{"id":"https://openalex.org/W4416738253","doi":"https://doi.org/10.1093/bib/bbaf622","title":"Single-cell omics arena: evaluation of large language models for automatic cell-type annotations on single-cell omics data via RNA-seq bridging","display_name":"Single-cell omics arena: evaluation of large language models for automatic cell-type annotations on single-cell omics data via RNA-seq bridging","publication_year":2025,"publication_date":"2025-11-01","ids":{"openalex":"https://openalex.org/W4416738253","doi":"https://doi.org/10.1093/bib/bbaf622","pmid":"https://pubmed.ncbi.nlm.nih.gov/41283813"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf622","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf622","pdf_url":"https://academic.oup.com/bib/article-pdf/26/6/bbaf622/65490434/bbaf622.pdf","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://academic.oup.com/bib/article-pdf/26/6/bbaf622/65490434/bbaf622.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Junhao Liu","orcid":"https://orcid.org/0009-0007-3694-7799"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]},{"id":"https://openalex.org/I4210140791","display_name":"Irvine University","ror":"https://ror.org/04ysmca02","country_code":"US","type":"education","lineage":["https://openalex.org/I4210140791"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Junhao Liu","raw_affiliation_strings":["Department of Computer Science , University of California, Irvine, 6210 Donald Bren Hall, Irvine, CA 92697,","Department of Computer Science, University of California, Irvine, 6210 Donald Bren Hall, Irvine, CA 92697, United States"],"raw_orcid":"https://orcid.org/0009-0007-3694-7799","affiliations":[{"raw_affiliation_string":"Department of Computer Science , University of California, Irvine, 6210 Donald Bren Hall, Irvine, CA 92697,","institution_ids":["https://openalex.org/I204250578","https://openalex.org/I4210140791"]},{"raw_affiliation_string":"Department of Computer Science, University of California, Irvine, 6210 Donald Bren Hall, Irvine, CA 92697, United States","institution_ids":["https://openalex.org/I204250578","https://openalex.org/I4210140791"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056041012","display_name":"Siwei Xu","orcid":"https://orcid.org/0000-0002-2828-3706"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]},{"id":"https://openalex.org/I4210140791","display_name":"Irvine University","ror":"https://ror.org/04ysmca02","country_code":"US","type":"education","lineage":["https://openalex.org/I4210140791"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Siwei Xu","raw_affiliation_strings":["Department of Computer Science , University of California, Irvine, 6210 Donald Bren Hall, Irvine, CA 92697,","Department of Computer Science, University of California, Irvine, 6210 Donald Bren Hall, Irvine, CA 92697, United States"],"raw_orcid":"https://orcid.org/0000-0002-2828-3706","affiliations":[{"raw_affiliation_string":"Department of Computer Science , University of California, Irvine, 6210 Donald Bren Hall, Irvine, CA 92697,","institution_ids":["https://openalex.org/I204250578","https://openalex.org/I4210140791"]},{"raw_affiliation_string":"Department of Computer Science, University of California, Irvine, 6210 Donald Bren Hall, Irvine, CA 92697, United States","institution_ids":["https://openalex.org/I204250578","https://openalex.org/I4210140791"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055160771","display_name":"Yongxian Wu","orcid":"https://orcid.org/0000-0003-1497-2444"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]},{"id":"https://openalex.org/I4210140791","display_name":"Irvine University","ror":"https://ror.org/04ysmca02","country_code":"US","type":"education","lineage":["https://openalex.org/I4210140791"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yongxian Wu","raw_affiliation_strings":["Department of Chemical and Biomolecular Engineering , University of California, Irvine, 5200 Engineering Hall, Irvine, CA 92697,","Department of Chemical and Biomolecular Engineering, University of California, Irvine, 5200 Engineering Hall, Irvine, CA 92697, United States"],"raw_orcid":"https://orcid.org/0000-0003-1497-2444","affiliations":[{"raw_affiliation_string":"Department of Chemical and Biomolecular Engineering , University of California, Irvine, 5200 Engineering Hall, Irvine, CA 92697,","institution_ids":["https://openalex.org/I204250578","https://openalex.org/I4210140791"]},{"raw_affiliation_string":"Department of Chemical and Biomolecular Engineering, University of California, Irvine, 5200 Engineering Hall, Irvine, CA 92697, United States","institution_ids":["https://openalex.org/I204250578","https://openalex.org/I4210140791"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100345410","display_name":"Jing Zhang","orcid":"https://orcid.org/0000-0002-5970-0509"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]},{"id":"https://openalex.org/I4210140791","display_name":"Irvine University","ror":"https://ror.org/04ysmca02","country_code":"US","type":"education","lineage":["https://openalex.org/I4210140791"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jing Zhang","raw_affiliation_strings":["Department of Computer Science , University of California, Irvine, 6210 Donald Bren Hall, Irvine, CA 92697,","Department of Computer Science, University of California, Irvine, 6210 Donald Bren Hall, Irvine, CA 92697, United States"],"raw_orcid":"https://orcid.org/0000-0002-5970-0509","affiliations":[{"raw_affiliation_string":"Department of Computer Science , University of California, Irvine, 6210 Donald Bren Hall, Irvine, CA 92697,","institution_ids":["https://openalex.org/I204250578","https://openalex.org/I4210140791"]},{"raw_affiliation_string":"Department of Computer Science, University of California, Irvine, 6210 Donald Bren Hall, Irvine, CA 92697, United States","institution_ids":["https://openalex.org/I204250578","https://openalex.org/I4210140791"]}]}],"institutions":[],"countries_distinct_count":1,"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":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.28502544,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"6","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":0.9842000007629395,"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":0.9842000007629395,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.0020000000949949026,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11307","display_name":"Domain Adaptation and Few-Shot Learning","score":0.0017999999690800905,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.8788999915122986},{"id":"https://openalex.org/keywords/bridging","display_name":"Bridging (networking)","score":0.5831999778747559},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.5304999947547913},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4246000051498413},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.40139999985694885},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.39910000562667847},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.36579999327659607},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.3628000020980835},{"id":"https://openalex.org/keywords/biological-database","display_name":"Biological database","score":0.35929998755455017}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.8788999915122986},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7760000228881836},{"id":"https://openalex.org/C174348530","wikidata":"https://www.wikidata.org/wiki/Q188635","display_name":"Bridging (networking)","level":2,"score":0.5831999778747559},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.5304999947547913},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4336000084877014},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4246000051498413},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.40139999985694885},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.39910000562667847},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.36980000138282776},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.36579999327659607},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.3628000020980835},{"id":"https://openalex.org/C20901353","wikidata":"https://www.wikidata.org/wiki/Q4117139","display_name":"Biological database","level":2,"score":0.35929998755455017},{"id":"https://openalex.org/C2779903281","wikidata":"https://www.wikidata.org/wiki/Q6888026","display_name":"Modalities","level":2,"score":0.33480000495910645},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.3230000138282776},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.32179999351501465},{"id":"https://openalex.org/C62230096","wikidata":"https://www.wikidata.org/wiki/Q275969","display_name":"Crowdsourcing","level":2,"score":0.31859999895095825},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3118000030517578},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.31060001254081726},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.30469998717308044},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.304500013589859},{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.29820001125335693},{"id":"https://openalex.org/C195344581","wikidata":"https://www.wikidata.org/wiki/Q2555318","display_name":"Automated reasoning","level":2,"score":0.2946000099182129},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.2930999994277954},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.28859999775886536},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.28700000047683716},{"id":"https://openalex.org/C170858558","wikidata":"https://www.wikidata.org/wiki/Q1394144","display_name":"Automatic