578},{"id":"https://openalex.org/C94375191","wikidata":"https://www.wikidata.org/wiki/Q11205","display_name":"Arithmetic","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","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":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster 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},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac790","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac790","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac790/48520788/btac790.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36478203","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36478203","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},{"id":"pmh:oai:pubmedcentral.nih.gov:9825778","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9825778","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac790","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac790","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac790/48520788/btac790.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1463133177","display_name":null,"funder_award_id":"61901238","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5435425164","display_name":null,"funder_award_id":"XAB2019AW12","funder_id":"https://openalex.org/F4320321133","funder_display_name":"Chinese Academy of Sciences"},{"id":"https://openalex.org/G6087093116","display_name":null,"funder_award_id":"XAB2019AW12","funder_id":"https://openalex.org/F4320328015","funder_display_name":"West Light Foundation of the Chinese Academy of Sciences"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321133","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35"},{"id":"https://openalex.org/F4320328015","display_name":"West Light Foundation of the Chinese Academy of Sciences","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4310947643.pdf","grobid_xml":"https://content.openalex.org/works/W4310947643.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1631320694","https://openalex.org/W1967304777","https://openalex.org/W2003094610","https://openalex.org/W2004232113","https://openalex.org/W2009569945","https://openalex.org/W2034629821","https://openalex.org/W2059300459","https://openalex.org/W2139790154","https://openalex.org/W2154068087","https://openalex.org/W2187089797","https://openalex.org/W2269040222","https://openalex.org/W2340974016","https://openalex.org/W2346273585","https://openalex.org/W2358053195","https://openalex.org/W2402730620","https://openalex.org/W2586389371","https://openalex.org/W2603523955","https://openalex.org/W2734435792","https://openalex.org/W2754025713","https://openalex.org/W2793271470","https://openalex.org/W2890035501","https://openalex.org/W2950983802","https://openalex.org/W2980586637","https://openalex.org/W3011144186","https://openalex.org/W3012280517","https://openalex.org/W3018522957","https://openalex.org/W3024013192","https://openalex.org/W3042807857","https://openalex.org/W3042855708","https://openalex.org/W3075371075","https://openalex.org/W3096831136","https://openalex.org/W3160758604","https://openalex.org/W3162373443","https://openalex.org/W3171986076","https://openalex.org/W4200405729","https://openalex.org/W4210782864","https://openalex.org/W4221135625","https://openalex.org/W4226106538"],"related_works":["https://openalex.org/W2159052453","https://openalex.org/W3013693939","https://openalex.org/W2566616303","https://openalex.org/W3131327266","https://openalex.org/W4297051394","https://openalex.org/W2752972570","https://openalex.org/W2734887215","https://openalex.org/W2803255133","https://openalex.org/W4310873165","https://openalex.org/W2355395139"],"abstract_inverted_index":{"MOTIVATION:":[0],"Genetic":[1],"intra-tumor":[2],"heterogeneity":[3,152],"(ITH)":[4],"characterizes":[5],"the":[6,56,62,91,115,135],"differences":[7],"in":[8,90,155,173],"genomic":[9],"variations":[10],"between":[11],"tumor":[12,46],"clones,":[13],"and":[14,58,84,102,130,150,157,176],"accurately":[15],"unmasking":[16],"ITH":[17,36],"is":[18,118,170,186],"important":[19],"for":[20,33,71],"personalized":[21],"cancer":[22],"therapy.":[23],"Single-cell":[24],"DNA":[25],"sequencing":[26],"now":[27],"emerges":[28],"as":[29,100,107,109],"a":[30,68,81],"powerful":[31],"means":[32],"deciphering":[34],"underlying":[35],"based":[37,79],"on":[38,80,137,162],"point":[39],"mutations":[40],"of":[41,61,76,122],"single":[42,77],"cells.":[43],"However,":[44],"detecting":[45],"clones":[47],"from":[48],"single-cell":[49,96],"mutation":[50,98],"data":[51,99,148,151,194],"remains":[52],"challenging":[53],"due":[54],"to":[55,120,179],"error-prone":[57],"discrete":[59],"nature":[60],"data.":[63],"RESULTS:":[64],"We":[65,133],"introduce":[66],"bmVAE,":[67],"bioinformatics":[69],"tool":[70],"learning":[72],"low-dimensional":[73],"latent":[74,92],"representation":[75],"cell":[78,105,128],"variational":[82],"autoencoder":[83],"then":[85],"clustering":[86,129],"cells":[87],"into":[88],"subpopulations":[89,106],"space.":[93],"bmVAE":[94,116,169,185],"takes":[95],"binary":[97],"inputs,":[101],"outputs":[103],"inferred":[104],"well":[108],"their":[110],"genotypes.":[111],"To":[112],"achieve":[113],"this,":[114],"framework":[117],"designed":[119],"consist":[121],"three":[123],"modules":[124],"including":[125,144],"dimensionality":[126],"reduction,":[127],"genotype":[131],"estimation.":[132],"assess":[134],"method":[136],"various":[138],"synthetic":[139],"datasets":[140],"where":[141],"different":[142],"factors":[143],"false":[145],"negative":[146],"rate,":[147],"size":[149],"are":[153,195],"considered":[154],"simulation,":[156],"further":[158],"demonstrate":[159],"its":[160],"effectiveness":[161],"two":[163],"real":[164],"datasets.":[165],"The":[166],"results":[167],"suggest":[168],"highly":[171],"effective":[172],"reasoning":[174],"ITH,":[175],"performs":[177],"competitive":[178],"existing":[180],"methods.":[181],"AVAILABILITY":[182],"AND":[183],"IMPLEMENTATION:":[184],"freely":[187],"available":[188,196],"at":[189,197],"https://github.com/zhyu-lab/bmvae.":[190],"SUPPLEMENTARY":[191],"INFORMATION:":[192],"Supplementary":[193],"Bioinformatics":[198],"online.":[199]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":4}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}