{"id":"https://openalex.org/W4410255551","doi":"https://doi.org/10.1093/bib/bbaf207","title":"An overview of computational methods in single-cell transcriptomic cell type annotation","display_name":"An overview of computational methods in single-cell transcriptomic cell type annotation","publication_year":2025,"publication_date":"2025-05-01","ids":{"openalex":"https://openalex.org/W4410255551","doi":"https://doi.org/10.1093/bib/bbaf207","pmid":"https://pubmed.ncbi.nlm.nih.gov/40347979"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf207","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf207","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/bbaf207","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070111623","display_name":"Tianhao Li","orcid":"https://orcid.org/0009-0007-2952-7788"},"institutions":[{"id":"https://openalex.org/I24201400","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I24201400"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tianhao Li","raw_affiliation_strings":["School of Computer Science , Chengdu University of Information Technology, No. 24 Block 1, Xuefu Road, 610225 Chengdu,"],"raw_orcid":"https://orcid.org/0009-0007-2952-7788","affiliations":[{"raw_affiliation_string":"School of Computer Science , Chengdu University of Information Technology, No. 24 Block 1, Xuefu Road, 610225 Chengdu,","institution_ids":["https://openalex.org/I24201400"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Zixuan Wang","orcid":"https://orcid.org/0009-0008-8503-6534"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zixuan Wang","raw_affiliation_strings":["College of Electronics and Information Engineering , Sichuan University, No. 24 South Section 1, 1st Ring Road, 610065 Chengdu,"],"raw_orcid":"https://orcid.org/0009-0008-8503-6534","affiliations":[{"raw_affiliation_string":"College of Electronics and Information Engineering , Sichuan University, No. 24 South Section 1, 1st Ring Road, 610065 Chengdu,","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yuhang Liu","orcid":"https://orcid.org/0000-0002-5949-344X"},"institutions":[{"id":"https://openalex.org/I49835588","display_name":"Macao Polytechnic University","ror":"https://ror.org/02sf5td35","country_code":"MO","type":"education","lineage":["https://openalex.org/I49835588"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Yuhang Liu","raw_affiliation_strings":["Faculty of Applied Sciences , Macao Polytechnic University, 999078 Macao,"],"raw_orcid":"https://orcid.org/0000-0002-5949-344X","affiliations":[{"raw_affiliation_string":"Faculty of Applied Sciences , Macao Polytechnic University, 999078 Macao,","institution_ids":["https://openalex.org/I49835588"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Sihan He","orcid":"https://orcid.org/0009-0004-4946-0478"},"institutions":[{"id":"https://openalex.org/I24201400","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I24201400"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Sihan He","raw_affiliation_strings":["School of Computer Science , Chengdu University of Information Technology, No. 24 Block 1, Xuefu Road, 610225 Chengdu,"],"raw_orcid":"https://orcid.org/0009-0004-4946-0478","affiliations":[{"raw_affiliation_string":"School of Computer Science , Chengdu University of Information Technology, No. 24 Block 1, Xuefu Road, 610225 Chengdu,","institution_ids":["https://openalex.org/I24201400"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017426085","display_name":"Quan Zou","orcid":"https://orcid.org/0000-0001-6406-1142"},"institutions":[{"id":"https://openalex.org/I150229711","display_name":"University of Electronic Science and Technology of China","ror":"https://ror.org/04qr3zq92","country_code":"CN","type":"education","lineage":["https://openalex.org/I150229711"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Quan Zou","raw_affiliation_strings":["Institute of Fundamental and Frontier Sciences , University of Electronic Science and Technology of China, Shahe Campus: No. 4, Section 2, North Jianshe Road, 611731 Chengdu,"],"raw_orcid":"https://orcid.org/0000-0001-6406-1142","affiliations":[{"raw_affiliation_string":"Institute of Fundamental and Frontier Sciences , University of Electronic Science and Technology of China, Shahe Campus: No. 4, Section 2, North Jianshe Road, 611731 Chengdu,","institution_ids":["https://openalex.org/I150229711"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100741917","display_name":"Yongqing Zhang","orcid":"https://orcid.org/0000-0003-3422-8305"},"institutions":[{"id":"https://openalex.org/I24201400","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I24201400"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yongqing Zhang","raw_affiliation_strings":["School of Computer Science , Chengdu University of Information Technology, No. 24 Block 1, Xuefu Road, 610225 Chengdu,"],"raw_orcid":"https://orcid.org/0000-0003-3422-8305","affiliations":[{"raw_affiliation_string":"School of Computer Science , Chengdu University of Information Technology, No. 24 Block 1, Xuefu Road, 610225 Chengdu,","institution_ids":["https://openalex.org/I24201400"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":9.0386,"has_fulltext":false,"cited_by_count":22,"citation_normalized_percentile":{"value":0.98570831,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"26","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10773","display_name":"Extracellular vesicles in disease","score":0.9851999878883362,"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":0.9476000070571899,"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/annotation","display_name":"Annotation","score":0.8767369985580444},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6345647573471069},{"id":"https://openalex.org/keywords/categorization","display_name":"Categorization","score":0.6094807982444763},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.5259994268417358},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.5143431425094604},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49029210209846497},{"id":"https://openalex.org/keywords/gene-annotation","display_name":"Gene