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Nevertheless, current SRT technologies exhibit limitations, manifesting as either low transcript detection sensitivity or restricted gene throughput. These constraints result in diminished precision and coverage in gene measurement. In response, we introduce SpaGDA, a sophisticated deep learning\u2013based graph domain adaptation framework for both scenarios of gene expression imputation and cell type identification in spatially resolved transcriptomics data by impartially transferring knowledge from reference scRNA-seq data. Systematic benchmarking analyses across several SRT datasets generated from different technologies have demonstrated SpaGDA's superior effectiveness compared to state-of-the-art methods in both scenarios. Further applied to three SRT datasets of different biological contexts, SpaGDA not only better recovers the well-established knowledge sourced from public atlases and existing scientific literature but also yields a more informative spatial expression pattern of genes. Together, these results demonstrate that SpaGDA can be used to overcome the challenges of current SRT data and provide more accurate insights into biological processes or disease development. The SpaGDA is available in https:\/\/github.com\/shenrb\/SpaGDA.<\/jats:p>","DOI":"10.1093\/bib\/bbae576","type":"journal-article","created":{"date-parts":[[2024,11,7]],"date-time":"2024-11-07T11:56:02Z","timestamp":1730980562000},"source":"Crossref","is-referenced-by-count":2,"title":["Graph domain adaptation\u2013based framework for gene expression enhancement and cell type identification in large-scale spatially resolved transcriptomics"],"prefix":"10.1093","volume":"25","author":[{"given":"Rongbo","family":"Shen","sequence":"first","affiliation":[{"name":"GMU-GIBH Joint School of Life Sciences , The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, , No. 1 Xinzao Road, Xinzao Town, Panyu District, Guangzhou 510005 ,","place":["China"]},{"name":"Guangzhou Medical University , The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, , No. 1 Xinzao Road, Xinzao Town, Panyu District, Guangzhou 510005 ,","place":["China"]},{"name":"Guangzhou National Laboratory , No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province ,","place":["China"]},{"name":"Tencent AI Lab , Shenzhen 518000 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Meiling","family":"Cheng","sequence":"additional","affiliation":[{"name":"Guangzhou National Laboratory , No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province ,","place":["China"]},{"name":"Key Laboratory of Molecular Biophysics of the Ministry of Education , Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, , Luoyu Road 1037, Wuhan 430074 ,","place":["China"]},{"name":"Huazhong University of Science and Technology , Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, , Luoyu Road 1037, Wuhan 430074 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wencang","family":"Wang","sequence":"additional","affiliation":[{"name":"Guangzhou National Laboratory , No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qi","family":"Fan","sequence":"additional","affiliation":[{"name":"Guangzhou National Laboratory , No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huan","family":"Yan","sequence":"additional","affiliation":[{"name":"Guangzhou National Laboratory , No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiayue","family":"Wen","sequence":"additional","affiliation":[{"name":"Guangzhou National Laboratory , No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhiyuan","family":"Yuan","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University , Handan Road, Shanghai 200433 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianhua","family":"Yao","sequence":"additional","affiliation":[{"name":"Tencent AI Lab , Shenzhen 518000 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yixue","family":"Li","sequence":"additional","affiliation":[{"name":"GMU-GIBH Joint School of Life Sciences , The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, , No. 1 Xinzao Road, Xinzao Town, Panyu District, Guangzhou 510005 ,","place":["China"]},{"name":"Guangzhou Medical University , The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, , No. 1 Xinzao Road, Xinzao Town, Panyu District, Guangzhou 510005 ,","place":["China"]},{"name":"Guangzhou National Laboratory , No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2597-2319","authenticated-orcid":false,"given":"Jiao","family":"Yuan","sequence":"additional","affiliation":[{"name":"GMU-GIBH Joint School of Life Sciences , The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, , No. 1 Xinzao Road, Xinzao Town, Panyu District, Guangzhou 510005 ,","place":["China"]},{"name":"Guangzhou Medical University , The 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