{"id":"https://openalex.org/W4213270761","doi":"https://doi.org/10.1093/bib/bbab531","title":"Deep learning tackles single-cell analysis\u2014a survey of deep learning for scRNA-seq analysis","display_name":"Deep learning tackles single-cell analysis\u2014a survey of deep learning for scRNA-seq analysis","publication_year":2021,"publication_date":"2021-11-20","ids":{"openalex":"https://openalex.org/W4213270761","doi":"https://doi.org/10.1093/bib/bbab531","pmid":"https://pubmed.ncbi.nlm.nih.gov/34929734"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbab531","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab531","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":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8769926","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024265492","display_name":"Mario Flores","orcid":"https://orcid.org/0000-0003-1255-3983"},"institutions":[{"id":"https://openalex.org/I45438204","display_name":"The University of Texas at San Antonio","ror":"https://ror.org/01kd65564","country_code":"US","type":"education","lineage":["https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mario Flores","raw_affiliation_strings":["Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA","institution_ids":["https://openalex.org/I45438204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008638025","display_name":"Zhentao Liu","orcid":"https://orcid.org/0000-0001-5188-3235"},"institutions":[{"id":"https://openalex.org/I45438204","display_name":"The University of Texas at San Antonio","ror":"https://ror.org/01kd65564","country_code":"US","type":"education","lineage":["https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhentao Liu","raw_affiliation_strings":["Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA","institution_ids":["https://openalex.org/I45438204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057799604","display_name":"Tinghe Zhang","orcid":"https://orcid.org/0000-0002-4595-6167"},"institutions":[{"id":"https://openalex.org/I45438204","display_name":"The University of Texas at San Antonio","ror":"https://ror.org/01kd65564","country_code":"US","type":"education","lineage":["https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tinghe Zhang","raw_affiliation_strings":["Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA","institution_ids":["https://openalex.org/I45438204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002768368","display_name":"Md Musaddaqui Hasib","orcid":null},"institutions":[{"id":"https://openalex.org/I45438204","display_name":"The University of Texas at San Antonio","ror":"https://ror.org/01kd65564","country_code":"US","type":"education","lineage":["https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Md Musaddaqui Hasib","raw_affiliation_strings":["Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA","institution_ids":["https://openalex.org/I45438204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028190064","display_name":"Yu\u2010Chiao Chiu","orcid":"https://orcid.org/0000-0003-1647-8634"},"institutions":[{"id":"https://openalex.org/I165951966","display_name":"The University of Texas Health Science Center at San Antonio","ror":"https://ror.org/02f6dcw23","country_code":"US","type":"education","lineage":["https://openalex.org/I165951966"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yu-Chiao Chiu","raw_affiliation_strings":["Greehey Children\u2019s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA","Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA"],"affiliations":[{"raw_affiliation_string":"Greehey Children\u2019s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA","institution_ids":["https://openalex.org/I165951966"]},{"raw_affiliation_string":"Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA","institution_ids":["https://openalex.org/I165951966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109394230","display_name":"Zhenqing Ye","orcid":null},"institutions":[{"id":"https://openalex.org/I165951966","display_name":"The University of Texas Health Science Center at San Antonio","ror":"https://ror.org/02f6dcw23","country_code":"US","type":"education","lineage":["https://openalex.org/I165951966"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhenqing Ye","raw_affiliation_strings":["Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA","Greehey Children\u2019s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA","Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA"],"affiliations":[{"raw_affiliation_string":"Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA","institution_ids":["https://openalex.org/I165951966"]},{"raw_affiliation_string":"Greehey Children\u2019s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA","institution_ids":["https://openalex.org/I165951966"]},{"raw_affiliation_string":"Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA","institution_ids":["https://openalex.org/I165951966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043302716","display_name":"Karla