{"id":"https://openalex.org/W4407114451","doi":"https://doi.org/10.1093/bib/bbaf031","title":"Cell-type deconvolution for bulk RNA-seq data using single-cell reference: a comparative analysis and recommendation guideline","display_name":"Cell-type deconvolution for bulk RNA-seq data using single-cell reference: a comparative analysis and recommendation guideline","publication_year":2024,"publication_date":"2024-11-22","ids":{"openalex":"https://openalex.org/W4407114451","doi":"https://doi.org/10.1093/bib/bbaf031","pmid":"https://pubmed.ncbi.nlm.nih.gov/39899596"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf031","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf031","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/bbaf031","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102773402","display_name":"Xintian Xu","orcid":"https://orcid.org/0000-0003-2234-371X"},"institutions":[{"id":"https://openalex.org/I4210165024","display_name":"Institute of Infection and Immunity","ror":"https://ror.org/05wdecy17","country_code":"CA","type":"facility","lineage":["https://openalex.org/I176337269","https://openalex.org/I4210165024"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CA","CN"],"is_corresponding":true,"raw_author_name":"Xintian Xu","raw_affiliation_strings":["Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences , 320 Yueyang Road, Xuhui District, Shanghai 200031 ,","University of Chinese Academy of Sciences, 1 Yanqihu East Road, Huairou District , Beijing 100039 ,"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences , 320 Yueyang Road, Xuhui District, Shanghai 200031 ,","institution_ids":["https://openalex.org/I4210165024"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, 1 Yanqihu East Road, Huairou District , Beijing 100039 ,","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101747523","display_name":"Rui Li","orcid":"https://orcid.org/0000-0002-8166-9667"},"institutions":[{"id":"https://openalex.org/I4210165024","display_name":"Institute of Infection and Immunity","ror":"https://ror.org/05wdecy17","country_code":"CA","type":"facility","lineage":["https://openalex.org/I176337269","https://openalex.org/I4210165024"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CA","CN"],"is_corresponding":false,"raw_author_name":"Rui Li","raw_affiliation_strings":["Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences , 320 Yueyang Road, Xuhui District, Shanghai 200031 ,","University of Chinese Academy of Sciences , 1 Yanqihu East Road, Huairou District, Beijing 100039 ,"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences , 320 Yueyang Road, Xuhui District, Shanghai 200031 ,","institution_ids":["https://openalex.org/I4210165024"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences , 1 Yanqihu East Road, Huairou District, Beijing 100039 ,","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071111073","display_name":"Ot\u00edlia M\u00f3","orcid":"https://orcid.org/0000-0003-2596-5987"},"institutions":[{"id":"https://openalex.org/I4210165024","display_name":"Institute of Infection and Immunity","ror":"https://ror.org/05wdecy17","country_code":"CA","type":"facility","lineage":["https://openalex.org/I176337269","https://openalex.org/I4210165024"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CA","CN"],"is_corresponding":false,"raw_author_name":"Ouyang Mo","raw_affiliation_strings":["Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences , 320 Yueyang Road, Xuhui District, Shanghai 200031 ,","University of Chinese Academy of Sciences , 1 Yanqihu East Road, Huairou District, Beijing 100039 ,"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences , 320 Yueyang Road, Xuhui District, Shanghai 200031 ,","institution_ids":["https://openalex.org/I4210165024"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences , 1 Yanqihu East Road, Huairou District, Beijing 100039 ,","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115602431","display_name":"Kai Liu","orcid":"https://orcid.org/0000-0002-1544-5518"},"institutions":[{"id":"https://openalex.org/I4210093194","display_name":"Fudan University Shanghai Cancer Center","ror":"https://ror.org/00my25942","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210093194"]},{"id":"https://openalex.org/I4210165024","display_name":"Institute of Infection and Immunity","ror":"https://ror.org/05wdecy17","country_code":"CA","type":"facility","lineage":["https://openalex.org/I176337269","https://openalex.org/I4210165024"]}],"countries":["CA","CN"],"is_corresponding":false,"raw_author_name":"Kai Liu","raw_affiliation_strings":["Department of Colorectal Surgery, Fudan University Shanghai Cancer Center , 270 Dong'an Road, Xuhui District, Shanghai 200032 ,","Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences , 320 Yueyang Road, Xuhui District, Shanghai 200031 ,"],"affiliations":[{"raw_affiliation_string":"Department