Nature Communications (Mar 2023)
Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST
- 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 Kim Lim,
- Longqi Liu,
- Jinmiao Chen
Affiliations
- Yahui Long
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove
- Kok Siong Ang
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove
- Mengwei Li
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove
- Kian Long Kelvin Chong
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove
- Raman Sethi
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove
- Chengwei Zhong
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove
- Hang Xu
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove
- Zhiwei Ong
- Neural Stem Cell Research Lab, Research Department, National Neuroscience Institute
- Karishma Sachaphibulkij
- Immunology Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore (NUS)
- Ao Chen
- BGI Research-Southwest, BGI
- Li Zeng
- Neural Stem Cell Research Lab, Research Department, National Neuroscience Institute
- Huazhu Fu
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR)
- Min Wu
- Institute for Infocomm Research (I2R), Agency for Science, Technology and Research (A*STAR)
- Lina Hsiu Kim Lim
- Immunology Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore (NUS)
- Longqi Liu
- BGI Research-ShenZhen, BGI
- Jinmiao Chen
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove
- DOI
- https://doi.org/10.1038/s41467-023-36796-3
- Journal volume & issue
-
Vol. 14,
no. 1
pp. 1 – 19
Abstract
Advances in spatial transcriptomics technologies have enabled the gene expression profiling of tissues while retaining spatial context. Here the authors present GraphST, a graph self-supervised contrastive learning method that learns informative and discriminative spot representations from spatial transcriptomics data.
