{"id":"https://openalex.org/W4414379651","doi":"https://doi.org/10.1093/bioinformatics/btaf521","title":"Conformal inference for reliable single cell RNA-seq annotation","display_name":"Conformal inference for reliable single cell RNA-seq annotation","publication_year":2025,"publication_date":"2025-09-18","ids":{"openalex":"https://openalex.org/W4414379651","doi":"https://doi.org/10.1093/bioinformatics/btaf521","pmid":"https://pubmed.ncbi.nlm.nih.gov/40973204"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf521","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf521","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf521/64316557/btaf521.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf521/64316557/btaf521.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050587161","display_name":"Marcos L\u00f3pez-De-Castro","orcid":"https://orcid.org/0000-0001-8179-3839"},"institutions":[{"id":"https://openalex.org/I4210091345","display_name":"Ayuntamiento de San Sebasti\u00e1n","ror":"https://ror.org/00g7vw110","country_code":"ES","type":"government","lineage":["https://openalex.org/I4210091345"]},{"id":"https://openalex.org/I4210113430","display_name":"Tecnalia","ror":"https://ror.org/02fv8hj62","country_code":"ES","type":"other","lineage":["https://openalex.org/I4210113430"]},{"id":"https://openalex.org/I4210135003","display_name":"Clinica Universidad de Navarra","ror":"https://ror.org/03phm3r45","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210135003"]},{"id":"https://openalex.org/I88155538","display_name":"Universidad de Navarra","ror":"https://ror.org/02rxc7m23","country_code":"ES","type":"education","lineage":["https://openalex.org/I88155538"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Marcos L\u00f3pez-De-Castro","raw_affiliation_strings":["Cancer Center CCUN, Cl\u00ednica Universidad de Navarra , Pamplona, Navarra, 31080,","Institute of Data Science and Artificial Intelligence (DATAI), University of Navarra , Pamplona, Navarra 31009,","TECNUN School of Engineering, University of Navarra , Donostia-San Sebasti\u00e1n, Basque Country, 20018,","Cl\u00ednica Universidad de Navarra Cancer Center CCUN, , Pamplona, Navarra","Institute of Data Science and Artificial Intelligence (DATAI), University of Navarra, Pamplona, Navarra 31009, Spain"],"raw_orcid":"https://orcid.org/0000-0001-8179-3839","affiliations":[{"raw_affiliation_string":"Cancer Center CCUN, Cl\u00ednica Universidad de Navarra , Pamplona, Navarra, 31080,","institution_ids":["https://openalex.org/I4210135003"]},{"raw_affiliation_string":"Institute of Data Science and Artificial Intelligence (DATAI), University of Navarra , Pamplona, Navarra 31009,","institution_ids":["https://openalex.org/I88155538"]},{"raw_affiliation_string":"TECNUN School of Engineering, University of Navarra , Donostia-San Sebasti\u00e1n, Basque Country, 20018,","institution_ids":["https://openalex.org/I4210113430","https://openalex.org/I4210091345"]},{"raw_affiliation_string":"Cl\u00ednica Universidad de Navarra Cancer Center CCUN, , Pamplona, Navarra","institution_ids":["https://openalex.org/I4210135003"]},{"raw_affiliation_string":"Institute of Data Science and Artificial Intelligence (DATAI), University of Navarra, Pamplona, Navarra 31009, Spain","institution_ids":["https://openalex.org/I88155538"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045186293","display_name":"Alberto Garc\u00eda\u2010Galindo","orcid":"https://orcid.org/0000-0001-7692-9113"},"institutions":[{"id":"https://openalex.org/I4210091345","display_name":"Ayuntamiento de San Sebasti\u00e1n","ror":"https://ror.org/00g7vw110","country_code":"ES","type":"government","lineage":["https://openalex.org/I4210091345"]},{"id":"https://openalex.org/I4210113430","display_name":"Tecnalia","ror":"https://ror.org/02fv8hj62","country_code":"ES","type":"other","lineage":["https://openalex.org/I4210113430"]},{"id":"https://openalex.org/I4210135003","display_name":"Clinica Universidad de Navarra","ror":"https://ror.org/03phm3r45","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210135003"]},{"id":"https://openalex.org/I88155538","display_name":"Universidad de Navarra","ror":"https://ror.org/02rxc7m23","country_code":"ES","type":"education","lineage":["https://openalex.org/I88155538"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Alberto Garc\u00eda-Galindo","raw_affiliation_strings":["Cancer Center CCUN, Cl\u00ednica Universidad de Navarra , Pamplona, Navarra, 31080,","Institute of Data Science and Artificial Intelligence (DATAI), University of Navarra , Pamplona, Navarra 31009,","TECNUN