of Colorectal Surgery, Fudan University Shanghai Cancer Center , 270 Dong'an Road, Xuhui District, Shanghai 200032 ,","institution_ids":["https://openalex.org/I4210093194"]},{"raw_affiliation_string":"Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences , 320 Yueyang Road, Xuhui District, Shanghai 200031 ,","institution_ids":["https://openalex.org/I4210165024"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057039557","display_name":"Justin Li","orcid":null},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Justin Li","raw_affiliation_strings":["Department of Mathematics, University of Connecticut , 352 Mansfield Road, Storrs, CT 06269 ,"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, University of Connecticut , 352 Mansfield Road, Storrs, CT 06269 ,","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084581495","display_name":"Pei Hao","orcid":"https://orcid.org/0000-0002-1498-7059"},"institutions":[{"id":"https://openalex.org/I4210165024","display_name":"Institute of Infection and Immunity","ror":"https://ror.org/05wdecy17","country_code":"CA","type":"facility","lineage":["https://openalex.org/I176337269","https://openalex.org/I4210165024"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CA","CN"],"is_corresponding":false,"raw_author_name":"Pei Hao","raw_affiliation_strings":["Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences , 320 Yueyang Road, Xuhui District, Shanghai 200031 ,","University of Chinese Academy of Sciences , 1 Yanqihu East Road, Huairou District, Beijing 100039 ,"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences , 320 Yueyang Road, Xuhui District, Shanghai 200031 ,","institution_ids":["https://openalex.org/I4210165024"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences , 1 Yanqihu East Road, Huairou District, Beijing 100039 ,","institution_ids":["https://openalex.org/I4210165038"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5102773402"],"corresponding_institution_ids":["https://openalex.org/I4210165024","https://openalex.org/I4210165038"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.3856,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.81844538,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"26","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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.998199999332428,"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/T10231","display_name":"Pancreatic and Hepatic Oncology Research","score":0.9588000178337097,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/deconvolution","display_name":"Deconvolution","score":0.9007643461227417},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7201566696166992},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.6774277687072754},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5621635913848877},{"id":"https://openalex.org/keywords/data-type","display_name":"Data type","score":0.4774375855922699},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3768593966960907},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32852715253829956},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15350207686424255},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07433271408081055},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.06715461611747742}],"concepts":[{"id":"https://openalex.org/C174576160","wikidata":"https://www.wikidata.org/wiki/Q1183700","display_name":"Deconvolution","level":2,"score":0.9007643461227417},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7201566696166992},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.6774277687072754},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5621635913848877},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.4774375855922699},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3768593966960907},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32852715253829956},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15350207686424255},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07433271408081055},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06715461611747742},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"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":"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":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D005434","descriptor_name":"Flow