{"id":"https://openalex.org/W4385295387","doi":"https://doi.org/10.1093/bib/bbad260","title":"A biology-driven deep generative model for cell-type annotation in cytometry","display_name":"A biology-driven deep generative model for cell-type annotation in cytometry","publication_year":2023,"publication_date":"2023-07-26","ids":{"openalex":"https://openalex.org/W4385295387","doi":"https://doi.org/10.1093/bib/bbad260","pmid":"https://pubmed.ncbi.nlm.nih.gov/37497716"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad260","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad260","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbad260/50973199/bbad260.pdf","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":"bronze","oa_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbad260/50973199/bbad260.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061877252","display_name":"Quentin Blampey","orcid":"https://orcid.org/0000-0002-3836-2889"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210107720","display_name":"CentraleSup\u00e9lec","ror":"https://ror.org/019tcpt25","country_code":"FR","type":"facility","lineage":["https://openalex.org/I277688954","https://openalex.org/I4210107720"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Quentin Blampey","raw_affiliation_strings":["Universit\u00e9 Paris-Saclay, CentraleSup\u00e9lec, Laboratory of Mathematics and Computer Science (MICS) , 3 rue Joliot Curie, 91190,Gif-sur-Yvette , France"],"raw_orcid":"https://orcid.org/0000-0002-3836-2889","affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay, CentraleSup\u00e9lec, Laboratory of Mathematics and Computer Science (MICS) , 3 rue Joliot Curie, 91190,Gif-sur-Yvette , France","institution_ids":["https://openalex.org/I4210107720","https://openalex.org/I277688954"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020180300","display_name":"Nad\u00e8ge Bercovici","orcid":"https://orcid.org/0000-0002-8449-0590"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I2801843802","display_name":"Institut Gustave Roussy","ror":"https://ror.org/0321g0743","country_code":"FR","type":"facility","lineage":["https://openalex.org/I2801843802"]},{"id":"https://openalex.org/I4210141964","display_name":"Institut Cochin","ror":"https://ror.org/051sk4035","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I4210096427","https://openalex.org/I4210141964"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Nad\u00e8ge Bercovici","raw_affiliation_strings":["Universit\u00e9 Paris Cit\u00e9, Institut Cochin , CNRS, Inserm, 22 Rue M\u00e9chain, 75014, Paris , France","Universit\u00e9 Paris-Saclay, Gustave Roussy , Inserm U981, 114 Rue Edouard Vaillant, 94805, Villejuif , France"],"raw_orcid":"https://orcid.org/0000-0002-8449-0590","affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris Cit\u00e9, Institut Cochin , CNRS, Inserm, 22 Rue M\u00e9chain, 75014, Paris , France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I4210141964","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay, Gustave Roussy , Inserm U981, 114 Rue Edouard Vaillant, 94805, Villejuif , France","institution_ids":["https://openalex.org/I2801843802","https://openalex.org/I154526488","https://openalex.org/I277688954"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027444394","display_name":"Charles\u2010Antoine Dutertre","orcid":"https://orcid.org/0000-0001-7950-3652"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I2801843802","display_name":"Institut Gustave Roussy","ror":"https://ror.org/0321g0743","country_code":"FR","type":"facility","lineage":["https://openalex.org/I2801843802"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Charles-Antoine Dutertre","raw_affiliation_strings":["Universit\u00e9 Paris-Saclay, Gustave Roussy , Inserm U1015, 114 Rue Edouard Vaillant, 94805, Villejuif , France"],"raw_orcid":"https://orcid.org/0000-0001-7950-3652","affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay, Gustave Roussy , Inserm U1015, 114 Rue Edouard Vaillant, 94805, Villejuif , France","institution_ids":["https://openalex.org/I2801843802","https://openalex.org/I154526488","https://openalex.org/I277688954"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034710988","display_name":"Isabelle Pic","orcid":null},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I2801843802","display_name":"Institut Gustave