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However, common methods for combining these datasets often merge data from multiple cells to generate pseudo-ST data, overlooking topological relationships and failing to represent spatial arrangements accurately. We introduce GTAD, a method utilizing the Graph Attention Network for deconvolution of integrated scRNA-seq and ST-seq data. GTAD effectively captures cell spatial relationships and topological structures within tissues using a graph-based approach, enhancing cell-type identification and our understanding of complex tissue cellular landscapes. By integrating scRNA-seq and ST data into a unified graph structure, GTAD outperforms traditional \u2018pseudo-ST\u2019 methods, providing robust and information-rich results. GTAD performs exceptionally well with synthesized spatial data and accurately identifies cell spatial composition in tissues like the mouse cerebral cortex, cerebellum, developing human heart and pancreatic ductal carcinoma. GTAD holds the potential to enhance our understanding of tissue microenvironments and cellular diversity in complex bio-logical systems. The source code is available at https:\/\/github.com\/zzhjs\/GTAD.<\/jats:p>","DOI":"10.1093\/bib\/bbad469","type":"journal-article","created":{"date-parts":[[2023,12,21]],"date-time":"2023-12-21T14:30:08Z","timestamp":1703169008000},"source":"Crossref","is-referenced-by-count":15,"title":["GTAD: a graph-based approach for cell spatial composition inference from integrated scRNA-seq and ST-seq data"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9807-8620","authenticated-orcid":false,"given":"Tianjiao","family":"Zhang","sequence":"first","affiliation":[{"name":"College of Computer and Control Engineering, Northeast Forestry University , Harbin 150040 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-0887-9795","authenticated-orcid":false,"given":"Ziheng","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Computer and Control Engineering, Northeast Forestry University , Harbin 150040 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-0594-5625","authenticated-orcid":false,"given":"Liangyu","family":"Li","sequence":"additional","affiliation":[{"name":"College of Computer and Control Engineering, Northeast Forestry University , Harbin 150040 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benzhi","family":"Dong","sequence":"additional","affiliation":[{"name":"College of Computer and Control Engineering, Northeast Forestry University , Harbin 150040 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guohua","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Computer and Control Engineering, Northeast Forestry University , Harbin 150040 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dandan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology, the First 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