{"id":"https://openalex.org/W4214854288","doi":"https://doi.org/10.1093/bib/bbac105","title":"JSNMF enables effective and accurate integrative analysis of single-cell multiomics data","display_name":"JSNMF enables effective and accurate integrative analysis of single-cell multiomics data","publication_year":2022,"publication_date":"2022-03-02","ids":{"openalex":"https://openalex.org/W4214854288","doi":"https://doi.org/10.1093/bib/bbac105","pmid":"https://pubmed.ncbi.nlm.nih.gov/35380624"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac105","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac105","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/A5061864295","display_name":"Yuanyuan Ma","orcid":"https://orcid.org/0000-0001-9103-5513"},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]},{"id":"https://openalex.org/I4210117382","display_name":"Anyang Normal University","ror":"https://ror.org/02g9nss57","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210117382"]}],"countries":["CN","HK"],"is_corresponding":false,"raw_author_name":"Yuanyuan Ma","raw_affiliation_strings":["Department of Statistics, The Chinese University of Hong Kong, Hong Kong SAR, China","School of Computer & Information Engineering, Anyang Normal University, Anyang Henan, China"],"raw_orcid":"https://orcid.org/0000-0001-9103-5513","affiliations":[{"raw_affiliation_string":"Department of Statistics, The Chinese University of Hong Kong, Hong Kong SAR, China","institution_ids":["https://openalex.org/I177725633"]},{"raw_affiliation_string":"School of Computer & Information Engineering, Anyang Normal University, Anyang Henan, China","institution_ids":["https://openalex.org/I4210117382"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041635540","display_name":"Zexuan Sun","orcid":null},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Zexuan Sun","raw_affiliation_strings":["Department of Statistics, The Chinese University of Hong Kong, Hong Kong SAR, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, The Chinese University of Hong Kong, Hong Kong SAR, China","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006697904","display_name":"Pengcheng Zeng","orcid":"https://orcid.org/0000-0002-0724-5313"},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Pengcheng Zeng","raw_affiliation_strings":["Department of Statistics, The Chinese University of Hong Kong, Hong Kong SAR, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, The Chinese University of Hong Kong, Hong Kong SAR, China","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100385201","display_name":"Wenyu Zhang","orcid":"https://orcid.org/0000-0002-2507-3033"},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Wenyu Zhang","raw_affiliation_strings":["Department of Statistics, The Chinese University of Hong Kong, Hong Kong SAR, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, The Chinese University of Hong Kong, Hong Kong SAR, China","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014111636","display_name":"Zhixiang Lin","orcid":"https://orcid.org/0000-0001-9301-947X"},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Zhixiang Lin","raw_affiliation_strings":["Department of Statistics, The Chinese University of Hong Kong, Hong Kong SAR, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, The Chinese University of Hong Kong, Hong Kong SAR, China","institution_ids":["https://openalex.org/I177725633"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5014111636"],"corresponding_institution_ids":["https://openalex.org/I177725633"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":3.1897,"has_fulltext":false,"cited_by_count":39,"citation_normalized_percentile":{"value":0.9316299,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"23","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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":1.0,"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":0.9941999912261963,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9815000295639038,"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/epigenomics","display_name":"Epigenomics","score":0.6835886240005493},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6002951860427856},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5647101998329163},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5314218997955322},{"id":"https://openalex.org/keywords/single-cell-analysis","display_name":"Single-cell analysis","score":0.4805639088153839},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.4313380718231201},{"id":"https://openalex.org/keywords/cell","display_name":"Cell","score":0.3396344780921936},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30918827652931213},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.20853522419929504},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.13896805047988892},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12630900740623474},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09159976243972778}],"concepts":[{"id":"https://openalex.org/C121912465","wikidata":"https://www.wikidata.org/wiki/Q3589153","display_name":"Epigenomics","level":5,"score":0.6835886240005493},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6002951860427856},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5647101998329163},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5314218997955322},{"id":"https://openalex.org/C2776950831","wikidata":"https://www.wikidata.org/wiki/Q15635432","display_name":"Single-cell