Roussy","ror":"https://ror.org/0321g0743","country_code":"FR","type":"facility","lineage":["https://openalex.org/I2801843802"]},{"id":"https://openalex.org/I4210131199","display_name":"Paris Cardiovascular Research Center","ror":"https://ror.org/03gvnh520","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I4210131199"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Isabelle Pic","raw_affiliation_strings":["Universit\u00e9 Paris-Saclay, Gustave Roussy , Inserm U981, 114 Rue Edouard Vaillant, 94805, Villejuif , France","PARCC (UMR_S 970/ U970) - Paris-Centre de Recherche Cardiovasculaire (56 rue Leblanc\r\n75015 PARIS\r\nFRANCE - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay, Gustave Roussy , Inserm U981, 114 Rue Edouard Vaillant, 94805, Villejuif , France","institution_ids":["https://openalex.org/I2801843802","https://openalex.org/I154526488","https://openalex.org/I277688954"]},{"raw_affiliation_string":"PARCC (UMR_S 970/ U970) - Paris-Centre de Recherche Cardiovasculaire (56 rue Leblanc\r\n75015 PARIS\r\nFRANCE - France)","institution_ids":["https://openalex.org/I4210131199"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101835488","display_name":"Joana Ribeiro","orcid":"https://orcid.org/0000-0001-7947-672X"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I2801843802","display_name":"Institut Gustave Roussy","ror":"https://ror.org/0321g0743","country_code":"FR","type":"facility","lineage":["https://openalex.org/I2801843802"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Joana Mourato Ribeiro","raw_affiliation_strings":["Gustave Roussy, D\u00e9partement de M\u00e9decine Oncologique , 114 Rue Edouard Vaillant, 94805, Villejuif , France","Universit\u00e9 Paris-Saclay, Gustave Roussy , Inserm U981, 114 Rue Edouard Vaillant, 94805, Villejuif , France"],"raw_orcid":"https://orcid.org/0000-0001-7947-672X","affiliations":[{"raw_affiliation_string":"Gustave Roussy, D\u00e9partement de M\u00e9decine Oncologique , 114 Rue Edouard Vaillant, 94805, Villejuif , France","institution_ids":["https://openalex.org/I2801843802"]},{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay, Gustave Roussy , Inserm U981, 114 Rue Edouard Vaillant, 94805, Villejuif , France","institution_ids":["https://openalex.org/I2801843802","https://openalex.org/I154526488","https://openalex.org/I277688954"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001814176","display_name":"Fabrice Andr\u00e9","orcid":"https://orcid.org/0000-0001-5795-8357"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I2801843802","display_name":"Institut Gustave Roussy","ror":"https://ror.org/0321g0743","country_code":"FR","type":"facility","lineage":["https://openalex.org/I2801843802"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Fabrice Andr\u00e9","raw_affiliation_strings":["Gustave Roussy, D\u00e9partement de M\u00e9decine Oncologique , 114 Rue Edouard Vaillant, 94805, Villejuif , France","Universit\u00e9 Paris-Saclay, Gustave Roussy , Inserm U981, 114 Rue Edouard Vaillant, 94805, Villejuif , France"],"raw_orcid":"https://orcid.org/0000-0001-5795-8357","affiliations":[{"raw_affiliation_string":"Gustave Roussy, D\u00e9partement de M\u00e9decine Oncologique , 114 Rue Edouard Vaillant, 94805, Villejuif , France","institution_ids":["https://openalex.org/I2801843802"]},{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay, Gustave Roussy , Inserm U981, 114 Rue Edouard Vaillant, 94805, Villejuif , France","institution_ids":["https://openalex.org/I2801843802","https://openalex.org/I154526488","https://openalex.org/I277688954"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048541433","display_name":"Paul-Henry Courn\u00e8de","orcid":"https://orcid.org/0000-0001-7679-6197"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210107720","display_name":"CentraleSup\u00e9lec","ror":"https://ror.org/019tcpt25","country_code":"FR","type":"facility","lineage":["https://openalex.org/I277688954","https://openalex.org/I4210107720"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Paul-Henry Courn\u00e8de","raw_affiliation_strings":["Universit\u00e9 Paris-Saclay, CentraleSup\u00e9lec, Laboratory of Mathematics and Computer Science (MICS) , 3 rue Joliot Curie, 91190,Gif-sur-Yvette , France"],"raw_orcid":"https://orcid.org/0000-0001-7679-6197","affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay, CentraleSup\u00e9lec, Laboratory of Mathematics and Computer Science (MICS) , 3 rue Joliot Curie, 91190,Gif-sur-Yvette , France","institution_ids":["https://openalex.org/I4210107720","https://openalex.org/I277688954"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.2216,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.79284672,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"24","issue":"5","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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9990000128746033,"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"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9677000045776367,"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/computer-science","display_name":"Computer science","score":0.7390289902687073},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.6919472217559814},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6769862174987793},{"id":"https://openalex.org/keywords/mass-cytometry","display_name":"Mass cytometry","score":0.6649874448776245},{"id":"https://openalex.org/keywords/cytometry","display_name":"Cytometry","score":0.6212617754936218},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5656232833862305},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5521251559257507},{"id":"https://openalex.org/keywords/flow-cytometry","display_name":"Flow cytometry","score":0.46365886926651},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.3929763734340668},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3879278600215912},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3721098303794861},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16928282380104065},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.10914260149002075}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7390289902687073},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.6919472217559814},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6769862174987793},{"id":"https://openalex.org/C2778015335","wikidata":"https://www.wikidata.org/wiki/Q17051163","display_name":"Mass cytometry","level":4,"score":0.6649874448776245},{"id":"https://openalex.org/C2780339063","wikidata":"https://www.wikidata.org/wiki/Q5201367","display_name":"Cytometry","level":3,"score":0.6212617754936218},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5656232833862305},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5521251559257507},{"id":"https://openalex.org/C553184892","wikidata":"https://www.wikidata.org/wiki/Q1141429","display_name":"Flow cytometry","level":2,"score":0.46365886926651},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.3929763734340668},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3879278600215912},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3721098303794861},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16928282380104065},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.10914260149002075},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D001695","descriptor_name":"Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001695","descriptor_name":"Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001695","descriptor_name":"Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005434","descriptor_name":"Flow Cytometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005434","descriptor_name":"Flow Cytometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005434","descriptor_name":"Flow Cytometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbad260","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad260","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbad260/50973199/bbad260.pdf","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:37497716","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37497716","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:HAL:hal-04287005v1","is_oa":true,"landing_page_url":"https://hal.science/hal-04287005","pdf_url":"https://hal.science/hal-04287005v1/file/Blampey%202023.pdf","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Briefings in Bioinformatics, 2023, 24 (5), ⟨10.1093/bib/bbad260⟩","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbad260","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad260","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbad260/50973199/bbad260.pdf","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"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4432323768","display_name":"PRecISion Medicine Institute in oncology","funder_award_id":"ANR-18-IBHU-0002","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G6876561401","display_name":null,"funder_award_id":"ANR-18","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4385295387.pdf","grobid_xml":"https://content.openalex.org/works/W4385295387.