{"id":"https://openalex.org/W4412650345","doi":"https://doi.org/10.1093/bib/bbaf371","title":"Benchmarking of computational demultiplexing methods for single-nucleus RNA sequencing data","display_name":"Benchmarking of computational demultiplexing methods for single-nucleus RNA sequencing data","publication_year":2025,"publication_date":"2025-07-01","ids":{"openalex":"https://openalex.org/W4412650345","doi":"https://doi.org/10.1093/bib/bbaf371","pmid":"https://pubmed.ncbi.nlm.nih.gov/40702707"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf371","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf371","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":true,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bib/bbaf371","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004541978","display_name":"Yile Fu","orcid":"https://orcid.org/0000-0003-0615-1152"},"institutions":[{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Yile Fu","raw_affiliation_strings":["Laboratory of Experimental Cardiology, Department of Cardiovascular Sciences, KU Leuven , Herestraat 49, 3000 Leuven ,"],"affiliations":[{"raw_affiliation_string":"Laboratory of Experimental Cardiology, Department of Cardiovascular Sciences, KU Leuven , Herestraat 49, 3000 Leuven ,","institution_ids":["https://openalex.org/I99464096"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101694282","display_name":"Mohamad Youness","orcid":"https://orcid.org/0000-0002-1159-4268"},"institutions":[{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Mohamad Youness","raw_affiliation_strings":["Laboratory of Experimental Cardiology, Department of Cardiovascular Sciences, KU Leuven , Herestraat 49, 3000 Leuven ,"],"affiliations":[{"raw_affiliation_string":"Laboratory of Experimental Cardiology, Department of Cardiovascular Sciences, KU Leuven , Herestraat 49, 3000 Leuven ,","institution_ids":["https://openalex.org/I99464096"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063575248","display_name":"Alessia Virz\u00ec","orcid":"https://orcid.org/0000-0002-0348-9601"},"institutions":[{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Alessia Virz\u00ec","raw_affiliation_strings":["Laboratory of Experimental Cardiology, Department of Cardiovascular Sciences, KU Leuven , Herestraat 49, 3000 Leuven ,"],"affiliations":[{"raw_affiliation_string":"Laboratory of Experimental Cardiology, Department of Cardiovascular Sciences, KU Leuven , Herestraat 49, 3000 Leuven ,","institution_ids":["https://openalex.org/I99464096"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090868938","display_name":"Xinran Song","orcid":"https://orcid.org/0009-0009-9704-9794"},"institutions":[{"id":"https://openalex.org/I4210098597","display_name":"Centre For Human Genetics","ror":"https://ror.org/00tw8zf26","country_code":"IN","type":"other","lineage":["https://openalex.org/I4210098597"]},{"id":"https://openalex.org/I4210105714","display_name":"Center for Human Genetics","ror":"https://ror.org/01gcrbc43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210105714"]}],"countries":["IN","US"],"is_corresponding":false,"raw_author_name":"Xinran Song","raw_affiliation_strings":["Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven , Herestraat 49, 3000 Leuven ,"],"affiliations":[{"raw_affiliation_string":"Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven , Herestraat 49, 3000 Leuven ,","institution_ids":["https://openalex.org/I4210105714","https://openalex.org/I4210098597"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042626064","display_name":"Michiel Tubeeckx","orcid":"https://orcid.org/0000-0002-1337-0727"},"institutions":[{"id":"https://openalex.org/I149213910","display_name":"University of Antwerp","ror":"https://ror.org/008x57b05","country_code":"BE","type":"education","lineage":["https://openalex.org/I149213910"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Michiel R L Tubeeckx","raw_affiliation_strings":["Laboratory of Physiopharmacology, Universiteitsplein 1, Building T (2nd Floor) , 2610 Antwerp ,"],"affiliations":[{"raw_affiliation_string":"Laboratory of Physiopharmacology, Universiteitsplein 1, Building T (2nd Floor) , 2610 Antwerp ,","institution_ids":["https://openalex.org/I149213910"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101474241","display_name":"Gilles W. De Keulenaer","orcid":"https://orcid.org/0000-0002-4238-4183"},"institutions":[{"id":"https://openalex.org/I149213910","display_name":"University of Antwerp","ror":"https://ror.org/008x57b05","country_code":"BE","type":"education","lineage":["https://openalex.org/I149213910"]},{"id":"https://openalex.org/I4210111370","display_name":"ZNA Middelheim Hospital","ror":"https://ror.org/01z5jvj74","country_code":"BE","type":"healthcare","lineage":["https://openalex.org/I4210111370"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Gilles W De Keulenaer","raw_affiliation_strings":["Department of Cardiology, ZNA Middelheim Hospital Antwerp , 2610 Antwerp ,","Laboratory of Physiopharmacology, Universiteitsplein 1, Building T (2nd Floor) , 2610 Antwerp ,"],"affiliations":[{"raw_affiliation_string":"Department of Cardiology, ZNA Middelheim Hospital Antwerp , 2610 Antwerp ,","institution_ids":["https://openalex.org/I4210111370"]},{"raw_affiliation_string":"Laboratory of Physiopharmacology, Universiteitsplein 1, Building T (2nd Floor) , 2610 Antwerp ,","institution_ids":["https://openalex.org/I149213910"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019955596","display_name":"Hein Heidb\u00fcchel","orcid":"https://orcid.org/0000-0001-9301-8127"},"institutions":[{"id":"https://openalex.org/I149213910","display_name":"University of Antwerp","ror":"https://ror.org/008x57b05","country_code":"BE","type":"education","lineage":["https://openalex.org/I149213910"]},{"id":"https://openalex.org/I4210102047","display_name":"Antwerp University Hospital","ror":"https://ror.org/01hwamj44","country_code":"BE","type":"funder","lineage":["https://openalex.org/I4210102047"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Hein Heidbuchel","raw_affiliation_strings":["Department of Cardiology, University Hospital Antwerp , 2610 Antwerp ,","Research Group Cardiovascular Diseases, GENCOR, University of Antwerp , 2610 Antwerp ,"],"affiliations":[{"raw_affiliation_string":"Department of Cardiology, University Hospital Antwerp , 2610 Antwerp ,","institution_ids":["https://openalex.org/I4210102047"]},{"raw_affiliation_string":"Research Group Cardiovascular Diseases, GENCOR, University of Antwerp , 2610 Antwerp ,","institution_ids":["https://openalex.org/I149213910"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024401015","display_name":"Vincent F. M. Segers","orcid":"https://orcid.org/0000-0001-7796-2222"},"institutions":[{"id":"https://openalex.org/I149213910","display_name":"University of Antwerp","ror":"https://ror.org/008x57b05","country_code":"BE","type":"education","lineage":["https://openalex.org/I149213910"]},{"id":"https://openalex.org/I4210102047","display_name":"Antwerp University Hospital","ror":"https://ror.org/01hwamj44","country_code":"BE","type":"funder","lineage":["https://openalex.org/I4210102047"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Vincent F M Segers","raw_affiliation_strings":["Department of Cardiology, University Hospital Antwerp , 2610 Antwerp ,","Laboratory of Physiopharmacology, Universiteitsplein 1, Building T (2nd Floor) , 2610 Antwerp ,"],"affiliations":[{"raw_affiliation_string":"Department of Cardiology, University Hospital Antwerp , 2610 Antwerp ,","institution_ids":["https://openalex.org/I4210102047"]},{"raw_affiliation_string":"Laboratory of Physiopharmacology, Universiteitsplein 1, Building T (2nd Floor) , 2610 Antwerp ,","institution_ids":["https://openalex.org/I149213910"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042788376","display_name":"Karin R. Sipido","orcid":"https://orcid.org/0000-0001-9609-5507"},"institutions":[{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Karin R Sipido","raw_affiliation_strings":["Laboratory of Experimental Cardiology, Department of Cardiovascular Sciences, KU Leuven , Herestraat 49, 3000 Leuven ,"],"affiliations":[{"raw_affiliation_string":"Laboratory of Experimental Cardiology, Department of Cardiovascular Sciences, KU Leuven , Herestraat 49, 3000 Leuven ,","institution_ids":["https://openalex.org/I99464096"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081498592","display_name":"Bernard Thienpont","orcid":"https://orcid.org/0000-0002-8772-6845"},"institutions":[{"id":"https://openalex.org/I4210098597","display_name":"Centre For Human Genetics","ror":"https://ror.org/00tw8zf26","country_code":"IN","type":"other","lineage":["https://openalex.org/I4210098597"]},{"id":"https://openalex.org/I4210105714","display_name":"Center for Human Genetics","ror":"https://ror.org/01gcrbc43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210105714"]}],"countries":["IN","US"],"is_corresponding":false,"raw_author_name":"Bernard Thienpont","raw_affiliation_strings":["Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven , Herestraat 49, 3000 Leuven ,"],"affiliations":[{"raw_affiliation_string":"Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven , Herestraat 49, 3000 Leuven ,","institution_ids":["https://openalex.org/I4210105714","https://openalex.org/I4210098597"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029465797","display_name":"H. Llewelyn Roderick","orcid":"https://orcid.org/0000-0001-7065-3523"},"institutions":[{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"H Llewelyn Roderick","raw_affiliation_strings":["Laboratory of Experimental Cardiology, Department of Cardiovascular Sciences, KU Leuven , Herestraat 49, 3000 Leuven ,"],"affiliations":[{"raw_affiliation_string":"Laboratory of Experimental Cardiology, Department of Cardiovascular Sciences, KU Leuven , Herestraat 49, 3000 Leuven ,","institution_ids":["https://openalex.org/I99464096"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5004541978"],"corresponding_institution_ids":["https://openalex.org/I99464096"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.7625,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.73526068,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"26","issue":"4","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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9957000017166138,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9951000213623047,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/multiplexing","display_name":"Multiplexing","score":0.7134021520614624},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5957008600234985},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5724009275436401},{"id":"https://openalex.org/keywords/pooling","display_name":"Pooling","score":0.41598159074783325},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.40940341353416443},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.17133817076683044}],"concepts":[{"id":"https://openalex.org/C19275194","wikidata":"https://www.wikidata.org/wiki/Q222903","display_name":"Multiplexing","level":2,"score":0.7134021520614624},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5957008600234985},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5724009275436401},{"id":"https://openalex.org/C70437156","wikidata":"https://www.wikidata.org/wiki/Q7228652","display_name":"Pooling","level":2,"score":0.41598159074783325},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40940341353416443},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.17133817076683044},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002467","descriptor_name":"Cell Nucleus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002467","descriptor_name":"Cell Nucleus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002467","descriptor_name":"Cell Nucleus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002467","descriptor_name":"Cell Nucleus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbaf371","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf371","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":true,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40702707","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40702707","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:lirias2repo.kuleuven.be:20.500.12942/770629","is_oa":true,"landing_page_url":"https://lirias.kuleuven.be/handle/20.500.12942/770629","pdf_url":null,"source":{"id":"https://openalex.org/S4306401954","display_name":"Lirias (KU Leuven)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I99464096","host_organization_name":"KU Leuven","host_organization_lineage":["https://openalex.org/I99464096"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Briefings In Bioinformatics, vol. 26 (4), Art.No. ARTN bbaf371","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:pubmedcentral.nih.gov:12286777","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12286777","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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf371","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf371","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":true,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1426318481","display_name":null,"funder_award_id":"grant","funder_id":"https://openalex.org/F4320322725","funder_display_name":"China Scholarship Council"},{"id":"https://openalex.org/G1717768553","display_name":null,"funder_award_id":"20-VLIR-iBOF-027","funder_id":"https://openalex.org/F4320323782","funder_display_name":"Vlaamse Interuniversitaire Raad"},{"id":"https://openalex.org/G3313827400","display_name":null,"funder_award_id":"20-VLIR-iBOF-027","funder_id":"https://openalex.org/F4320322308","funder_display_name":"KU Leuven"},{"id":"https://openalex.org/G3769692487","display_name":null,"funder_award_id":"20-VLIR-iBOF-027","funder_id":"https://openalex.org/F4320335227","funder_display_name":"Bijzonder Onderzoeksfonds UGent"},{"id":"https://openalex.org/G512459777","display_name":null,"funder_award_id":"G0C7319N","funder_id":"https://openalex.org/F4320321730","funder_display_name":"Fonds Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G6286167507","display_name":null,"funder_award_id":"C14/21/093","funder_id":"https://openalex.org/F4320322308","funder_display_name":"KU Leuven"},{"id":"https://openalex.org/G8589651859","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320322725","funder_display_name":"China Scholarship Council"},{"id":"https://openalex.org/G8863810249","display_name":null,"funder_award_id":"C1 project","funder_id":"https://openalex.org/F4320322308","funder_display_name":"KU Leuven"}],"funders":[{"id":"https://openalex.org/F4320321730","display_name":"Fonds Wetenschappelijk Onderzoek","ror":"https://ror.org/03qtxy027"},{"id":"https://openalex.org/F4320322308","display_name":"KU Leuven","ror":"https://ror.org/05f950310"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"},{"id":"https://openalex.org/F4320323782","display_name":"Vlaamse Interuniversitaire Raad","ror":"https://ror.org/00q3h2974"},{"id":"https://openalex.org/F4320327336","display_name":"Vlaamse regering","ror":null},{"id":"https://openalex.org/F4320335227","display_name":"Bijzonder