School of Engineering, University of Navarra , Donostia-San Sebasti\u00e1n, Basque Country, 20018,","Cl\u00ednica Universidad de Navarra Cancer Center CCUN, , Pamplona, Navarra","Institute of Data Science and Artificial Intelligence (DATAI), University of Navarra, Pamplona, Navarra 31009, Spain"],"raw_orcid":"https://orcid.org/0000-0001-7692-9113","affiliations":[{"raw_affiliation_string":"Cancer Center CCUN, Cl\u00ednica Universidad de Navarra , Pamplona, Navarra, 31080,","institution_ids":["https://openalex.org/I4210135003"]},{"raw_affiliation_string":"Institute of Data Science and Artificial Intelligence (DATAI), University of Navarra , Pamplona, Navarra 31009,","institution_ids":["https://openalex.org/I88155538"]},{"raw_affiliation_string":"TECNUN School of Engineering, University of Navarra , Donostia-San Sebasti\u00e1n, Basque Country, 20018,","institution_ids":["https://openalex.org/I4210113430","https://openalex.org/I4210091345"]},{"raw_affiliation_string":"Cl\u00ednica Universidad de Navarra Cancer Center CCUN, , Pamplona, Navarra","institution_ids":["https://openalex.org/I4210135003"]},{"raw_affiliation_string":"Institute of Data Science and Artificial Intelligence (DATAI), University of Navarra, Pamplona, Navarra 31009, Spain","institution_ids":["https://openalex.org/I88155538"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039064555","display_name":"Jos\u00e9 Gonz\u00e1lez-Gomariz","orcid":"https://orcid.org/0000-0002-8549-0453"},"institutions":[{"id":"https://openalex.org/I4210091345","display_name":"Ayuntamiento de San Sebasti\u00e1n","ror":"https://ror.org/00g7vw110","country_code":"ES","type":"government","lineage":["https://openalex.org/I4210091345"]},{"id":"https://openalex.org/I4210113430","display_name":"Tecnalia","ror":"https://ror.org/02fv8hj62","country_code":"ES","type":"other","lineage":["https://openalex.org/I4210113430"]},{"id":"https://openalex.org/I4210135003","display_name":"Clinica Universidad de Navarra","ror":"https://ror.org/03phm3r45","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210135003"]},{"id":"https://openalex.org/I88155538","display_name":"Universidad de Navarra","ror":"https://ror.org/02rxc7m23","country_code":"ES","type":"education","lineage":["https://openalex.org/I88155538"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Jos\u00e9 Gonz\u00e1lez-Gomariz","raw_affiliation_strings":["Cancer Center CCUN, Cl\u00ednica Universidad de Navarra , Pamplona, Navarra, 31080,","Institute of Data Science and Artificial Intelligence (DATAI), University of Navarra , Pamplona, Navarra 31009,","TECNUN School of Engineering, University of Navarra , Donostia-San Sebasti\u00e1n, Basque Country, 20018,","Institute of Data Science and Artificial Intelligence (DATAI), University of Navarra, Pamplona, Navarra 31009, Spain","Cl\u00ednica Universidad de Navarra Cancer Center CCUN, , Pamplona, Navarra"],"raw_orcid":"https://orcid.org/0000-0002-8549-0453","affiliations":[{"raw_affiliation_string":"Cancer Center CCUN, Cl\u00ednica Universidad de Navarra , Pamplona, Navarra, 31080,","institution_ids":["https://openalex.org/I4210135003"]},{"raw_affiliation_string":"Institute of Data Science and Artificial Intelligence (DATAI), University of Navarra , Pamplona, Navarra 31009,","institution_ids":["https://openalex.org/I88155538"]},{"raw_affiliation_string":"TECNUN School of Engineering, University of Navarra , Donostia-San Sebasti\u00e1n, Basque Country, 20018,","institution_ids":["https://openalex.org/I4210113430","https://openalex.org/I4210091345"]},{"raw_affiliation_string":"Institute of Data Science and Artificial Intelligence (DATAI), University of Navarra, Pamplona, Navarra 31009, Spain","institution_ids":["https://openalex.org/I88155538"]},{"raw_affiliation_string":"Cl\u00ednica Universidad de Navarra Cancer Center CCUN, , Pamplona, Navarra","institution_ids":["https://openalex.org/I4210135003"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041627450","display_name":"Rub\u00e9n Arma\u00f1anzas","orcid":"https://orcid.org/0000-0003-4049-0000"},"institutions":[{"id":"https://openalex.org/I4210091345","display_name":"Ayuntamiento de San Sebasti\u00e1n","ror":"https://ror.org/00g7vw110","country_code":"ES","type":"government","lineage":["https://openalex.org/I4210091345"]},{"id":"https://openalex.org/I4210113430","display_name":"Tecnalia","ror":"https://ror.org/02fv8hj62","country_code":"ES","type":"other","lineage":["https://openalex.org/I4210113430"]},{"id":"https://openalex.org/I4210135003","display_name":"Clinica Universidad de