{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,14]],"date-time":"2025-12-14T08:26:43Z","timestamp":1765700803417,"version":"3.41.2"},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,1,21]],"date-time":"2025-01-21T00:00:00Z","timestamp":1737417600000},"content-version":"vor","delay-in-days":60,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62173282","62472363"],"award-info":[{"award-number":["62173282","62472363"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Fuzhou Inter-institutional Science and Technology Cooperation Project","award":["2024-Y-018"],"award-info":[{"award-number":["2024-Y-018"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Understanding cell destiny requires unraveling the intricate mechanism of gene regulation, where transcription factors (TFs) play a pivotal role. However, the actual contribution of TFs, that is TF activity, is not only determined by TF expression, but also accessibility of corresponding chromatin regions. Therefore, we introduce BIOTIC, an advanced Bayesian model with a well-established gene regulation structure that harnesses the power of single-cell multi-omics data to model the gene expression process under the control of regulatory elements, thereby defining the regulatory activity of TFs with variational inference. We demonstrated that the TF activity inferred by BIOTIC can serve as a characterization of cell identity, and outperforms baseline methods for the tasks of cell typing, cell development tracking, and batch effect correction. Additionally, BIOTIC trained on multi-omics data can flexibly be applied to the scenario where merely single-cell transcriptome sequencing is available, to infer TF activity and annotate the cell type by mapping the query cell into the reference TF activity space, as an emerging application of cell atlases. The structure of BIOTIC has been determined to be adaptable for the inclusion of additional biological factors, allowing for flexible and more comprehensive gene regulation analysis. BIOTIC introduces a pioneering biological-mechanism-driven framework to infer TF activity and elucidate cell identity states at gene regulatory level, paving the way for a deeper understanding of the complex interplay between TFs and gene expression in living systems.<\/jats:p>","DOI":"10.1093\/bib\/bbaf013","type":"journal-article","created":{"date-parts":[[2025,1,21]],"date-time":"2025-01-21T01:34:11Z","timestamp":1737423251000},"source":"Crossref","is-referenced-by-count":1,"title":["BIOTIC: a Bayesian framework to integrate single-cell multi-omics for transcription factor activity inference and improve identity characterization of cells"],"prefix":"10.1093","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-6141-6864","authenticated-orcid":false,"given":"Lan","family":"Cao","sequence":"first","affiliation":[{"name":"Department of Automation, Xiamen University , Xiang'an South Road, Xiang'an, 361102, Xiamen, Fujian ,","place":["China"]}]},{"given":"Wenhao","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Automation, Xiamen University , Xiang'an South Road, Xiang'an, 361102, Xiamen, Fujian ,","place":["China"]}]},{"given":"Fan","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Automation, Xiamen University , Xiang'an South Road, Xiang'an, 361102, Xiamen, Fujian ,","place":["China"]},{"name":"National Institute for Data Science in Health and Medicine, Xiamen University , Xiang'an South Road, Xiang'an, 361102, Xiamen, Fujian ,","place":["China"]},{"name":"Xiamen Key Laboratory of Big Data Intelligent Analysis and Decision, Xiamen University , Xiang'an South Road, Xiang'an, 361102, Xiamen, Fujian ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3503-9306","authenticated-orcid":false,"given":"Shengquan","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Mathematical Sciences and LPMC, Nankai University , Weijing Road, Nankai, 300071, Tianjin ,","place":["China"]}]},{"given":"Xiaobing","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Medical Oncology , Fuzhou First Hospital Affiliated with Fujian Medical University, Chating Road, Taijiang, 350000, Fuzhou, Fujian,","place":["China"]}]},{"given":"Feng","family":"Zeng","sequence":"additional","affiliation":[{"name":"Department of Automation, Xiamen University , Xiang'an South Road, Xiang'an, 361102, Xiamen, Fujian ,","place":["China"]},{"name":"National Institute for Data Science in Health and Medicine, Xiamen University , Xiang'an South Road, Xiang'an, 361102, Xiamen, Fujian ,","place":["China"]},{"name":"Xiamen Key Laboratory of Big Data Intelligent Analysis and Decision, Xiamen University , Xiang'an South Road, Xiang'an, 361102, Xiamen, Fujian 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