Deciphering tissue structure and function using spatial transcriptomics

BL Walker, Z Cang, H Ren, E Bourgain-Chang… - Communications …, 2022 - nature.com
The rapid development of spatial transcriptomics (ST) techniques has allowed the
measurement of transcriptional levels across many genes together with the spatial positions …

Computational approaches and challenges in spatial transcriptomics

S Fang, B Chen, Y Zhang, H Sun, L Liu… - Genomics …, 2023 - academic.oup.com
The development of spatial transcriptomics (ST) technologies has transformed genetic
research from a single-cell data level to a two-dimensional spatial coordinate system and …

Spatially informed cell-type deconvolution for spatial transcriptomics

Y Ma, X Zhou - Nature biotechnology, 2022 - nature.com
Many spatially resolved transcriptomic technologies do not have single-cell resolution but
measure the average gene expression for each spot from a mixture of cells of potentially …

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

K Dong, S Zhang - Nature communications, 2022 - nature.com
Recent advances in spatially resolved transcriptomics have enabled comprehensive
measurements of gene expression patterns while retaining the spatial context of the tissue …

Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST

Y Long, KS Ang, M Li, KLK Chong, R Sethi… - Nature …, 2023 - nature.com
Spatial transcriptomics technologies generate gene expression profiles with spatial context,
requiring spatially informed analysis tools for three key tasks, spatial clustering, multisample …

DeepST: identifying spatial domains in spatial transcriptomics by deep learning

C Xu, X Jin, S Wei, P Wang, M Luo, Z Xu… - Nucleic Acids …, 2022 - academic.oup.com
Recent advances in spatial transcriptomics (ST) have brought unprecedented opportunities
to understand tissue organization and function in spatial context. However, it is still …

SODB facilitates comprehensive exploration of spatial omics data

Z Yuan, W Pan, X Zhao, F Zhao, Z Xu, X Li, Y Zhao… - Nature …, 2023 - nature.com
Spatial omics technologies generate wealthy but highly complex datasets. Here we present
Spatial Omics DataBase (SODB), a web-based platform providing both rich data resources …

Identifying multicellular spatiotemporal organization of cells with SpaceFlow

H Ren, BL Walker, Z Cang, Q Nie - Nature communications, 2022 - nature.com
One major challenge in analyzing spatial transcriptomic datasets is to simultaneously
incorporate the cell transcriptome similarity and their spatial locations. Here, we introduce …

Cell clustering for spatial transcriptomics data with graph neural networks

J Li, S Chen, X Pan, Y Yuan, HB Shen - Nature Computational Science, 2022 - nature.com
Spatial transcriptomics data can provide high-throughput gene expression profiling and the
spatial structure of tissues simultaneously. Most studies have relied on only the gene …

Benchmarking spatial clustering methods with spatially resolved transcriptomics data

Z Yuan, F Zhao, S Lin, Y Zhao, J Yao, Y Cui… - Nature …, 2024 - nature.com
Spatial clustering, which shares an analogy with single-cell clustering, has expanded the
scope of tissue physiology studies from cell-centroid to structure-centroid with spatially …