Navarra","ror":"https://ror.org/03phm3r45","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210135003"]},{"id":"https://openalex.org/I88155538","display_name":"Universidad de Navarra","ror":"https://ror.org/02rxc7m23","country_code":"ES","type":"education","lineage":["https://openalex.org/I88155538"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Rub\u00e9n Arma\u00f1anzas","raw_affiliation_strings":["Cancer Center CCUN, Cl\u00ednica Universidad de Navarra , Pamplona, Navarra, 31080,","Institute of Data Science and Artificial Intelligence (DATAI), University of Navarra , Pamplona, Navarra 31009,","TECNUN School of Engineering, University of Navarra , Donostia-San Sebasti\u00e1n, Basque Country, 20018,","Institute of Data Science and Artificial Intelligence (DATAI), University of Navarra, Pamplona, Navarra 31009, Spain","Cl\u00ednica Universidad de Navarra Cancer Center CCUN, , Pamplona, Navarra"],"raw_orcid":"https://orcid.org/0000-0003-4049-0000","affiliations":[{"raw_affiliation_string":"Cancer Center CCUN, Cl\u00ednica Universidad de Navarra , Pamplona, Navarra, 31080,","institution_ids":["https://openalex.org/I4210135003"]},{"raw_affiliation_string":"Institute of Data Science and Artificial Intelligence (DATAI), University of Navarra , Pamplona, Navarra 31009,","institution_ids":["https://openalex.org/I88155538"]},{"raw_affiliation_string":"TECNUN School of Engineering, University of Navarra , Donostia-San Sebasti\u00e1n, Basque Country, 20018,","institution_ids":["https://openalex.org/I4210113430","https://openalex.org/I4210091345"]},{"raw_affiliation_string":"Institute of Data Science and Artificial Intelligence (DATAI), University of Navarra, Pamplona, Navarra 31009, Spain","institution_ids":["https://openalex.org/I88155538"]},{"raw_affiliation_string":"Cl\u00ednica Universidad de Navarra Cancer Center CCUN, , Pamplona, Navarra","institution_ids":["https://openalex.org/I4210135003"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.19528601,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"10","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":0.9984999895095825,"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":0.9984999895095825,"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":0.0005000000237487257,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.00019999999494757503,"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":0.7224000096321106},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6930999755859375},{"id":"https://openalex.org/keywords/conformal-map","display_name":"Conformal map","score":0.3889000117778778},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.37929999828338623},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.37599998712539673}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.770799994468689},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7224000096321106},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6930999755859375},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5180000066757202},{"id":"https://openalex.org/C98214594","wikidata":"https://www.wikidata.org/wiki/Q850275","display_name":"Conformal map","level":2,"score":0.3889000117778778},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.37929999828338623},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.37599998712539673},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3675999939441681},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3240000009536743},{"id":"https://openalex.org/C3019831412","wikidata":"https://www.wikidata.org/wiki/Q5778278","display_name":"Fully automatic","level":2,"score":0.30820000171661377},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.2831000089645386},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.26190000772476196},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2517000138759613}],"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":"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":"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":"D000465","descriptor_name":"Algorithms","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":"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":"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":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":"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":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","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":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaf521","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf521","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf521/64316557/btaf521.