Annotation","score":0.4438438415527344},{"id":"https://openalex.org/keywords/data-type","display_name":"Data type","score":0.4317149817943573},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.42897799611091614},{"id":"https://openalex.org/keywords/cell-type","display_name":"Cell type","score":0.4148893654346466},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.36702919006347656},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2961466908454895},{"id":"https://openalex.org/keywords/cell","display_name":"Cell","score":0.2636166214942932},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.25987279415130615},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2491624355316162},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.21199694275856018},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09342297911643982}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.8767369985580444},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6345647573471069},{"id":"https://openalex.org/C94124525","wikidata":"https://www.wikidata.org/wiki/Q912550","display_name":"Categorization","level":2,"score":0.6094807982444763},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.5259994268417358},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5143431425094604},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49029210209846497},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.4438438415527344},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.4317149817943573},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.42897799611091614},{"id":"https://openalex.org/C189014844","wikidata":"https://www.wikidata.org/wiki/Q189118","display_name":"Cell type","level":3,"score":0.4148893654346466},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36702919006347656},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2961466908454895},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.2636166214942932},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.25987279415130615},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2491624355316162},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.21199694275856018},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09342297911643982},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"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":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf207","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf207","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:40347979","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40347979","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:12065632","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12065632","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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/bbaf207","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf207","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":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.44999998807907104}],"awards":[{"id":"https://openalex.org/G5133105583","display_name":null,"funder_award_id":"62131004","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8617958116","display_name":null,"funder_award_id":"62272067","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"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":159,"referenced_works":["https://openalex.org/W92469554","https://openalex.org/W1573528873","https://openalex.org/W1574447377","https://openalex.org/W1985690171","https://openalex.org/W1998214135","https://openalex.org/W2040895929","https://openalex.org/W2050604187","https://openalex.org/W2056710301","https://openalex.org/W2068767807","https://openalex.org/W2069089843","https://openalex.org/W2102212449","https://openalex.org/W2103868202","https://openalex.org/W2107518278","https://openalex.org/W2117767331","https://openalex.org/W2118258530","https://openalex.org/W2136453261","https://openalex.org/W2145463997","https://openalex.org/W2166291251","https://openalex.org/W2467604901","https://openalex.org/W2560647685","https://openalex.org/W2598326928","https://openalex.org/W2601450892","https://openalex.org/W2735831688","https://openalex.org/W2739492614","https://openalex.org/W2740711073","https://openalex.org/W2747545374","https://openalex.org/W2766959028","https://openalex.org/W2788348358","https://openalex.org/W2791285756","https://openalex.org/W2794521141","https://openalex.org/W2796170779","https://openalex.org/W2894687190","https://openalex.org/W2895456557","https://openalex.org/W2897044695","https://openalex.org/W2899971546","https://openalex.org/W2901677030","https://openalex.org/W2907514116","https://openalex.org/W2912390237","https://openalex.org/W2913389840","https://openalex.org/W2926010705","https://openalex.org/W2931036699","https://openalex.org/W2942380588","https://openalex.org/W2949177718","https://openalex.org/W2951068020","https://openalex.org/W2951158909","https://openalex.org/W2951444558","https://openalex.org/W2951506174","https://openalex.org/W2951914955","https://openalex.org/W2954540134","https://openalex.org/W2959295202","https://openalex.org/W2964643116","https://openalex.org/W2966569571","https://openalex.org/W2969948459","https://openalex.org/W2971653850","https://openalex.org/W2973034691","https://openalex.org/W2984472267","https://openalex.org/W2989899726","https://openalex.org/W2993894543","https://openalex.org/W2995410603","https://openalex.org/W2