{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,31]],"date-time":"2026-05-31T14:03:56Z","timestamp":1780236236820,"version":"3.54.0"},"reference-count":80,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2026,5,31]],"date-time":"2026-05-31T00:00:00Z","timestamp":1780185600000},"content-version":"vor","delay-in-days":30,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003725","name":"National Research Foundation (NRF) of Korea","doi-asserted-by":"crossref","award":["RS-2025-16652968 to J.Y.A."],"award-info":[{"award-number":["RS-2025-16652968 to J.Y.A."]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,5,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Reference-based annotation tools have become standard for cell type assignment in single-cell RNA sequencing, leveraging large-scale atlases to transfer labels to new datasets. However, a substantial fraction of cells often receive uncertain or ambiguous annotations\u2014low confidence scores, competing label probabilities, or high entropy across cell types. These cells are typically treated as technical artifacts and filtered out, yet in perturbation experiments they may represent the biologically interesting deviations that investigators seek to identify. We present AnnQ (Annotation Quantification of cellular identity uncertainty), a Python framework that repurposes annotation uncertainty as a quantitative measure of cellular abnormality. AnnQ extracts uncertainty-aware features from probabilistic cell type assignments\u2014including confidence, confidence gap, admixture ratio, and entropy\u2014and computes an out-of-reference (OOR) score measuring each cell\u2019s deviation from a reference population in multivariate uncertainty space. Applying AnnQ to genetic perturbation and drug resistance datasets, we show that OOR scores detect aberrant cellular states that are not resolved by conventional clustering or differential abundance analyses. AnnQ provides a complementary approach for characterizing transitional and abnormal cell states at single-cell resolution. AnnQ is implemented in Python, and its source code and documentation are available on https:\/\/github.com\/joonan-lab\/AnnQ.git.<\/jats:p>","DOI":"10.1093\/bib\/bbag278","type":"journal-article","created":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T11:46:49Z","timestamp":1778845609000},"source":"Crossref","is-referenced-by-count":0,"title":["AnnQ: reference-based quantification of cellular abnormality at single-cell resolution"],"prefix":"10.1093","volume":"27","author":[{"given":"Davin","family":"Lee","sequence":"first","affiliation":[{"name":"Department of Integrated Biomedical and Life Science, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","place":["Republic of Korea"]},{"name":"Interdisciplinary Major Program in Targeted Degradation-based Innovative Therapeutics, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","place":["Republic of Korea"]},{"name":"National Research Laboratory for Convergence Degradation Biology, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","place":["Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gaeun","family":"Byeon","sequence":"additional","affiliation":[{"name":"Department of Integrated Biomedical and Life Science, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","place":["Republic of Korea"]},{"name":"National Research Laboratory for Convergence Degradation Biology, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","place":["Republic of Korea"]},{"name":"L-HOPE Program for Community-Based Total Learning Health Systems, Korea University , Republic of Korea ,","place":["Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seojin","family":"Chung","sequence":"additional","affiliation":[{"name":"School of Biosystem and Biomedical Science, College of Health Science, Korea University , Republic of Korea ,","place":["Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongmin","family":"Shin","sequence":"additional","affiliation":[{"name":"Department of Integrated Biomedical and Life Science, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","place":["Republic of Korea"]},{"name":"National Research Laboratory for Convergence Degradation Biology, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","place":["Republic of Korea"]},{"name":"L-HOPE Program for Community-Based Total Learning Health Systems, Korea University , Republic of Korea ,","place":["Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jongseo","family":"Park","sequence":"additional","affiliation":[{"name":"School of Health and Environmental Science, College of Health Science, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","place":["Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ingyeon","family":"Koh","sequence":"additional","affiliation":[{"name":"Department of Integrated Biomedical and Life Science, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","place":["Republic of Korea"]},{"name":"National Research Laboratory for Convergence Degradation Biology, Korea University , 145 Anam-ro, Seongbuk-gu, Seoul 02841 ,","place":["Republic of Korea"]},{"name":"L-HOPE Program for Community-Based Total Learning Health Systems, Korea University , Republic of Korea ,","place":["Republic of Korea"]},{"name":"Genetics and Genome Biology Program, The Hospital for Sick Children ; Toronto, ON M5G 0A4 ,","place":["Canada"]},{"name":"The Centre for Applied Genomics, The Hospital for Sick Children ; Toronto, ON M5G 0A4 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joon-Yong","family":"An","sequence":"additional","affiliation":[{"name":"Department of 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