analysis","level":3,"score":0.4805639088153839},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.4313380718231201},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.3396344780921936},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30918827652931213},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.20853522419929504},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.13896805047988892},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12630900740623474},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09159976243972778},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"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":"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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac105","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac105","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35380624","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35380624","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4329023745","display_name":null,"funder_award_id":"4053423","funder_id":"https://openalex.org/F4320322942","funder_display_name":"Chinese University of Hong Kong"},{"id":"https://openalex.org/G7010797735","display_name":null,"funder_award_id":"4053476","funder_id":"https://openalex.org/F4320322942","funder_display_name":"Chinese University of Hong Kong"},{"id":"https://openalex.org/G768243115","display_name":null,"funder_award_id":"4930181","funder_id":"https://openalex.org/F4320322942","funder_display_name":"Chinese University of Hong Kong"}],"funders":[{"id":"https://openalex.org/F4320322942","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48"},{"id":"https://openalex.org/F4320335728","display_name":"Pusat Pengurusan Penyelidikan dan Instrumentasi","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":55,"referenced_works":["https://openalex.org/W1902027874","https://openalex.org/W1979594866","https://openalex.org/W1987219048","https://openalex.org/W2015583498","https://openalex.org/W2019338222","https://openalex.org/W2023461603","https://openalex.org/W2043545458","https://openalex.org/W2108119513","https://openalex.org/W2131681506","https://openalex.org/W2156718197","https://openalex.org/W2162833336","https://openalex.org/W2235245651","https://openalex.org/W2328735579","https://openalex.org/W2507998592","https://openalex.org/W2574988253","https://openalex.org/W2762237834","https://openalex.org/W2798368076","https://openalex.org/W2808845633","https://openalex.org/W2889236955","https://openalex.org/W2897249806","https://openalex.org/W2928665623","https://openalex.org/W2945628008","https://openalex.org/W2948469692","https://openalex.org/W2949177718","https://openalex.org/W2951217100","https://openalex.org/W2979670855","https://openalex.org/W2979911343","https://openalex.org/W2984472267","https://openalex.org/W2985765936","https://openalex.org/W2989061519","https://openalex.org/W2992957227","https://openalex.org/W3012788672","https://openalex.org/W3026606665","https://openalex.org/W3027051073","https://openalex.org/W3093858607","https://openalex.org/W3099768174","https://openalex.org/W3106188259","https://openalex.org/W3112466552","https://openalex.org/W3131450268","https://openalex.org/W3153110198","https://openalex.org/W3164692211","https://openalex.org/W3164839005","https://openalex.org/W3165062450","https://openalex.org/W3165519561","https://openalex.org/W4200438609","https://openalex.org/W4252676770","https://openalex.org/W4318977936","https://openalex.org/W6634702315","https://openalex.org/W6676321539","https://openalex.org/W6682755970","https://openalex.org/W6684050148","https://openalex.org/W6748816842","https://openalex.org/W6761319427","https://openalex.org/W6775249418","https://openalex.org/W6793405004"],"related_works":["https://openalex.org/W2930001795","https://openalex.org/W2415013816","https://openalex.org/W3013151148","https://openalex.org/W4229068595","https://openalex.org/W4247819660","https://openalex.org/W4231548908","https://openalex.org/W4396903217","https://openalex.org/W2975378934","https://openalex.org/W3104133195","https://openalex.org/W2781745374"],"abstract_inverted_index":{"The":[0,89,155],"single-cell":[1,139,146,178,182],"multiomics":[2,140,147,179,183],"technologies":[3,25],"provide":[4],"an":[5,94],"unprecedented":[6],"opportunity":[7],"to":[8,27,145],"study":[9],"the":[10,20,52,62,72,80,107,113,127,158,169,192,202,208,211],"cellular":[11],"heterogeneity":[12],"from":[13,23,61,149],"different":[14,103,135,150,153],"layers":[15],"of":[16,31,55,71,82,91,115,132,161,168,176,210],"transcriptional":[17],"regulation.":[18],"However,":[19],"datasets":[21,148],"generated":[22],"these":[24],"tend":[26],"have":[28],"high":[29],"levels":[30,131],"noise,":[32],"making":[33],"data":[34,59,67,119,166,184],"analysis":[35,54,175],"challenging.":[36],"Here,":[37],"we":[38],"propose":[39],"jointly":[40],"semi-orthogonal":[41],"nonnegative":[42],"matrix":[43],"factorization":[44],"(JSNMF),":[45],"which":[46,124],"is":[47,93],"a":[48],"versatile":[49],"toolkit":[50],"for":[51,106],"integrative":[53],"transcriptomic":[56,116],"and":[57,69,74,84,111,117,130,152,165,181,207],"epigenomic":[58,118],"profiled":[60,190],"same":[63,193],"cell.":[64,194],"JSNMF":[65,92,144,162,171,195],"enables":[66],"visualization":[68,167],"clustering":[70,164],"cells":[73],"also":[75,172,196],"facilitates":[76],"downstream":[77],"analysis,":[78],"including":[79],"characterization":[81],"markers":[83],"functional":[85],"pathway":[86],"enrichment":[87],"analysis.":[88],"core":[90],"unsupervised":[95],"method":[96],"based":[97],"on":[98,191,201],"JSNMF,":[99],"where":[100],"it":[101],"assumes":[102],"latent":[104],"variables":[105],"two":[108,188],"molecular":[109,136],"modalities,":[110],"integrates":[112],"information":[114],"with":[120,185],"consensus":[121],"graph":[122],"fusion,":[123],"better":[125],"tackles":[126],"distinct":[128],"characteristics":[129],"noise":[133],"across":[134],"modalities":[137,189],"in":[138,163],"data.":[141],"We":[142],"applied":[143],"tissues":[151],"technologies.":[154],"results":[156],"demonstrate":[157],"superior":[159],"performance":[160],"cells.":[170],"allows":[173],"joint":[174],"multiple":[177],"experiments":[180],"more":[186],"than":[187],"provides":[197],"rich":[198],"biological":[199],"insight":[200],"markers,":[203],"cell-type-specific":[204],"region-gene":[205],"associations":[206],"functions":[209],"identified":[212],"cell":[213],"subpopulation.":[214]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":16},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":4}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}