Statistical and computational methods for enabling the clinical and translational application of spatial transcriptomics

Peijun Wu; Xiang Zhou

doi:10.1002/ctm2.70119

Clinical and Translational Medicine ›› 2024, Vol. 14 ›› Issue (12) : e70119 DOI: 10.1002/ctm2.70119

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Statistical and computational methods for enabling the clinical and translational application of spatial transcriptomics

Peijun Wu ¹^,²
, Xiang Zhou ¹^,²^,^†

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Computational Methods / Clinical Applications / Spatial Transcriptomics / Statistical Methods

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Peijun Wu, Xiang Zhou. Statistical and computational methods for enabling the clinical and translational application of spatial transcriptomics. Clinical and Translational Medicine, 2024, 14(12): e70119 DOI:10.1002/ctm2.70119

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References

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[1]	Liu L, Chen A, Li Y, Mulder J, Heyn H, Xu X. Spatiotemporal omics for biology and medicine. Cell. 2024; 187(17): 4488-4519.

[2]	Ma Y, Zhou X. Spatially informed cell-type deconvolution for spatial transcriptomics. Nat Biotechnol. 2022; 40(9): 1349-1359.

[3]	Ma Y, Zhou X. Accurate and efficient integrative reference-informed spatial domain detection for spatial transcriptomics. Nat Methods. 2024; 21(7): 1231-1244.

[4]	Shang L, Zhou X. Spatially aware dimension reduction for spatial transcriptomics. Nat Commun. 2022; 13(1): 7203.

[5]	Shang L, Wu P, Zhou X. Statistical identification of cell type-specific spatially variable genes in spatial transcriptomics. Nat Commun. 2024. in press.

[6]	Sun S, Zhu J, Zhou X. Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies. Nat Methods. 2020; 17(2): 193-200.

[7]	Zhu J, Sun S, Zhou X. SPARK-X: non-parametric modeling enables scalable and robust detection of spatial expression patterns for large spatial transcriptomic studies. Genome Biol. 2021; 22(1): 184.

[8]	Wang X, Zhou X. ELLA: modeling subcellular spatial variation of gene expression within cells in high-resolution spatial transcriptomics. bioRxiv. 2024:2024.09.23.614515.

[9]	Li Z, Zhou X. BASS: multi-scale and multi-sample analysis enables accurate cell type clustering and spatial domain detection in spatial transcriptomic studies. Genome Biol. 2022; 23(1): 168.

[10]	Allen Institute for Brain Science, Allen Reference Atlas. Mouse Brain [brain atlas]. Available from: https://atlas.brain-map.org/2024

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2024 The Author(s). Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics.