{"id":"https://openalex.org/W7162958713","doi":"https://doi.org/10.1093/bib/bbag278","title":"AnnQ: reference-based quantification of cellular abnormality at single-cell resolution","display_name":"AnnQ: reference-based quantification of cellular abnormality at single-cell resolution","publication_year":2026,"publication_date":"2026-05-01","ids":{"openalex":"https://openalex.org/W7162958713","doi":"https://doi.org/10.1093/bib/bbag278","pmid":"https://pubmed.ncbi.nlm.nih.gov/42218718"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbag278","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag278","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/bbag278","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030357259","display_name":"Davin Lee","orcid":"https://orcid.org/0000-0002-1506-5304"},"institutions":[{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]},{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]},{"id":"https://openalex.org/I4210161052","display_name":"Korea University","ror":"https://ror.org/05m1gnk07","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210161052"]}],"countries":["JP","KR"],"is_corresponding":false,"raw_author_name":"Davin Lee","raw_affiliation_strings":["Department of Integrated Biomedical and Life Science, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","Interdisciplinary Major Program in Targeted Degradation-based Innovative Therapeutics, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","National Research Laboratory for Convergence Degradation Biology, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Integrated Biomedical and Life Science, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","institution_ids":["https://openalex.org/I197347611","https://openalex.org/I4210161052"]},{"raw_affiliation_string":"Interdisciplinary Major Program in Targeted Degradation-based Innovative Therapeutics, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","institution_ids":["https://openalex.org/I4210161052"]},{"raw_affiliation_string":"National Research Laboratory for Convergence Degradation Biology, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","institution_ids":["https://openalex.org/I139264467"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5137475858","display_name":"Gaeun Byeon","orcid":null},"institutions":[{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]},{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]},{"id":"https://openalex.org/I4210161052","display_name":"Korea University","ror":"https://ror.org/05m1gnk07","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210161052"]}],"countries":["JP","KR"],"is_corresponding":false,"raw_author_name":"Gaeun Byeon","raw_affiliation_strings":["Department of Integrated Biomedical and Life Science, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","L-HOPE Program for Community-Based Total Learning Health Systems, Korea University , Republic of Korea ,","National Research Laboratory for Convergence Degradation Biology, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Integrated Biomedical and Life Science, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","institution_ids":["https://openalex.org/I197347611","https://openalex.org/I4210161052"]},{"raw_affiliation_string":"L-HOPE Program for Community-Based Total Learning Health Systems, Korea University , Republic of Korea ,","institution_ids":["https://openalex.org/I4210161052"]},{"raw_affiliation_string":"National Research Laboratory for Convergence Degradation Biology, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","institution_ids":["https://openalex.org/I139264467"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103520849","display_name":"S W Chung","orcid":null},"institutions":[{"id":"https://openalex.org/I4210161052","display_name":"Korea University","ror":"https://ror.org/05m1gnk07","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210161052"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Seojin Chung","raw_affiliation_strings":["School of Biosystem and Biomedical Science, College of Health Science, Korea University , Republic of Korea ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biosystem and Biomedical Science, College of Health Science, Korea University , Republic of Korea ,","institution_ids":["https://openalex.org/I4210161052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5121383814","display_name":"Dongmin Shin","orcid":null},"institutions":[{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]},{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]},{"id":"https://openalex.org/I4210161052","display_name":"Korea University","ror":"https://ror.org/05m1gnk07","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210161052"]}],"countries":["JP","KR"],"is_corresponding":false,"raw_author_name":"Dongmin Shin","raw_affiliation_strings":["Department of Integrated Biomedical and Life Science, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","L-HOPE Program for Community-Based Total Learning Health Systems, Korea University , Republic of Korea ,","National Research Laboratory for Convergence Degradation Biology, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Integrated Biomedical and Life Science, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","institution_ids":["https://openalex.org/I197347611","https://openalex.org/I4210161052"]},{"raw_affiliation_string":"L-HOPE Program for Community-Based Total Learning Health Systems, Korea University , Republic of Korea ,","institution_ids":["https://openalex.org/I4210161052"]},{"raw_affiliation_string":"National Research Laboratory for Convergence Degradation Biology, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","institution_ids":["https://openalex.org/I139264467"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5137473972","display_name":"Jongseo Park","orcid":null},"institutions":[{"id":"https://openalex.org/I4210161052","display_name":"Korea University","ror":"https://ror.org/05m1gnk07","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210161052"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Jongseo Park","raw_affiliation_strings":["School of Health and Environmental Science, College of Health Science, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Health and Environmental Science, College of Health Science, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","institution_ids":["https://openalex.org/I4210161052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5137475897","display_name":"Ingyeon Koh","orcid":null},"institutions":[{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]},{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]},{"id":"https://openalex.org/I2801317318","display_name":"Hospital for Sick Children","ror":"https://ror.org/057q4rt57","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I2801317318"]},{"id":"https://openalex.org/I4210161052","display_name":"Korea University","ror":"https://ror.org/05m1gnk07","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210161052"]}],"countries":["CA","JP","KR"],"is_corresponding":false,"raw_author_name":"Ingyeon Koh","raw_affiliation_strings":["Department of Integrated Biomedical and Life Science, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","Genetics and Genome Biology Program, The Hospital for Sick Children ; Toronto, ON M5G 0A4 ,","L-HOPE Program for Community-Based Total Learning Health Systems, Korea University , Republic of Korea ,","National Research Laboratory for Convergence Degradation Biology, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","The Centre for Applied Genomics, The Hospital for Sick Children ; Toronto, ON M5G 0A4 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Integrated Biomedical and Life Science, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","institution_ids":["https://openalex.org/I197347611","https://openalex.org/I4210161052"]},{"raw_affiliation_string":"Genetics and Genome Biology Program, The Hospital for Sick Children ; Toronto, ON M5G 0A4 ,","institution_ids":["https://openalex.org/I2801317318"]},{"raw_affiliation_string":"L-HOPE Program for Community-Based Total Learning Health Systems, Korea University , Republic of Korea ,","institution_ids":["https://openalex.org/I4210161052"]},{"raw_affiliation_string":"National Research Laboratory for Convergence Degradation Biology, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","institution_ids":["https://openalex.org/I139264467"]},{"raw_affiliation_string":"The Centre for Applied Genomics, The Hospital for Sick Children ; Toronto, ON M5G 0A4 ,","institution_ids":["https://openalex.org/I2801317318"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041088179","display_name":"Joon\u2010Yong An","orcid":"https://orcid.org/0000-0001-8839-6297"},"institutions":[{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]},{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]},{"id":"https://openalex.org/I4210161052","display_name":"Korea University","ror":"https://ror.org/05m1gnk07","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210161052"]}],"countries":["JP","KR"],"is_corresponding":true,"raw_author_name":"Joon-Yong An","raw_affiliation_strings":["Department of Integrated Biomedical and Life Science, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","Interdisciplinary Major Program in Targeted Degradation-based Innovative Therapeutics, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","L-HOPE Program for Community-Based Total Learning Health Systems, Korea University , Republic of Korea ,","National Research Laboratory for Convergence Degradation Biology, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","School of Biosystem and Biomedical Science, College of Health Science, Korea University , Republic of Korea ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Integrated Biomedical and Life Science, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","institution_ids":["https://openalex.org/I197347611","https://openalex.org/I4210161052"]},{"raw_affiliation_string":"Interdisciplinary Major Program in Targeted Degradation-based Innovative Therapeutics, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","institution_ids":["https://openalex.org/I4210161052"]},{"raw_affiliation_string":"L-HOPE Program for Community-Based Total Learning Health Systems, Korea University , Republic of Korea ,","institution_ids":["https://openalex.org/I4210161052"]},{"raw_affiliation_string":"National Research Laboratory for Convergence Degradation Biology, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","institution_ids":["https://openalex.org/I139264467"]},{"raw_affiliation_string":"School of Biosystem and Biomedical Science, College of Health Science, Korea University , Republic of Korea ,","institution_ids":["https://openalex.org/I4210161052"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5041088179"],"corresponding_institution_ids":["https://openalex.org/I139264467","https://openalex.org/I197347611","https://openalex.org/I4210161052"],"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":0.68278813,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","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":0.9941999912261963,"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":0.9941999912261963,"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":0.00419999985024333,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.00019999999494757503,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6568999886512756},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.6274999976158142},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5309000015258789},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4756999909877777},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4343000054359436},{"id":"https://openalex.org/keywords/entropy","display_name":"Entropy (arrow of time)","score":0.3937000036239624},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.3926999866962433},{"id":"https://openalex.org/keywords/confidence-interval","display_name":"Confidence interval","score":0.3756999969482422}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6568999886512756},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6503000259399414},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.6274999976158142},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5309000015258789},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4756999909877777},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4713999927043915},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4343000054359436},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41350001096725464},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4088999927043915},{"id":"https://openalex.org/C106301342","wikidata":"https://www.wikidata.org/wiki/Q4117933","display_name":"Entropy (arrow of time)","level":2,"score":0.3937000036239624},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.3926999866962433},{"id":"https://openalex.org/C44249647","wikidata":"https://www.wikidata.org/wiki/Q208498","display_name":"Confidence interval","level":2,"score":0.3756999969482422},{"id":"https://openalex.org/C189014844","wikidata":"https://www.wikidata.org/wiki/Q189118","display_name":"Cell type","level":3,"score":0.37229999899864197},{"id":"https://openalex.org/C161584116","wikidata":"https://www.wikidata.org/wiki/Q1952580","display_name":"Multivariate statistics","level":2,"score":0.36160001158714294},{"id":"https://openalex.org/C50965678","wikidata":"https://www.wikidata.org/wiki/Q2724302","display_name":"Abnormality","level":2,"score":0.3497999906539917},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.3151000142097473},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.3100000023841858},{"id":"https://openalex.org/C138268822","wikidata":"https://www.wikidata.org/wiki/Q1051925","display_name":"Resolution (logic)","level":2,"score":0.3068999946117401},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.27900001406669617},{"id":"https://openalex.org/C22679943","wikidata":"https://www.wikidata.org/wiki/Q159375","display_name":"Standard deviation","level":2,"score":0.2689000070095062},{"id":"https://openalex.org/C66782513","wikidata":"https://www.wikidata.org/wiki/Q864601","display_name":"Biomedicine","level":2,"score":0.26660001277923584},{"id":"https://openalex.org/C3020402766","wikidata":"https://www.wikidata.org/wiki/Q104376712","display_name":"Prior information","level":2,"score":0.2596000134944916},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.2587999999523163},{"id":"https://openalex.org/C3020199158","wikidata":"https://www.wikidata.org/wiki/Q210521","display_name":"High resolution","level":2,"score":0.2581000030040741}],"mesh":[{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","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":"D000465","descriptor_name":"Algorithms","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbag278","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag278","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:42218718","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42218718","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:13222523","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13222523/","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/bbag278","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag278","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1823355532","display_name":null,"funder_award_id":"RS-2025-16652968 to J.Y.A.","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"},{"id":"https://openalex.org/G1866764127","display_name":null,"funder_award_id":"RS-2025-16652968","funder_id":"https://openalex.org/F4320320671","funder_display_name":"National Research Foundation"},{"id":"https://openalex.org/G3506292433","display_name":null,"funder_award_id":"RS-2024-00467876","funder_id":"https://openalex.org/F4320320671","funder_display_name":"National Research Foundation"},{"id":"https://openalex.org/G4080463709","display_name":null,"funder_award_id":"RS-2024-00467876","funder_id":"https://openalex.org/F4320328359","funder_display_name":"Ministry of Science and ICT, South Korea"},{"id":"https://openalex.org/G4377333866","display_name":null,"funder_award_id":"RS-2025-16652968","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"}],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320322120","display_name":"National Research Foundation of Korea","ror":"https://ror.org/013aysd81"},{"id":"https://openalex.org/F4320322724","display_name":"Ministry of Education, India","ror":"https://ror.org/048xjjh50"},{"id":"https://openalex.org/F4320328359","display_name":"Ministry