Paniagua","orcid":"https://orcid.org/0000-0003-3639-4403"},"institutions":[{"id":"https://openalex.org/I45438204","display_name":"The University of Texas at San Antonio","ror":"https://ror.org/01kd65564","country_code":"US","type":"education","lineage":["https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Karla Paniagua","raw_affiliation_strings":["Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA","institution_ids":["https://openalex.org/I45438204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073343116","display_name":"Sumin Jo","orcid":null},"institutions":[{"id":"https://openalex.org/I45438204","display_name":"The University of Texas at San Antonio","ror":"https://ror.org/01kd65564","country_code":"US","type":"education","lineage":["https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sumin Jo","raw_affiliation_strings":["Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA","institution_ids":["https://openalex.org/I45438204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087249630","display_name":"Jianqiu Zhang","orcid":"https://orcid.org/0000-0002-5220-3200"},"institutions":[{"id":"https://openalex.org/I45438204","display_name":"The University of Texas at San Antonio","ror":"https://ror.org/01kd65564","country_code":"US","type":"education","lineage":["https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jianqiu Zhang","raw_affiliation_strings":["Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA","institution_ids":["https://openalex.org/I45438204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010896860","display_name":"Shou\u2010Jiang Gao","orcid":"https://orcid.org/0000-0001-6194-1742"},"institutions":[{"id":"https://openalex.org/I4210128526","display_name":"UPMC Hillman Cancer Center","ror":"https://ror.org/03bw34a45","country_code":"US","type":"facility","lineage":["https://openalex.org/I170201317","https://openalex.org/I4210128526"]},{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shou-Jiang Gao","raw_affiliation_strings":["Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, PA 15232, USA","UPMC Hillman Cancer Center, University of Pittsburgh, PA 15232, USA"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, PA 15232, USA","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"UPMC Hillman Cancer Center, University of Pittsburgh, PA 15232, USA","institution_ids":["https://openalex.org/I4210128526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046855484","display_name":"Yufang Jin","orcid":"https://orcid.org/0000-0002-9049-9807"},"institutions":[{"id":"https://openalex.org/I45438204","display_name":"The University of Texas at San Antonio","ror":"https://ror.org/01kd65564","country_code":"US","type":"education","lineage":["https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yu-Fang Jin","raw_affiliation_strings":["Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA","institution_ids":["https://openalex.org/I45438204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100689057","display_name":"Yidong Chen","orcid":"https://orcid.org/0000-0001-6806-2185"},"institutions":[{"id":"https://openalex.org/I165951966","display_name":"The University of Texas Health Science Center at San Antonio","ror":"https://ror.org/02f6dcw23","country_code":"US","type":"education","lineage":["https://openalex.org/I165951966"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yidong Chen","raw_affiliation_strings":["Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA","Greehey Children\u2019s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA","Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA"],"affiliations":[{"raw_affiliation_string":"Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA","institution_ids":["https://openalex.org/I165951966"]},{"raw_affiliation_string":"Greehey Children\u2019s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA","institution_ids":["https://openalex.org/I165951966"]},{"raw_affiliation_string":"Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA","institution_ids":["https://openalex.org/I165951966"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068887242","display_name":"Yufei Huang","orcid":"https://orcid.org/0000-0001-6268-5357"},"institutions":[{"id":"https://openalex.org/I4210128526","display_name":"UPMC Hillman Cancer Center","ror":"https://ror.org/03bw34a45","country_code":"US","type":"facility","lineage":["https://openalex.org/I170201317","https://openalex.org/I4210128526"]},{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yufei Huang","raw_affiliation_strings":["Department of Medicine, School of Medicine, University of Pittsburgh, PA 15232, USA","UPMC Hillman Cancer Center, University of Pittsburgh, PA 15232, USA"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, School