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W1522301498","https://openalex.org/W1631320694","https://openalex.org/W1970170720","https://openalex.org/W1981480494","https://openalex.org/W2024626836","https://openalex.org/W2042492924","https://openalex.org/W2052221015","https://openalex.org/W2073256527","https://openalex.org/W2101234009","https://openalex.org/W2107665951","https://openalex.org/W2112493011","https://openalex.org/W2346039638","https://openalex.org/W2485014704","https://openalex.org/W2559588458","https://openalex.org/W2585179645","https://openalex.org/W2585665652","https://openalex.org/W2612538354","https://openalex.org/W2761095749","https://openalex.org/W2786672974","https://openalex.org/W2884964182","https://openalex.org/W2897249806","https://openalex.org/W2901677030","https://openalex.org/W2920999075","https://openalex.org/W2962788902","https://openalex.org/W2972495911","https://openalex.org/W2972623358","https://openalex.org/W2973034691","https://openalex.org/W2978541146","https://openalex.org/W2984472267","https://openalex.org/W3021526713","https://openalex.org/W3106188259","https://openalex.org/W3164882886","https://openalex.org/W4237142329","https://openalex.org/W4252684946","https://openalex.org/W4295312788","https://openalex.org/W4297798428","https://openalex.org/W6610566761","https://openalex.org/W6631190155","https://openalex.org/W6675354045","https://openalex.org/W6714644935","https://openalex.org/W6748816842","https://openalex.org/W6754561918","https://openalex.org/W6766978945","https://openalex.org/W6767520560","https://openalex.org/W6770847983","https://openalex.org/W6772175390"],"related_works":["https://openalex.org/W2176701861","https://openalex.org/W4224000552","https://openalex.org/W2053129129","https://openalex.org/W4365211920","https://openalex.org/W4251194061","https://openalex.org/W2470680194","https://openalex.org/W2944792102","https://openalex.org/W1576959934","https://openalex.org/W4313381864","https://openalex.org/W3014948380"],"abstract_inverted_index":{"Cytometry":[0,59],"enables":[1],"precise":[2],"single-cell":[3],"phenotyping":[4],"within":[5],"heterogeneous":[6],"populations.":[7],"These":[8],"cell":[9,65,137],"types":[10,66],"are":[11],"traditionally":[12],"annotated":[13],"via":[14,42],"manual":[15,43],"gating,":[16],"but":[17],"this":[18,132],"method":[19],"lacks":[20],"reproducibility":[21],"and":[22,37,47,114,128,135,141],"sensitivity":[23],"to":[24],"batch":[25],"effect.":[26],"Also,":[27],"the":[28,73,103],"most":[29],"recent":[30],"cytometers-spectral":[31],"flow":[32],"or":[33],"mass":[34],"cytometers-create":[35],"rich":[36],"high-dimensional":[38],"data":[39],"whose":[40],"analysis":[41],"gating":[44],"becomes":[45],"challenging":[46],"time-consuming.":[48],"To":[49],"tackle":[50],"these":[51],"limitations,":[52],"we":[53],"introduce":[54],"Scyan":[55,100,118],"https://github.com/MICS-Lab/scyan,":[56],"a":[57,80,92],"Single-cell":[58],"Annotation":[60],"Network":[61],"that":[62,99],"automatically":[63],"annotates":[64],"using":[67],"only":[68],"prior":[69],"expert":[70],"knowledge":[71],"about":[72],"cytometry":[74],"panel.":[75],"For":[76],"this,":[77],"it":[78],"uses":[79],"normalizing":[81],"flow-a":[82],"type":[83],"of":[84],"deep":[85],"generative":[86],"model-that":[87],"maps":[88],"protein":[89],"expressions":[90],"into":[91],"biologically":[93],"relevant":[94],"latent":[95],"space.":[96],"We":[97],"demonstrate":[98],"significantly":[101],"outperforms":[102],"related":[104],"state-of-the-art":[105],"models":[106],"on":[107],"multiple":[108],"public":[109],"datasets":[110],"while":[111],"being":[112],"faster":[113],"interpretable.":[115],"In":[116],"addition,":[117],"overcomes":[119],"several":[120],"complementary":[121],"tasks,":[122],"such":[123],"as":[124],"batch-effect":[125],"correction,":[126],"debarcoding":[127],"population":[129,138],"discovery.":[130],"Overall,":[131],"model":[133],"accelerates":[134],"eases":[136],"characterization,":[139],"quantification":[140],"discovery":[142],"in":[143],"cytometry.":[144]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":3}],"updated_date":"2026-07-03T08:13:44.112507","created_date":"2025-10-10T00:00:00"}