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A masked generative graph representation learning framework empowering precise spatial domain identification

delete2026-05-22
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OA
AI
C
Chuyao Wang
T
Tongdong Zhang
H
Hang Sun
Z
Zhipeng Wu
S
Shuo Liang
X
Xueting Wang
M
Meirong Du
Y
Yanchun Liang
X
Xin Gao
Q
Qi Tang
D
Dong Xu
丰
丰小月 (Xiaoyue Feng) *
A
An Zeng *
R
Renchu Guan *
DOI:10.1093/bioinformatics/btag333delete
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Abstract

Abstract

En 中文
Spatial transcriptomics (ST) enables the measurement of gene expression while preserving the spatial context of tissues. However, the sparsity of ST data leads to poor usage of gene expression and spatial information, resulting in the embeddings that are not well represented and challenging for downstream analyses.
Keywords:
Spatial transcriptomics
Gene expression
Graph representation learning
Spatial domain identification
Data sparsity

Journal

Bioinformatics cover
Bioinformatics
IF:
5.4
Papers:
1.3K
Citations:
17.9W

Organization

T
tongji university
Scholars:
7.9W
Papers: 6.0W
Citations: 98
K
king abdullah university of science and technology
Scholars:
1.7K
Papers: 630
Citations: 0
U
university of missouri
Scholars:
1.3K
Papers: 620
Citations: 0
J
Jilin University
Scholars:
8.7W
Papers: 5.6W
Citations: 8.9K
C
chinese academy of sciences
Scholars:
56.7W
Papers: 45.0W
Citations: 704
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Cited Papers

Cited Papers

Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
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errOAAI
errKristen R. Maynard; Leonardo Collado-Torres; Lukas M. Weber; Cedric Uytingco; Brianna K. Barry; Stephen R. Williams; Joseph L. Catallini; Matthew N. Tran; Zachary Besich; Madhavi Tippani; Jennifer Chew; Yifeng Yin; Joel E. Kleinman; Thomas M. Hyde; Nikhil Rao; Stephanie C. Hicks; Keri Martinowich; Andrew E. Jaffe
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Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis
err2021-09-06
err147
errOAAI
errLohoff, T.; Ghazanfar, S.; Missarova, A.; Koulena, N.; Pierson, N.; Griffiths, J. A.; Bardot, E. S.; Eng, C. -H. L.; Tyser, R. C. V.; Argelaguet, R.; Guibentif, C.; Srinivas, S.; Briscoe, J.; Simons, B. D.; Hadjantonakis, A. -K.; Gottgens, B.; Reik, W.; Nichols, J.; Cai, L.; Marioni, J. C.
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Integrated analysis of multimodal single-cell data
errCell
IF0
err2021-06-01
err0
errOAAI
errYuhan Hao; Stephanie Hao; Erica Andersen-Nissen; William M. Mauck; Shiwei Zheng; Andrew Butler; Maddie J. Lee; Aaron J. Wilk; Charlotte Darby; Michael Zager; Paul Hoffman; Marlon Stoeckius; Efthymia Papalexi; Eleni P. Mimitou; Jaison Jain; Avi Srivastava; Tim Stuart; Lamar M. Fleming; Bertrand Yeung; Angela J. Rogers; Juliana M. McElrath; Catherine A. Blish; Raphael Gottardo; Peter Smibert; Rahul Satija
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Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST
err2023-03-01
err115
errOAAI
errLong, Yahui; Ang, Kok Siong; Li, Mengwei; Chong, Kian Long Kelvin; Sethi, Raman; Zhong, Chengwei; Xu, Hang; Ong, Zhiwei; Sachaphibulkij, Karishma; Chen, Ao; Zeng, Li; Fu, Huazhu; Wu, Min; Lim, Lina Hsiu Kim; Liu, Longqi; Chen, Jinmiao
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Cortical development: Layers of complexity
err1997-04-01
err48
errOAAI
errGilmore, EC; Herrup, K
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Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays
errCell
IF0
err2022-05-01
err0
errOAAI
errAo Chen; Sha Liao; Mengnan Cheng; Kailong Ma; Liang Wu; Yiwei Lai; Xiaojie Qiu; Jin Yang; Jiangshan Xu; Shijie Hao; Xin Wang; Huifang Lu; Xi Chen; Xing Liu; Xin Huang; Zhao Li; Yan Hong; Yujia Jiang; Jian Peng; Shuai Liu; Mengzhe Shen; Chuanyu Liu; Quanshui Li; Yue Yuan; Xiaoyu Wei; Huiwen Zheng; Weimin Feng; Zhifeng Wang; Yang Liu; Zhaohui Wang; Yunzhi Yang; Haitao Xiang; Lei Han; Baoming Qin; Pengcheng Guo; Guangyao Lai; Pura Muñoz-Cánoves; Patrick H. Maxwell; Jean Paul Thiery; Qing-Feng Wu; Fuxiang Zhao; Bichao Chen; Mei Li; Xi Dai; Shuai Wang; Haoyan Kuang; Junhou Hui; Liqun Wang; Ji-Feng Fei; Ou Wang; Xiaofeng Wei; Haorong Lu; Bo Wang; Shiping Liu; Ying Gu; Ming Ni; Wenwei Zhang; Feng Mu; Ye Yin; Huanming Yang; Michael Lisby; Richard J. Cornall; Jan Mulder; Mathias Uhlén; Miguel A. Esteban; Yuxiang Li; Longqi Liu; Xun Xu; Jian Wang
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Identifying multicellular spatiotemporal organization of cells with SpaceFlow
err2022-07-14
err56
errOAAI
errRen, Honglei; Walker, Benjamin L.; Cang, Zixuan; Nie, Qing
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