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Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder

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Cited by:

  1. Jingyang Qian & Hudong Bao & Xin Shao & Yin Fang & Jie Liao & Zhuo Chen & Chengyu Li & Wenbo Guo & Yining Hu & Anyao Li & Yue Yao & Xiaohui Fan & Yiyu Cheng, 2024. "Simulating multiple variability in spatially resolved transcriptomics with scCube," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
  2. Zhiyuan Liu & Dafei Wu & Weiwei Zhai & Liang Ma, 2023. "SONAR enables cell type deconvolution with spatially weighted Poisson-Gamma model for spatial transcriptomics," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  3. Jingyang Qian & Jie Liao & Ziqi Liu & Ying Chi & Yin Fang & Yanrong Zheng & Xin Shao & Bingqi Liu & Yongjin Cui & Wenbo Guo & Yining Hu & Hudong Bao & Penghui Yang & Qian Chen & Mingxiao Li & Bing Zha, 2023. "Reconstruction of the cell pseudo-space from single-cell RNA sequencing data with scSpace," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
  4. Yitao Yang & Yang Cui & Xin Zeng & Yubo Zhang & Martin Loza & Sung-Joon Park & Kenta Nakai, 2025. "STAIG: Spatial transcriptomics analysis via image-aided graph contrastive learning for domain exploration and alignment-free integration," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
  5. Jingyang Qian & Xin Shao & Hudong Bao & Yin Fang & Wenbo Guo & Chengyu Li & Anyao Li & Hua Hua & Xiaohui Fan, 2025. "Identification and characterization of cell niches in tissue from spatial omics data at single-cell resolution," Nature Communications, Nature, vol. 16(1), pages 1-21, December.
  6. Yuqiu Zhou & Wei He & Weizhen Hou & Ying Zhu, 2024. "Pianno: a probabilistic framework automating semantic annotation for spatial transcriptomics," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  7. Xiaomeng Wan & Jiashun Xiao & Sindy Sing Ting Tam & Mingxuan Cai & Ryohichi Sugimura & Yang Wang & Xiang Wan & Zhixiang Lin & Angela Ruohao Wu & Can Yang, 2023. "Integrating spatial and single-cell transcriptomics data using deep generative models with SpatialScope," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
  8. Kaichen Xu & Yan Lu & Suyang Hou & Kainan Liu & Yihang Du & Mengqian Huang & Hao Feng & Hao Wu & Xiaobo Sun, 2024. "Detecting anomalous anatomic regions in spatial transcriptomics with STANDS," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
  9. Chunman Zuo & Yijian Zhang & Chen Cao & Jinwang Feng & Mingqi Jiao & Luonan Chen, 2022. "Elucidating tumor heterogeneity from spatially resolved transcriptomics data by multi-view graph collaborative learning," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  10. Yahui Long & Kok Siong Ang & Mengwei Li & Kian Long Kelvin Chong & Raman Sethi & Chengwei Zhong & Hang Xu & Zhiwei Ong & Karishma Sachaphibulkij & Ao Chen & Li Zeng & Huazhu Fu & Min Wu & Lina Hsiu Ki, 2023. "Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
  11. Yuchen Liang & Guowei Shi & Runlin Cai & Yuchen Yuan & Ziying Xie & Long Yu & Yingjian Huang & Qian Shi & Lizhe Wang & Jun Li & Zhonghui Tang, 2024. "PROST: quantitative identification of spatially variable genes and domain detection in spatial transcriptomics," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
  12. Zhiyuan Yuan, 2024. "MENDER: fast and scalable tissue structure identification in spatial omics data," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
  13. Chunman Zuo & Junjie Xia & Luonan Chen, 2024. "Dissecting tumor microenvironment from spatially resolved transcriptomics data by heterogeneous graph learning," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  14. Tianci Song & Charles Broadbent & Rui Kuang, 2023. "GNTD: reconstructing spatial transcriptomes with graph-guided neural tensor decomposition informed by spatial and functional relations," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  15. Linhua Wang & Mirjana Maletic-Savatic & Zhandong Liu, 2022. "Region-specific denoising identifies spatial co-expression patterns and intra-tissue heterogeneity in spatially resolved transcriptomics data," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  16. Chen-Rui Xia & Zhi-Jie Cao & Xin-Ming Tu & Ge Gao, 2023. "Spatial-linked alignment tool (SLAT) for aligning heterogenous slices," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
  17. Quentin Blampey & Kevin Mulder & Margaux Gardet & Stergios Christodoulidis & Charles-Antoine Dutertre & Fabrice André & Florent Ginhoux & Paul-Henry Cournède, 2024. "Sopa: a technology-invariant pipeline for analyses of image-based spatial omics," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
  18. Rongbo Shen & Lin Liu & Zihan Wu & Ying Zhang & Zhiyuan Yuan & Junfu Guo & Fan Yang & Chao Zhang & Bichao Chen & Wanwan Feng & Chao Liu & Jing Guo & Guozhen Fan & Yong Zhang & Yuxiang Li & Xun Xu & Ji, 2022. "Spatial-ID: a cell typing method for spatially resolved transcriptomics via transfer learning and spatial embedding," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  19. Rafael dos Santos Peixoto & Brendan F. Miller & Maigan A. Brusko & Gohta Aihara & Lyla Atta & Manjari Anant & Mark A. Atkinson & Todd M. Brusko & Clive H. Wasserfall & Jean Fan, 2025. "Characterizing cell-type spatial relationships across length scales in spatially resolved omics data," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
  20. Peng Zhang & Chaofei Gao & Zhuoyu Zhang & Zhiyuan Yuan & Qian Zhang & Ping Zhang & Shiyu Du & Weixun Zhou & Yan Li & Shao Li, 2025. "Systematic inference of super-resolution cell spatial profiles from histology images," Nature Communications, Nature, vol. 16(1), pages 1-21, December.
  21. Benjamin L. Walker & Qing Nie, 2023. "NeST: nested hierarchical structure identification in spatial transcriptomic data," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  22. Guanshen Cui & Kangning Dong & Jia-Yi Zhou & Shang Li & Ying Wu & Qinghua Han & Bofei Yao & Qunlun Shen & Yong-Liang Zhao & Ying Yang & Jun Cai & Shihua Zhang & Yun-Gui Yang, 2023. "Spatiotemporal transcriptomic atlas reveals the dynamic characteristics and key regulators of planarian regeneration," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  23. Hao Xu & Shuyan Wang & Minghao Fang & Songwen Luo & Chunpeng Chen & Siyuan Wan & Rirui Wang & Meifang Tang & Tian Xue & Bin Li & Jun Lin & Kun Qu, 2023. "SPACEL: deep learning-based characterization of spatial transcriptome architectures," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
  24. Zhiyuan Yuan & Yisi Li & Minglei Shi & Fan Yang & Juntao Gao & Jianhua Yao & Michael Q. Zhang, 2022. "SOTIP is a versatile method for microenvironment modeling with spatial omics data," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
  25. Ankit Agrawal & Stefan Thomann & Sukanya Basu & Dominic Grün, 2024. "NiCo identifies extrinsic drivers of cell state modulation by niche covariation analysis," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
  26. Biao Zhang & Shuqin Zhang & Shihua Zhang, 2024. "Whole brain alignment of spatial transcriptomics between humans and mice with BrainAlign," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
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