of Science and ICT, South Korea","ror":"https://ror.org/01wpjm123"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":79,"referenced_works":["https://openalex.org/W1984883254","https://openalex.org/W2015964634","https://openalex.org/W2079777624","https://openalex.org/W2100801632","https://openalex.org/W2106391833","https://openalex.org/W2214074259","https://openalex.org/W2560648000","https://openalex.org/W2561754210","https://openalex.org/W2620676965","https://openalex.org/W2734283649","https://openalex.org/W2756868900","https://openalex.org/W2767055857","https://openalex.org/W2791731597","https://openalex.org/W2794083495","https://openalex.org/W2891688308","https://openalex.org/W2907514116","https://openalex.org/W2908670724","https://openalex.org/W2910923792","https://openalex.org/W2918950867","https://openalex.org/W2948578084","https://openalex.org/W2951914955","https://openalex.org/W2985456447","https://openalex.org/W2995410603","https://openalex.org/W3009606620","https://openalex.org/W3043086101","https://openalex.org/W3045497066","https://openalex.org/W3131916754","https://openalex.org/W3132715010","https://openalex.org/W3133712085","https://openalex.org/W3133859624","https://openalex.org/W3164692211","https://openalex.org/W3174228953","https://openalex.org/W3175922295","https://openalex.org/W3184208286","https://openalex.org/W3184729641","https://openalex.org/W3198123874","https://openalex.org/W3203496375","https://openalex.org/W3217151720","https://openalex.org/W4280596398","https://openalex.org/W4280598116","https://openalex.org/W4280624033","https://openalex.org/W4281716291","https://openalex.org/W4283157828","https://openalex.org/W4286491754","https://openalex.org/W4320896645","https://openalex.org/W4320913125","https://openalex.org/W4323360805","https://openalex.org/W4377565738","https://openalex.org/W4380991813","https://openalex.org/W4382359456","https://openalex.org/W4384561857","https://openalex.org/W4385290032","https://openalex.org/W4386333999","https://openalex.org/W4386334053","https://openalex.org/W4386693811","https://openalex.org/W4387251835","https://openalex.org/W4389670555","https://openalex.org/W4389788467","https://openalex.org/W4390778893","https://openalex.org/W4391991523","https://openalex.org/W4395469459","https://openalex.org/W4400606143","https://openalex.org/W4401047144","https://openalex.org/W4401637494","https://openalex.org/W4402503335","https://openalex.org/W4402943211","https://openalex.org/W4403082643","https://openalex.org/W4403095045","https://openalex.org/W4403468233","https://openalex.org/W4404566892","https://openalex.org/W4404566935","https://openalex.org/W4406002944","https://openalex.org/W4406117135","https://openalex.org/W4406357615","https://openalex.org/W4406500383","https://openalex.org/W4408149462","https://openalex.org/W4410841060","https://openalex.org/W4413688376","https://openalex.org/W7126033895"],"related_works":[],"abstract_inverted_index":{"Reference-based":[0],"annotation":[1,87],"tools":[2],"have":[3],"become":[4],"standard":[5],"for":[6,163],"cell":[7,44,102,168],"type":[8,103],"assignment":[9],"in":[10,58,125,176],"single-cell":[11,171],"RNA":[12],"sequencing,":[13],"leveraging":[14],"large-scale":[15],"atlases":[16],"to":[17,20,71,131],"transfer":[18],"labels":[19],"new":[21],"datasets.":[22],"However,":[23],"a":[24,82,90,122,160],"substantial":[25],"fraction":[26],"of":[27,78,93],"cells":[28,47],"often":[29],"receive":[30],"uncertain":[31],"or":[32,40,154],"ambiguous":[33],"annotations-low":[34],"confidence":[35,106],"scores,":[36],"competing":[37],"label":[38],"probabilities,":[39],"high":[41],"entropy":[42],"across":[43],"types.":[45],"These":[46],"are":[48,148,184],"typically":[49],"treated":[50],"as":[51,89],"technical":[52],"artifacts":[53],"and":[54,110,134,166,178,182],"filtered":[55],"out,":[56],"yet":[57],"perturbation":[59,133],"experiments":[60],"they":[61],"may":[62],"represent":[63],"the":[64],"biologically":[65],"interesting":[66],"deviations":[67],"that":[68,85,140,147],"investigators":[69],"seek":[70],"identify.":[72],"We":[73],"present":[74],"AnnQ":[75,96,130,158,173],"(Annotation":[76],"Quantification":[77],"cellular":[79,94,145],"identity":[80],"uncertainty),":[81],"Python":[83],"framework":[84],"repurposes":[86],"uncertainty":[88,127],"quantitative":[91],"measure":[92],"abnormality.":[95],"extracts":[97],"uncertainty-aware":[98],"features":[99],"from":[100,121],"probabilistic":[101],"assignments-including":[104],"confidence,":[105],"gap,":[107],"admixture":[108],"ratio,":[109],"entropy-and":[111],"computes":[112],"an":[113],"out-of-reference":[114],"(OOR)":[115],"score":[116],"measuring":[117],"each":[118],"cell's":[119],"deviation":[120],"reference":[123],"population":[124],"multivariate":[126],"space.":[128],"Applying":[129],"genetic":[132],"drug":[135],"resistance":[136],"datasets,":[137],"we":[138],"show":[139],"OOR":[141],"scores":[142],"detect":[143],"aberrant":[144],"states":[146,169],"not":[149],"resolved":[150],"by":[151],"conventional":[152],"clustering":[153],"differential":[155],"abundance":[156],"analyses.":[157],"provides":[159],"complementary":[161],"approach":[162],"characterizing":[164],"transitional":[165],"abnormal":[167],"at":[170],"resolution.":[172],"is":[174],"implemented":[175],"Python,":[177],"its":[179],"source":[180],"code":[181],"documentation":[183],"available":[185],"on":[186],"https://github.com/joonan-lab/AnnQ.git.":[187]},"counts_by_year":[],"updated_date":"2026-07-05T07:55:05.734416","created_date":"2026-06-01T00:00:00"}
