{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,3]],"date-time":"2024-09-03T10:54:18Z","timestamp":1725360858514},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2024,7,8]],"date-time":"2024-07-08T00:00:00Z","timestamp":1720396800000},"content-version":"vor","delay-in-days":46,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62102319"],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Natural Science Project of Shaanxi Provincial Department of Education","award":["23JK0562"]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,5,23]]},"abstract":"Abstract<\/jats:title>\n Spatial transcriptomics provides valuable insights into gene expression within the native tissue context, effectively merging molecular data with spatial information to uncover intricate cellular relationships and tissue organizations. In this context, deciphering cellular spatial domains becomes essential for revealing complex cellular dynamics and tissue structures. However, current methods encounter challenges in seamlessly integrating gene expression data with spatial information, resulting in less informative representations of spots and suboptimal accuracy in spatial domain identification. We introduce stCluster, a novel method that integrates graph contrastive learning with multi-task learning to refine informative representations for spatial transcriptomic data, consequently improving spatial domain identification. stCluster first leverages graph contrastive learning technology to obtain discriminative representations capable of recognizing spatially coherent patterns. Through jointly optimizing multiple tasks, stCluster further fine-tunes the representations to be able to capture complex relationships between gene expression and spatial organization. Benchmarked against six state-of-the-art methods, the experimental results reveal its proficiency in accurately identifying complex spatial domains across various datasets and platforms, spanning tissue, organ, and embryo levels. Moreover, stCluster can effectively denoise the spatial gene expression patterns and enhance the spatial trajectory inference. The source code of stCluster is freely available at https:\/\/github.com\/hannshu\/stCluster.<\/jats:p>","DOI":"10.1093\/bib\/bbae329","type":"journal-article","created":{"date-parts":[[2024,7,8]],"date-time":"2024-07-08T12:47:08Z","timestamp":1720442828000},"source":"Crossref","is-referenced-by-count":1,"title":["Accurately deciphering spatial domains for spatially resolved transcriptomics with stCluster"],"prefix":"10.1093","volume":"25","author":[{"given":"Tao","family":"Wang","sequence":"first","affiliation":[{"name":"School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Rd., Xi'an 710072 , China"},{"name":"Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China"},{"name":"Northwestern Polytechnical University , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China"}]},{"given":"Han","family":"Shu","sequence":"additional","affiliation":[{"name":"School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Rd., Xi'an 710072 , China"},{"name":"Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China"},{"name":"Northwestern Polytechnical University , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China"}]},{"given":"Jialu","family":"Hu","sequence":"additional","affiliation":[{"name":"School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Rd., Xi'an 710072 , China"},{"name":"Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China"},{"name":"Northwestern Polytechnical University , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China"}]},{"given":"Yongtian","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Rd., Xi'an 710072 , China"},{"name":"Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China"},{"name":"Northwestern Polytechnical University , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China"}]},{"given":"Jing","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Xi'an University of Technology , No.5 South Jinhua rd., Xi'an 710048 , China"}]},{"given":"Jiajie","family":"Peng","sequence":"additional","affiliation":[{"name":"School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Rd., Xi'an 710072 , China"},{"name":"Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China"},{"name":"Northwestern Polytechnical University , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China"}]},{"given":"Xuequn","family":"Shang","sequence":"additional","affiliation":[{"name":"School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Rd., Xi'an 710072 , China"},{"name":"Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China"},{"name":"Northwestern Polytechnical University , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China"}]}],"member":"286","published-online":{"date-parts":[[2024,7,8]]},"reference":[{"key":"2024070812372851500_ref1","doi-asserted-by":"crossref","first-page":"1219","DOI":"10.1016\/j.jhep.2020.06.004","article-title":"Single-cell genomics and spatial transcriptomics: discovery of novel cell states and cellular interactions in liver 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