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40973204","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40973204","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:11314756","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12506889","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12506889","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12506889/","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf521","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf521","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf521/64316557/btaf521.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414379651.pdf"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1982433617","https://openalex.org/W2016026777","https://openalex.org/W2069089843","https://openalex.org/W2115627867","https://openalex.org/W2514278201","https://openalex.org/W2794480084","https://openalex.org/W2907514116","https://openalex.org/W2907783748","https://openalex.org/W2912272542","https://openalex.org/W2936414047","https://openalex.org/W2971398276","https://openalex.org/W2971653850","https://openalex.org/W2984472267","https://openalex.org/W2997207862","https://openalex.org/W3156397721","https://openalex.org/W3165190053","https://openalex.org/W4200452132","https://openalex.org/W4214857593","https://openalex.org/W4220837089","https://openalex.org/W4220856587","https://openalex.org/W4280596398","https://openalex.org/W4312294904","https://openalex.org/W4361012985","https://openalex.org/W4362521490","https://openalex.org/W4391746981","https://openalex.org/W4392529462","https://openalex.org/W4410841060"],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"Despite":[1],"the":[2,20,53,68,76,80,104,114,124,128,180,188],"inherent":[3],"complexity":[4],"associated":[5],"to":[6,57,88],"automatic":[7,202],"cell":[8,101,115,166],"type":[9],"assignments,":[10],"most":[11],"supervised":[12],"learning":[13],"models":[14],"overlook":[15],"rigorous":[16,173],"uncertainty":[17,111],"quantification":[18,112],"on":[19,35,52,67],"annotations.":[21,61],"Although":[22],"some":[23],"existing":[24],"pipelines":[25],"incorporate":[26],"rejection":[27],"options":[28],"under":[29],"predefined":[30],"circumstances,":[31],"they":[32],"usually":[33],"rely":[34],"arbitrary":[36],"assumptions":[37],"and":[38,127,148,209],"do":[39],"not":[40],"provide":[41,58],"statistical":[42,65],"guarantees.":[43],"In":[44],"this":[45],"work,":[46],"we":[47,140,185],"propose":[48],"a":[49],"methodology":[50],"based":[51],"conformal":[54,86,191],"prediction":[55,63,119,170,192],"framework":[56],"reliable":[59,110],"single-cell":[60,94],"Conformal":[62],"provides":[64],"guarantees":[66],"outcome":[69],"predictions":[70],"without":[71],"making":[72],"any":[73],"assumption":[74],"about":[75],"underlying":[77],"distribution":[78],"of":[79,113,190],"data.":[81],"Our":[82],"methodological":[83],"proposal":[84],"leverages":[85],"inference":[87],"address":[89],"two":[90],"critical":[91],"challenges":[92],"in":[93,103,131],"RNA":[95],"sequencing":[96],"annotations:":[97],"(i)":[98],"detect":[99],"out-of-distribution":[100],"types":[102],"query":[105],"data;":[106],"and,":[107],"(ii)":[108],"perform":[109],"annotations":[116],"through":[117],"well-calibrated":[118,169],"sets.":[120,171],"RESULTS:":[121],"We":[122],"evaluated":[123],"anomaly":[125,160],"detector":[126,161],"uncertainty-aware":[129],"annotator":[130,204],"10":[132],"batched":[133],"experiments":[134],"derived":[135],"from":[136],"various":[137],"tissues.":[138],"Specifically,":[139],"studied":[141],"three":[142,151],"different":[143,152],"annotation":[144,174],"taxonomies":[145],"(standard,":[146],"classwise,":[147],"cluster)":[149],"alongside":[150],"non-conformity":[153],"measures.":[154],"The":[155,201],"results":[156],"showed":[157],"that":[158],"our":[159],"effectively":[162],"identified":[163],"previously":[164],"unseen":[165],"types,":[167],"producing":[168],"This":[172],"helped":[175],"maintain":[176],"coverage":[177],"probabilities":[178],"at":[179,207],"expected":[181],"significance":[182],"level.":[183],"Finally,":[184],"illustrate":[186],"how":[187],"integration":[189],"outputs":[193],"enhanced":[194],"further":[195],"downstream":[196],"analyses.":[197],"AVAILABILITY":[198],"AND":[199],"IMPLEMENTATION:":[200],"scRNA-seq":[203],"is":[205],"available":[206],"https://github.com/digital-medicine-research-group-UNAV/conformalized_single_cell_annotator":[208],"https://doi.org/10.5281/zenodo.15870599.":[210]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}