{"id":"https://openalex.org/W4214932646","doi":"https://doi.org/10.1093/bioinformatics/btac141","title":"scGate: marker-based purification of cell types from heterogeneous single-cell RNA-seq datasets","display_name":"scGate: marker-based purification of cell types from heterogeneous single-cell RNA-seq datasets","publication_year":2022,"publication_date":"2022-03-04","ids":{"openalex":"https://openalex.org/W4214932646","doi":"https://doi.org/10.1093/bioinformatics/btac141","pmid":"https://pubmed.ncbi.nlm.nih.gov/35258562"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac141","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac141","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/9/2642/43481072/btac141.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/38/9/2642/43481072/btac141.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003717199","display_name":"Massimo Andreatta","orcid":"https://orcid.org/0000-0002-8036-2647"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I4210117758","display_name":"Ludwig Cancer Research","ror":"https://ror.org/02cn3rm21","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I4210117758","https://openalex.org/I4210150094"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Massimo Andreatta","raw_affiliation_strings":["Ludwig Institute for Cancer Research, Lausanne Branch, and Department of Oncology, CHUV and University of Lausanne , 1011 Lausanne, Switzerland","Swiss Institute of Bioinformatics , 1015 Lausanne, Switzerland"],"affiliations":[{"raw_affiliation_string":"Ludwig Institute for Cancer Research, Lausanne Branch, and Department of Oncology, CHUV and University of Lausanne , 1011 Lausanne, Switzerland","institution_ids":["https://openalex.org/I4210117758","https://openalex.org/I97565354"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics , 1015 Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068676336","display_name":"Ariel Berenstein","orcid":"https://orcid.org/0000-0001-8540-5389"},"institutions":[{"id":"https://openalex.org/I151201029","display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","ror":"https://ror.org/03cqe8w59","country_code":"AR","type":"government","lineage":["https://openalex.org/I151201029","https://openalex.org/I4210123736","https://openalex.org/I4387155568"]},{"id":"https://openalex.org/I4210165869","display_name":"Instituto Multidisciplinario de Biolog\u00eda Celular","ror":"https://ror.org/05p6vdy67","country_code":"AR","type":"facility","lineage":["https://openalex.org/I151201029","https://openalex.org/I4210123736","https://openalex.org/I4210138160","https://openalex.org/I4210165869","https://openalex.org/I4387155568","https://openalex.org/I874386039"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"Ariel J Berenstein","raw_affiliation_strings":["Laboratorio de Biolog\u00eda Molecular, Divisi\u00f3n Patolog\u00eda, Instituto Multidisciplinario de Investigaciones en Patolog\u00edas Pedi\u00e1tricas (IMIPP), CONICET-GCBA , Buenos Aires C1425EFD, Argentina"],"affiliations":[{"raw_affiliation_string":"Laboratorio de Biolog\u00eda Molecular, Divisi\u00f3n Patolog\u00eda, Instituto Multidisciplinario de Investigaciones en Patolog\u00edas Pedi\u00e1tricas (IMIPP), CONICET-GCBA , Buenos Aires C1425EFD, Argentina","institution_ids":["https://openalex.org/I4210165869","https://openalex.org/I151201029"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009921267","display_name":"Santiago J. Carmona","orcid":"https://orcid.org/0000-0002-2495-0671"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I4210117758","display_name":"Ludwig Cancer Research","ror":"https://ror.org/02cn3rm21","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I4210117758","https://openalex.org/I4210150094"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Santiago J Carmona","raw_affiliation_strings":["Ludwig Institute for Cancer Research, Lausanne Branch, and Department of Oncology, CHUV and University of Lausanne , 1011 Lausanne, Switzerland","Swiss Institute of Bioinformatics , 1015 Lausanne, Switzerland"],"affiliations":[{"raw_affiliation_string":"Ludwig Institute for Cancer Research, Lausanne Branch, and Department of Oncology, CHUV and University of Lausanne , 1011 Lausanne, Switzerland","institution_ids":["https://openalex.org/I4210117758","https://openalex.org/I97565354"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics , 1015 Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5009921267"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I4210117758","https://openalex.org/I97565354"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":8.2455,"has_fulltext":true,"cited_by_count":101,"citation_normalized_percentile":{"value":0.98596345,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"38","issue":"9","first_page":"2642","last_page":"2644"},"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":0.9686999917030334,"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/T11313","display_name":"Immune cells in cancer","score":0.9678999781608582,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.7299858331680298},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6755785942077637},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5962313413619995},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5850448608398438},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5123151540756226},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.44904154539108276},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.3932628333568573},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37873485684394836},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35531342029571533},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3552725315093994},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.22880524396896362},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13961714506149292},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12061578035354614},{"id":"https://openalex.org/keywords/cartography","display_name":"Cartography","score":0.0723564624786377}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7299858331680298},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6755785942077637},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5962313413619995},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5850448608398438},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5123151540756226},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.44904154539108276},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.3932628333568573},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37873485684394836},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35531342029571533},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3552725315093994},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.22880524396896362},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13961714506149292},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12061578035354614},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.0723564624786377},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btac141","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac141","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/9/2642/43481072/btac141.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:35258562","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35258562","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:serval.unil.ch:BIB_241F222A7909","is_oa":true,"landing_page_url":"https://serval.unil.ch/notice/serval:BIB_241F222A7909","pdf_url":null,"source":{"id":"https://openalex.org/S4306401797","display_name":"SERVAL (Universit\u00e9 de Lausanne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210093590","host_organization_name":"Swiss School of Archaeology in Greece","host_organization_lineage":["https://openalex.org/I4210093590"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics, vol. 38, no. 9, pp. 2642-2644","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:iris.unil.ch:iris/90298","is_oa":true,"landing_page_url":"https://iris.unil.ch/handle/iris/90298","pdf_url":"https://iris.unil.ch/bitstreams/a7873a6a-c8e4-4c1b-a791-a537de8cbc20/download","source":{"id":"https://openalex.org/S7407055444","display_name":"IRIS","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":null,"raw_type":"journal article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9048671","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9048671","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":"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/btac141","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac141","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/9/2642/43481072/btac141.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/G4183234989","display_name":null,"funder_award_id":"180010","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G65162470","display_name":null,"funder_award_id":"Swiss National Science Foundation (SNF)","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G6691483310","display_name":null,"funder_award_id":"Ambizione","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"id":"https://openalex.org/F4320321594","display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","ror":"https://ror.org/03cqe8w59"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4214932646.pdf","grobid_xml":"https://content.openalex.org/works/W4214932646.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W2887886950","https://openalex.org/W2898830231","https://openalex.org/W2907514116","https://openalex.org/W2936414047","https://openalex.org/W2959295202","https://openalex.org/W2966465234","https://openalex.org/W2971398276","https://openalex.org/W2971653850","https://openalex.org/W3117771127","https://openalex.org/W3124814274","https://openalex.org/W3164692211","https://openalex.org/W3174072032","https://openalex.org/W3210860076"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W4321353415","https://openalex.org/W2130974462","https://openalex.org/W972276598","https://openalex.org/W2086519370","https://openalex.org/W2028665553","https://openalex.org/W2087343574","https://openalex.org/W2535915176","https://openalex.org/W2105860728","https://openalex.org/W3081644756"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":27},{"year":2024,"cited_by_count":44},{"year":2023,"cited_by_count":16},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":1}],"updated_date":"2026-04-14T08:04:32.555800","created_date":"2025-10-10T00:00:00"}