of Medicine, University of Pittsburgh, PA 15232, USA","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"UPMC Hillman Cancer Center, University of Pittsburgh, PA 15232, USA","institution_ids":["https://openalex.org/I4210128526"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":13,"corresponding_author_ids":["https://openalex.org/A5024265492","https://openalex.org/A5068887242","https://openalex.org/A5100689057"],"corresponding_institution_ids":["https://openalex.org/I165951966","https://openalex.org/I170201317","https://openalex.org/I4210128526","https://openalex.org/I45438204"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":3.9749,"has_fulltext":false,"cited_by_count":72,"citation_normalized_percentile":{"value":0.95226109,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"23","issue":"1","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/T10773","display_name":"Extracellular vesicles in disease","score":0.9760000109672546,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9700000286102295,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/autoencoder","display_name":"Autoencoder","score":0.748907208442688},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7415990829467773},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.7108316421508789},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.678801417350769},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.6211657524108887},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.5941727757453918},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5827707052230835},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.47580987215042114},{"id":"https://openalex.org/keywords/presentation","display_name":"Presentation (obstetrics)","score":0.44303441047668457},{"id":"https://openalex.org/keywords/adversarial-system","display_name":"Adversarial system","score":0.4114637076854706},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4087217450141907},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3290301263332367}],"concepts":[{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.748907208442688},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7415990829467773},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7108316421508789},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.678801417350769},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6211657524108887},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.5941727757453918},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5827707052230835},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.47580987215042114},{"id":"https://openalex.org/C2777601897","wikidata":"https://www.wikidata.org/wiki/Q3409113","display_name":"Presentation (obstetrics)","level":2,"score":0.44303441047668457},{"id":"https://openalex.org/C37736160","wikidata":"https://www.wikidata.org/wiki/Q1801315","display_name":"Adversarial system","level":2,"score":0.4114637076854706},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4087217450141907},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3290301263332367},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C126838900","wikidata":"https://www.wikidata.org/wiki/Q77604","display_name":"Radiology","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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":"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":"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":"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":"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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","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},{"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":3,"locations":[{"id":"doi:10.1093/bib/bbab531","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab531","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:34929734","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34929734","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},{"id":"pmh:oai:pubmedcentral.nih.gov:8769926","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8769926","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:8769926","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8769926","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.5699999928474426}],"awards":[{"id":"https://openalex.org/G1851233220","display_name":null,"funder_award_id":"1UL1RR025767","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3299191655","display_name":null,"funder_award_id":"R01GM113245","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4864431264","display_name":null,"funder_award_id":"RP160732","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"},{"id":"https://openalex.org/G5502230245","display_name":null,"funder_award_id":"RP190346","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"},{"id":"https://openalex.org/G6209358963","display_name":null,"funder_award_id":"2051113","funder_id":"https://openalex.org/F4320335353","funder_display_name":"National