summarization","level":2,"score":0.2827000021934509},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.271699994802475},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.26809999346733093},{"id":"https://openalex.org/C115901376","wikidata":"https://www.wikidata.org/wiki/Q184199","display_name":"Automation","level":2,"score":0.26660001277923584}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","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":"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":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"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":"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":"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":"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":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf622","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf622","pdf_url":"https://academic.oup.com/bib/article-pdf/26/6/bbaf622/65490434/bbaf622.pdf","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:41283813","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41283813","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:europepmc.org:11448392","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12641614","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf622","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf622","pdf_url":"https://academic.oup.com/bib/article-pdf/26/6/bbaf622/65490434/bbaf622.pdf","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/G4902214262","display_name":null,"funder_award_id":"R01HG012572","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8387611733","display_name":null,"funder_award_id":"R01DA063316","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4416738253.pdf","grobid_xml":"https://content.openalex.org/works/W4416738253.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W2090037139","https://openalex.org/W2101105183","https://openalex.org/W2131660156","https://openalex.org/W2142112143","https://openalex.org/W2788348358","https://openalex.org/W2800392236","https://openalex.org/W2907514116","https://openalex.org/W2912390237","https://openalex.org/W2922020904","https://openalex.org/W2963748441","https://openalex.org/W3013151148","https://openalex.org/W3013823153","https://openalex.org/W3022968840","https://openalex.org/W3027774968","https://openalex.org/W3144696998","https://openalex.org/W4200575396","https://openalex.org/W4221065117","https://openalex.org/W4280598116","https://openalex.org/W4280633014","https://openalex.org/W4297977428","https://openalex.org/W4307432965","https://openalex.org/W4322768301","https://openalex.org/W4378838672","https://openalex.org/W4379521442","https://openalex.org/W4380357680","https://openalex.org/W4392168151","https://openalex.org/W4393153069","https://openalex.org/W4398250269","https://openalex.org/W4401042394","https://openalex.org/W4403577864"],"related_works":[],"abstract_inverted_index":{"The":[0],"single-cell":[1,114],"sequencing":[2,116,208],"revolution":[3],"enables":[4,198],"simultaneous":[5],"molecular":[6],"profiling":[7],"of":[8,13,23,83,161,168,202,228],"various":[9],"modalities":[10],"across":[11,123],"thousands":[12],"individual":[14,32],"cells,":[15],"allowing":[16],"scientists":[17],"to":[18,34,64,157,173,179,187,206],"investigate":[19],"the":[20,28,81,88,159,166,199,226],"diverse":[21],"functions":[22],"complex":[24],"tissues.":[25],"Among":[26],"all":[27],"analysis":[29],"steps,":[30],"assigning":[31],"cells":[33],"specific":[35],"types":[36],"is":[37,46],"fundamental":[38],"for":[39,133,231],"understanding":[40],"cellular":[41],"heterogeneity.":[42],"However,":[43],"this":[44,149],"process":[45],"labor-intensive":[47],"and":[48,75,119,164,224],"requires":[49],"extensive":[50],"expert":[51],"knowledge.":[52],"Recent":[53],"advances":[54],"in":[55,86],"large":[56],"language":[57],"models":[58],"(LLMs)":[59],"have":[60],"demonstrated":[61],"their":[62],"ability":[63],"automatically":[65],"extract":[66],"biological":[67,170],"knowledge,":[68],"such":[69,143,190],"as":[70,144,191],"marker":[71],"genes,":[72],"promoting":[73],"efficient,":[74],"automated":[76,96,134,218],"cell-type":[77,89,97,125,135,162,204,219],"annotations.":[78],"To":[79],"evaluate":[80],"capability":[82],"modern":[84],"LLMs":[85,122],"automating":[87],"identification":[90],"process,":[91],"we":[92,107,151,177],"first":[93],"introduce":[94],"an":[95],"annotation":[98,136,163,205,220],"method":[99],"with":[100],"comprehensive":[101],"benchmark:":[102],"Single-cell":[103],"Omics":[104],"Arena).":[105],"Specifically,":[106],"began":[108],"by":[109],"compiling":[110],"11":[111],"publicly":[112],"available":[113],"RNA":[115],"(scRNA-seq)":[117],"datasets":[118],"evaluating":[120],"eight":[121],"1226":[124],"annotation-related":[126],"tasks.":[127],"This":[128],"effort":[129],"established":[130],"a":[131,181],"foundation":[132],"from":[137,221],"scRNA-seq":[138,222],"data":[139,223],"using":[140],"interpretable":[141,195],"features":[142,189],"gene":[145],"names.":[146],"Building":[147],"upon":[148],"benchmark,":[150],"introduced":[152],"domain-specific":[153],"chain-of-thought":[154],"prompting":[155],"techniques":[156],"enhance":[158],"accuracy":[160],"facilitate":[165],"extraction":[167],"relevant":[169],"insights.":[171],"Finally,":[172],"accommodate":[174],"non-interpretable":[175,233],"features,":[176],"proposed":[178],"leverage":[180],"pretrained":[182],"VAE-based":[183],"cross-modality":[184,229],"translation":[185,230],"module":[186],"convert":[188],"epigenetic":[192],"marks":[193],"into":[194,217],"representations,":[196],"which":[197],"seamless":[200],"extension":[201],"LLM-based":[203],"non-RNA-based":[207],"technologies.":[209],"In":[210],"summary,":[211],"our":[212],"benchmark":[213],"provides":[214],"key":[215],"insights":[216],"demonstrates":[225],"potential":[227],"handling":[232],"features.":[234]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-11-25T00:00:00"}