{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T18:13:33Z","timestamp":1767636813348,"version":"3.48.0"},"reference-count":68,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,12,3]],"date-time":"2025-12-03T00:00:00Z","timestamp":1764720000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"RGC Collaborative Research Fund","award":["C7046-23G"],"award-info":[{"award-number":["C7046-23G"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Single-cell technologies enable high-resolution cellular studies but face challenges in identifying differential features due to data complexity.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present OTMODE, a non-parametric method using unbalanced Sinkhorn algorithm and Wald test to improve differential feature identification in single-cell multi-omics data. Under simulation, OTMODE achieved superior performance (average 90% F1 score; average 92% AUC score) with high efficiency (2.2\u2009s for 5000 cells). In practice, it shows greater sensitivity than other state-of-the-art methods in detecting meaningful processes and can evaluate annotation accuracy by identifying potentially misannotated clusters from auto-annotation tools. Furthermore, OTMODE integrates seamlessly with Scanpy, offering a user-friendly solution for researchers.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>OTMODE is freely available at https:\/\/github.com\/Eggong\/OTMODE and also available at https:\/\/pypi.org\/project\/OTMODE\/.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf650","type":"journal-article","created":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T12:30:24Z","timestamp":1764592224000},"source":"Crossref","is-referenced-by-count":0,"title":["OTMODE: an optimal transport theory-based framework for identifying differential features in single-cell multi-omics data"],"prefix":"10.1093","volume":"42","author":[{"given":"Huidong","family":"Su","sequence":"first","affiliation":[{"name":"Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong , Hong Kong SAR, 999077,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Caicai","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong , Hong Kong SAR, 999077,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Frank Qingyun","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong , Hong Kong SAR, 999077,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chun Hing","family":"She","sequence":"additional","affiliation":[{"name":"Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong , Hong Kong SAR, 999077,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinxin","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong , Hong Kong SAR, 999077,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiao","family":"Dang","sequence":"additional","affiliation":[{"name":"Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong , Hong Kong SAR, 999077,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yao","family":"Lei","sequence":"additional","affiliation":[{"name":"Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong , Hong Kong SAR, 999077,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ke","family":"Ni","sequence":"additional","affiliation":[{"name":"Joint Carnegie Mellon\u2013University of Pittsburgh Program in Computational Biology Computational Biology Department, , Pittsburgh, PA, 15213,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zewei","family":"Xiong","sequence":"additional","affiliation":[{"name":"Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong , Hong Kong SAR, 999077,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Danqing","family":"Yin","sequence":"additional","affiliation":[{"name":"Laboratory of Data Discovery for Health Limited (D24H) , Hong Kong SAR, 999077,","place":["China"]},{"name":"School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam , Hong Kong SAR, 999077,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xingtian","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong , Hong Kong SAR, 999077,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hong","family":"Feng","sequence":"additional","affiliation":[{"name":"Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong , Hong Kong SAR, 999077,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Philip H","family":"Li","sequence":"additional","affiliation":[{"name":"Division of Rheumatology & Clinical Immunology, Department of Medicine, Queen Mary Hospital, The University of Hong Kong , Hong Kong SAR, 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