Science Foundation of Sri Lanka"}],"funders":[{"id":"https://openalex.org/F4320308129","display_name":"Cancer Prevention and Research Institute of Texas","ror":"https://ror.org/0003xa228"},{"id":"https://openalex.org/F4320317949","display_name":"Fund for Innovation in Cancer Informatics","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320335353","display_name":"National Science Foundation of Sri Lanka","ror":"https://ror.org/010xaa060"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":176,"referenced_works":["https://openalex.org/W839653734","https://openalex.org/W1552434751","https://openalex.org/W1613448136","https://openalex.org/W1631320694","https://openalex.org/W1967327758","https://openalex.org/W1979283544","https://openalex.org/W1989277387","https://openalex.org/W2007439698","https://openalex.org/W2010653277","https://openalex.org/W2019552331","https://openalex.org/W2023887100","https://openalex.org/W2027557822","https://openalex.org/W2030017878","https://openalex.org/W2033072655","https://openalex.org/W2051658465","https://openalex.org/W2053186076","https://openalex.org/W2074192627","https://openalex.org/W2076513103","https://openalex.org/W2079296583","https://openalex.org/W2097455931","https://openalex.org/W2102212449","https://openalex.org/W2120205807","https://openalex.org/W2130410032","https://openalex.org/W2130430382","https://openalex.org/W2135937351","https://openalex.org/W2138621090","https://openalex.org/W2139232457","https://openalex.org/W2151936673","https://openalex.org/W2164943005","https://openalex.org/W2165363188","https://openalex.org/W2177432730","https://openalex.org/W2181255501","https://openalex.org/W2187089797","https://openalex.org/W2190545194","https://openalex.org/W2307567449","https://openalex.org/W2332292689","https://openalex.org/W2343956310","https://openalex.org/W2344887288","https://openalex.org/W2407916594","https://openalex.org/W2465917013","https://openalex.org/W2489812534","https://openalex.org/W2510746232","https://openalex.org/W2511896561","https://openalex.org/W2523419694","https://openalex.org/W2523620612","https://openalex.org/W2526262591","https://openalex.org/W2528543174","https://openalex.org/W2533508881","https://openalex.org/W2534008312","https://openalex.org/W2546514099","https://openalex.org/W2557334921","https://openalex.org/W2559588208","https://openalex.org/W2559655401","https://openalex.org/W2571353615","https://openalex.org/W2580989000","https://openalex.org/W2600132724","https://openalex.org/W2600453489","https://openalex.org/W2607471016","https://openalex.org/W2610509384","https://openalex.org/W2611919322","https://openalex.org/W2612519453","https://openalex.org/W2612690371","https://openalex.org/W2618735189","https://openalex.org/W2626990934","https://openalex.org/W2739492614","https://openalex.org/W2741564801","https://openalex.org/W2747545374","https://openalex.org/W2747877289","https://openalex.org/W2767423581","https://openalex.org/W2773035279","https://openalex.org/W2774307122","https://openalex.org/W2786672974","https://openalex.org/W2787579267","https://openalex.org/W2788263670","https://openalex.org/W2788348358","https://openalex.org/W2792693509","https://openalex.org/W2794190081","https://openalex.org/W2794480084","https://openalex.org/W2794521141","https://openalex.org/W2799273685","https://openalex.org/W2800392236","https://openalex.org/W2804847416","https://openalex.org/W2805516822","https://openalex.org/W2805619986","https://openalex.org/W2810097927","https://openalex.org/W2897249806","https://openalex.org/W2897346235","https://openalex.org/W2897748644","https://openalex.org/W2899948177","https://openalex.org/W2901677030","https://openalex.org/W2902652978","https://openalex.org/W2905317377","https://openalex.org/W2912272542","https://openalex.org/W2916020270","https://openalex.org/W2924067995","https://openalex.org/W2926010705","https://openalex.org/W2935703330","https://openalex.org/W2937917790","https://openalex.org/W2942880491","https://openalex.org/W2944189019","https://openalex.org/W2949067670","https://openalex.org/W2949177718","https://openalex.org/W2949272108","https://openalex.org/W2950983802","https://openalex.org/W2951217100","https://openalex.org/W2951381561","https://openalex.org/W2951506174","https://openalex.org/W2952001873","https://openalex.org/W2952016241","https://openalex.org/W2952303649","https://openalex.org/W2953251392","https://openalex.org/W2955621471","https://openalex.org/W2960029024","https://openalex.org/W2965552103","https://openalex.org/W2967177832","https://openalex.org/W2968352143","https://openalex.org/W2970372573","https://openalex.org/W2970633838","https://openalex.org/W2971653850","https://openalex.org/W2978541146