Cytometry","qualifier_ui":"Q000592","qualifier_name":"standards","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":"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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":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":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":false},{"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":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"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":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf031","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf031","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39899596","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39899596","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:11789683","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11789683","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11789683/pdf/bbaf031.pdf","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf031","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf031","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G391238517","display_name":null,"funder_award_id":", and","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4020255992","display_name":null,"funder_award_id":"Project","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4113151966","display_name":null,"funder_award_id":"32270695","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5939423041","display_name":null,"funder_award_id":"Technology","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8955107213","display_name":null,"funder_award_id":"Major","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320329860","display_name":"National Science and Technology Major Project","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W2049491375","https://openalex.org/W2104950932","https://openalex.org/W2107940314","https://openalex.org/W2128599926","https://openalex.org/W2140683554","https://openalex.org/W2142300779","https://openalex.org/W2176487248","https://openalex.org/W2406250479","https://openalex.org/W2464319238","https://openalex.org/W2509106468","https://openalex.org/W2512899508","https://openalex.org/W2523620612","https://openalex.org/W2582743722","https://openalex.org/W2737082469","https://openalex.org/W2788357641","https://openalex.org/W2892164007","https://openalex.org/W2907564726","https://openalex.org/W2911922390","https://openalex.org/W2921330004","https://openalex.org/W2952240309","https://openalex.org/W2953757801","https://openalex.org/W2953866345","https://openalex.org/W2972438906","https://openalex.org/W2988153676","https://openalex.org/W2991604058","https://openalex.org/W2999977864","https://openalex.org/W3000010184","https://openalex.org/W3015184839","https://openalex.org/W3016360824","https://openalex.org/W3019556496","https://openalex.org/W3027382471","https://openalex.org/W3096486123","https://openalex.org/W3110779225","https://openalex.org/W3119889556","https://openalex.org/W3124296497","https://openalex.org/W3164692211","https://openalex.org/W3166868467","https://openalex.org/W3167821357","https://openalex.org/W4224470052","https://openalex.org/W4254687493","https://openalex.org/W4386801555","https://openalex.org/W4387814741"],"related_works":["https://openalex.org/W4250106855","https://openalex.org/W2037261263","https://openalex.org/W3149087629","https://openalex.org/W4231036715","https://openalex.org/W2032074591","https://openalex.org/W1986156575","https://openalex.org/W3193619106","https://openalex.org/W2751689993","https://openalex.org/W1966302070","https://openalex.org/W2064421023"],"abstract_inverted_index":{"The":[0],"accurate":[1],"estimation":[2],"of":[3,19,42,64,108,128,136],"cell":[4,84,117,121],"type":[5,118,122],"proportions":[6,85],"in":[7,48,142],"tissues":[8],"is":[9,51],"crucial":[10],"for":[11,139],"various":[12],"downstream":[13],"analyses.":[14],"With":[15],"the":[16,60,106,124],"increasing":[17],"availability":[18],"single-cell":[20,28,70,99],"sequencing":[21,30,72,101],"data,":[22],"numerous":[23],"deconvolution":[24,45,66,129],"methods":[25,67],"that":[26,68],"use":[27,69],"RNA":[29,71,100],"data":[31,73,82,95],"as":[32,74,90,92],"a":[33,39,75,134],"reference":[34,111],"have":[35],"been":[36],"developed.":[37],"However,":[38],"unified":[40],"understanding":[41],"how":[43],"these":[44],"approaches":[46],"perform":[47],"practical":[49],"applications":[50],"still":[52],"lacking.":[53],"To":[54],"address":[55],"this,":[56],"we":[57],"systematically":[58],"assessed":[59],"accuracy":[61,125],"and":[62,120,126],"robustness":[63,127],"nine":[65],"reference,":[76],"evaluating":[77],"them":[78],"on":[79],"real":[80],"bulk":[81,94],"with":[83],"verified":[86],"through":[87],"flow":[88],"cytometry,":[89],"well":[91],"simulated":[93],"generated":[96],"from":[97],"five":[98],"datasets.":[102],"Our":[103],"study":[104],"highlights":[105],"importance":[107],"several":[109],"factors-including":[110],"dataset":[112,115],"construction":[113],"strategies,":[114],"size,":[116],"subdivision,":[119],"inconsistency-on":[123],"results.":[130],"We":[131],"also":[132],"propose":[133],"set":[135],"recommended":[137],"guidelines":[138],"software":[140],"users":[141],"diverse":[143],"scenarios.":[144]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4}],"updated_date":"2026-04-06T07:47:59.780226","created_date":"2025-10-10T00:00:00"}