Onderzoeksfonds UGent","ror":"https://ror.org/00cv9y106"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W839653734","https://openalex.org/W1580018887","https://openalex.org/W1596062789","https://openalex.org/W2069295116","https://openalex.org/W2102212449","https://openalex.org/W2104549677","https://openalex.org/W2110417468","https://openalex.org/W2121964616","https://openalex.org/W2774307122","https://openalex.org/W2785085486","https://openalex.org/W2794891507","https://openalex.org/W2817838603","https://openalex.org/W2899348912","https://openalex.org/W2946232537","https://openalex.org/W2949237386","https://openalex.org/W2949787845","https://openalex.org/W2949829455","https://openalex.org/W2951068818","https://openalex.org/W2951624434","https://openalex.org/W2951638683","https://openalex.org/W2953151710","https://openalex.org/W2995043840","https://openalex.org/W2997393200","https://openalex.org/W3023290106","https://openalex.org/W3037482866","https://openalex.org/W3046099861","https://openalex.org/W3113268000","https://openalex.org/W3125409863","https://openalex.org/W3131055609","https://openalex.org/W3157353881","https://openalex.org/W3160731134","https://openalex.org/W3164185283","https://openalex.org/W3164692211","https://openalex.org/W3199486250","https://openalex.org/W4213286472","https://openalex.org/W4225764874","https://openalex.org/W4283257569","https://openalex.org/W4320914072","https://openalex.org/W4360829845","https://openalex.org/W4362521601","https://openalex.org/W4365513261","https://openalex.org/W4367668197","https://openalex.org/W4377011406","https://openalex.org/W4394808545","https://openalex.org/W4398166518","https://openalex.org/W4398239554","https://openalex.org/W4399474248","https://openalex.org/W4405078072"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2953234277","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694"],"abstract_inverted_index":{"Single-nucleus":[0],"RNA":[1],"sequencing":[2,45],"(snRNA-Seq)":[3],"has":[4],"transformed":[5],"our":[6],"understanding":[7],"of":[8,36,78,114,188,219,222,226],"complex":[9],"tissues,":[10],"providing":[11],"insights":[12],"into":[13],"cellular":[14],"composition":[15],"and":[16,23,28,41,61,116,142,150,152,161,170,183,236,248],"heterogeneity":[17],"in":[18,26],"gene":[19],"expression":[20],"between":[21,67,85,148],"cells,":[22],"their":[24,42],"alterations":[25],"development":[27],"disease.":[29],"High":[30],"costs":[31],"however":[32],"constrain":[33],"the":[34,90,192,201,216,233],"number":[35],"samples":[37,144],"analysed.":[38],"Sample":[39],"pooling":[40],"demultiplexing":[43,80,100,155,223],"following":[44],"based":[46],"on":[47,135],"prior":[48],"labelling":[49],"with":[50,145,185,205,215],"antibodies":[51],"or":[52,63],"lipid":[53],"anchors":[54],"conjugated":[55],"to":[56,82],"DNA":[57],"barcodes":[58],"(cell":[59],"hashing":[60],"MULTI-seq),":[62],"using":[64,101,122,156],"genetic":[65,102,108],"differences":[66],"samples,":[68],"provides":[69],"a":[70],"solution.":[71],"However,":[72],"there":[73],"remains":[74],"no":[75],"comprehensive":[76],"evaluation":[77],"these":[79],"tools":[81,127,177,196],"guide":[83],"selection":[84],"them.":[86],"Here,":[87],"we":[88],"benchmark":[89],"leading":[91],"software":[92],"(Vireo,":[93],"Souporcell,":[94],"Freemuxlet,":[95],"scSplit)":[96],"used":[97],"for":[98,245],"sample":[99],"variants.":[103],"We":[104],"further":[105],"compared":[106],"obtaining":[107],"variants":[109],"from":[110,117,232,237],"SNP":[111],"array":[112],"analysis":[113,225],"gDNA":[115],"sample-matched":[118],"bulk-RNA-Seq":[119],"data,":[120],"identified":[121],"three":[123],"different":[124,238],"variant":[125,202],"calling":[126,203],"(BCFtools,":[128],"cellSNP,":[129],"FreeBayes).":[130],"Demultiplexing":[131,195],"performance":[132],"was":[133,208],"evaluated":[134,164],"simulated":[136],"multiplexed":[137],"datasets":[138],"comprising":[139],"two,":[140],"four,":[141],"six":[143],"doublet":[146,246],"percentages":[147],"0%":[149],"30%,":[151],"validated":[153],"against":[154],"sex-linked":[157],"genes.":[158],"Software":[159],"implementation":[160],"execution":[162],"were":[163,197],"by":[165,200],"run":[166],"speed,":[167],"robustness,":[168],"scalability,":[169],"usability.":[171],"Our":[172],"results":[173],"show":[174],"that":[175],"all":[176,211],"excluding":[178],"scSplit":[179],"provide":[180],"high":[181],"recall":[182],"precision":[184],"an":[186],"accuracy":[187,213],"80%-85%.":[189],"Vireo":[190],"achieved":[191],"best":[193],"accuracy.":[194],"differentially":[198],"affected":[199],"tool":[204],"which":[206],"it":[207],"paired.":[209],"For":[210],"tools,":[212],"decreased":[214],"increasing":[217],"percentage":[218],"doublets.":[220],"Deployment":[221],"during":[224],"pooled":[227],"real-world":[228],"10x":[229],"RNA-Seq":[230],"data":[231],"human":[234],"heart":[235],"species":[239],"is":[240],"shown,":[241],"as":[242],"are":[243],"advantages":[244],"detection":[247],"removal.":[249]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