","https://openalex.org/W2980495984","https://openalex.org/W2981732942","https://openalex.org/W2984472267","https://openalex.org/W2996140569","https://openalex.org/W2997280954","https://openalex.org/W3000350302","https://openalex.org/W3001485171","https://openalex.org/W3002417351","https://openalex.org/W3003517652","https://openalex.org/W3005127469","https://openalex.org/W3010280657","https://openalex.org/W3012280517","https://openalex.org/W3019420398","https://openalex.org/W3021272327","https://openalex.org/W3022248657","https://openalex.org/W3024013192","https://openalex.org/W3035266582","https://openalex.org/W3036962145","https://openalex.org/W3037216933","https://openalex.org/W3045713985","https://openalex.org/W3095964485","https://openalex.org/W3096831136","https://openalex.org/W3097029961","https://openalex.org/W3100015175","https://openalex.org/W3105146463","https://openalex.org/W3106188259","https://openalex.org/W3113251307","https://openalex.org/W3121168830","https://openalex.org/W3121756359","https://openalex.org/W3125073942","https://openalex.org/W3130617412","https://openalex.org/W3132357920","https://openalex.org/W3137392859","https://openalex.org/W3138479716","https://openalex.org/W3159754263","https://openalex.org/W3197283953","https://openalex.org/W3198138654","https://openalex.org/W4212774754","https://openalex.org/W4213108508","https://openalex.org/W4233698560","https://openalex.org/W4234552385","https://openalex.org/W4235169531","https://openalex.org/W4292560509","https://openalex.org/W4295274059","https://openalex.org/W4295521014","https://openalex.org/W6636447677","https://openalex.org/W6735913928","https://openalex.org/W6736155344","https://openalex.org/W6736677004","https://openalex.org/W6748655329","https://openalex.org/W6748816842","https://openalex.org/W6751796012","https://openalex.org/W6779669310","https://openalex.org/W6779698138","https://openalex.org/W6785155162","https://openalex.org/W6800106536"],"related_works":["https://openalex.org/W3013693939","https://openalex.org/W2159052453","https://openalex.org/W2566616303","https://openalex.org/W3131327266","https://openalex.org/W2734887215","https://openalex.org/W2502115930","https://openalex.org/W4297051394","https://openalex.org/W2752972570","https://openalex.org/W2145836866","https://openalex.org/W2803255133"],"abstract_inverted_index":{"Since":[0],"its":[1],"selection":[2],"as":[3,64,171],"the":[4,7,25,72,94,119,130,140,162,178],"method":[5],"of":[6,27,82,107,133,139,180,189,196],"year":[8],"in":[9,38,45,93,161,199],"2013,":[10],"single-cell":[11,28,42,69,204],"technologies":[12],"have":[13],"become":[14],"mature":[15],"enough":[16],"to":[17,20,48,136,150,191],"provide":[18],"answers":[19],"complex":[21],"research":[22],"questions.":[23],"With":[24],"growth":[26],"profiling":[29],"technologies,":[30],"there":[31],"has":[32],"also":[33],"been":[34],"a":[35,65,80,90,103,145,193],"significant":[36],"increase":[37],"data":[39,141],"collected":[40],"from":[41],"profilings,":[43],"resulting":[44],"computational":[46],"challenges":[47,198],"process":[49],"these":[50,57,126,134],"massive":[51],"and":[52,86,114,122,128,185,202],"complicated":[53],"datasets.":[54],"To":[55],"address":[56,192],"challenges,":[58],"deep":[59],"learning":[60,75,177],"(DL)":[61],"is":[62],"positioned":[63],"competitive":[66],"alternative":[67],"for":[68,89,125,154,176,182],"analyses":[70],"besides":[71],"traditional":[73],"machine":[74],"approaches.":[76],"Here,":[77],"we":[78,101],"survey":[79,168],"total":[81],"25":[83],"DL":[84,116,181,190],"algorithms":[85,153],"their":[87,155],"applicability":[88],"specific":[91,137],"step":[92,160],"single":[95],"cell":[96],"RNA-seq":[97],"processing":[98,142],"pipeline.":[99,163],"Specifically,":[100],"establish":[102],"unified":[104],"mathematical":[105],"representation":[106],"variational":[108],"autoencoder,":[109,110],"generative":[111],"adversarial":[112],"network":[113],"supervised":[115],"models,":[117,127],"compare":[118],"training":[120],"strategies":[121],"loss":[123,131],"functions":[124,132],"relate":[129],"models":[135],"objectives":[138],"step.":[143],"Such":[144],"presentation":[146],"will":[147,169],"allow":[148],"readers":[149],"choose":[151],"suitable":[152],"particular":[156],"objective":[157],"at":[158],"each":[159],"We":[164],"envision":[165],"that":[166],"this":[167],"serve":[170],"an":[172],"important":[173],"information":[174],"portal":[175],"application":[179],"scRNA-seq":[183],"analysis":[184],"inspire":[186],"innovative":[187],"uses":[188],"broader":[194],"range":[195],"new":[197],"emerging":[200],"multi-omics":[201],"spatial":[203],"sequencing.":[205]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":19},{"year":2024,"cited_by_count":24},{"year":2023,"cited_by_count":15},{"year":2022,"cited_by_count":10}],"updated_date":"2026-03-12T08:34:05.389933","created_date":"2025-10-10T00:00:00"}