997280954","https://openalex.org/W3004512212","https://openalex.org/W3013151148","https://openalex.org/W3013731060","https://openalex.org/W3015184839","https://openalex.org/W3016020856","https://openalex.org/W3024842005","https://openalex.org/W3024992482","https://openalex.org/W3027051073","https://openalex.org/W3029148360","https://openalex.org/W3034368386","https://openalex.org/W3041129226","https://openalex.org/W3092295864","https://openalex.org/W3093900604","https://openalex.org/W3096486351","https://openalex.org/W3096831136","https://openalex.org/W3124814274","https://openalex.org/W3129866267","https://openalex.org/W3130453114","https://openalex.org/W3133859624","https://openalex.org/W3135159941","https://openalex.org/W3138154797","https://openalex.org/W3149361930","https://openalex.org/W3149376923","https://openalex.org/W3157103618","https://openalex.org/W3163842339","https://openalex.org/W3164839005","https://openalex.org/W3176693948","https://openalex.org/W3178911446","https://openalex.org/W3185674647","https://openalex.org/W3193974171","https://openalex.org/W3195317458","https://openalex.org/W3196650609","https://openalex.org/W3198628780","https://openalex.org/W3205594709","https://openalex.org/W4205514149","https://openalex.org/W4205916264","https://openalex.org/W4210922136","https://openalex.org/W4212766485","https://openalex.org/W4221065117","https://openalex.org/W4225598893","https://openalex.org/W4225858647","https://openalex.org/W4243363028","https://openalex.org/W4293237882","https://openalex.org/W4295083893","https://openalex.org/W4296029724","https://openalex.org/W4297243391","https://openalex.org/W4301419755","https://openalex.org/W4306404361","https://openalex.org/W4307402399","https://openalex.org/W4307432965","https://openalex.org/W4309793872","https://openalex.org/W4311484399","https://openalex.org/W4313527252","https://openalex.org/W4318913348","https://openalex.org/W4323066405","https://openalex.org/W4361284397","https://openalex.org/W4366465247","https://openalex.org/W4376615697","https://openalex.org/W4377029825","https://openalex.org/W4382361760","https://openalex.org/W4385245566","https://openalex.org/W4385405421","https://openalex.org/W4385421874","https://openalex.org/W4385768116","https://openalex.org/W4387267581","https://openalex.org/W4387764879","https://openalex.org/W4388562978","https://openalex.org/W4391432211","https://openalex.org/W4391815397","https://openalex.org/W4391920551","https://openalex.org/W4392112958","https://openalex.org/W4392168151","https://openalex.org/W4396229708","https://openalex.org/W4396918877","https://openalex.org/W4399387478","https://openalex.org/W4399430319","https://openalex.org/W4400408070","https://openalex.org/W4401023515","https://openalex.org/W4401024607","https://openalex.org/W4401455022","https://openalex.org/W4403516090","https://openalex.org/W4404126723","https://openalex.org/W4404442837","https://openalex.org/W4404566651","https://openalex.org/W4405666966","https://openalex.org/W4406262333","https://openalex.org/W6603695430","https://openalex.org/W6720208624","https://openalex.org/W6735236233","https://openalex.org/W6737135848","https://openalex.org/W6739901393","https://openalex.org/W6765696844","https://openalex.org/W6776331362","https://openalex.org/W6779304910","https://openalex.org/W6783944145","https://openalex.org/W6797671258","https://openalex.org/W6861173722","https://openalex.org/W6866686367","https://openalex.org/W6876343941"],"related_works":["https://openalex.org/W2059565715","https://openalex.org/W2901823680","https://openalex.org/W2009940763","https://openalex.org/W4386637333","https://openalex.org/W2946410450","https://openalex.org/W4361192415","https://openalex.org/W2126804125","https://openalex.org/W2162782320","https://openalex.org/W2137318037","https://openalex.org/W1760213857"],"abstract_inverted_index":{"The":[0],"rapid":[1],"accumulation":[2],"of":[3,21,41,51,87,118],"single-cell":[4],"RNA":[5],"sequencing":[6],"data":[7,108],"has":[8],"provided":[9],"unprecedented":[10],"computational":[11],"resources":[12],"for":[13],"cell":[14,36,63,112,133],"type":[15],"annotation,":[16],"significantly":[17],"advancing":[18],"our":[19],"understanding":[20],"cellular":[22],"heterogeneity.":[23],"Leveraging":[24],"gene":[25,77],"expression":[26,78],"profiles":[27,79],"derived":[28],"from":[29,107],"transcriptomic":[30],"data,":[31],"researchers":[32],"can":[33],"accurately":[34],"infer":[35],"types,":[37],"sparking":[38],"the":[39,94,98,102,116],"development":[40],"numerous":[42],"innovative":[43],"annotation":[44,72,99],"methods.":[45,89],"These":[46],"methods":[47],"utilize":[48],"a":[49,82],"range":[50],"strategies,":[52],"including":[53],"marker":[54],"genes,":[55],"correlation-based":[56],"matching,":[57],"and":[58,80,85,126],"supervised":[59],"learning,":[60],"to":[61,122],"classify":[62],"types.":[64,113],"In":[65],"this":[66],"review,":[67],"we":[68,91],"systematically":[69],"examine":[70],"these":[71,88,124],"approaches":[73],"based":[74],"on":[75,93],"transcriptomics-specific":[76],"provide":[81],"comprehensive":[83],"comparison":[84],"categorization":[86],"Furthermore,":[90],"focus":[92],"main":[95],"challenges":[96],"in":[97,110,130],"process,":[100],"especially":[101],"long-tail":[103],"distribution":[104],"problem":[105],"arising":[106],"imbalance":[109],"rare":[111],"We":[114],"discuss":[115],"potential":[117],"deep":[119],"learning":[120],"techniques":[121],"address":[123],"issues":[125],"enhance":[127],"model":[128],"capability":[129],"recognizing":[131],"novel":[132],"types":[134],"within":[135],"an":[136],"open-world":[137],"framework.":[138]},"counts_by_year":[{"year":2026,"cited_by_count":14},{"year":2025,"cited_by_count":8}],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2025-10-10T00:00:00"}
