Exploring tissue architecture using spatial transcriptomics

A Rao, D Barkley, V Singhal, N Chou, J Lee, Y Yue, J Liu, WK Chock… - Nature …, 2024‏ - nature.com
Spatial omics data are clustered to define both cell types and tissue domains. We present
Building Aggregates with a Neighborhood Kernel and Spatial Yardstick (BANKSY), an …

Clinical and translational values of spatial transcriptomics

L Zhang, D Chen, D Song, X Liu, Y Zhang… - … and Targeted Therapy, 2022‏ - nature.com
The combination of spatial transcriptomics (ST) and single cell RNA sequencing (scRNA-
seq) acts as a pivotal component to bridge the pathological phenomes of human tissues with …

SCS: cell segmentation for high-resolution spatial transcriptomics

H Chen, D Li, Z Bar-Joseph - Nature methods, 2023‏ - nature.com
Spatial transcriptomics promises to greatly improve our understanding of tissue organization
and cell–cell interactions. While most current platforms for spatial transcriptomics only offer …

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 …

BASS: multi-scale and multi-sample analysis enables accurate cell type clustering and spatial domain detection in spatial transcriptomic studies

Z Li, X Zhou - Genome biology, 2022‏ - Springer
Spatial transcriptomic studies are reaching single-cell spatial resolution, with data often
collected from multiple tissue sections. Here, we present a computational method, BASS …

Annotation of spatially resolved single-cell data with STELLAR

M Brbić, K Cao, JW Hickey, Y Tan, MP Snyder… - Nature …, 2022‏ - nature.com
Accurate cell-type annotation from spatially resolved single cells is crucial to understand
functional spatial biology that is the basis of tissue organization. However, current …

[HTML][HTML] A guidebook of spatial transcriptomic technologies, data resources and analysis approaches

L Yue, F Liu, J Hu, P Yang, Y Wang, J Dong… - Computational and …, 2023‏ - Elsevier
Advances in transcriptomic technologies have deepened our understanding of the cellular
gene expression programs of multicellular organisms and provided a theoretical basis for …

SONAR enables cell type deconvolution with spatially weighted Poisson-Gamma model for spatial transcriptomics

Z Liu, D Wu, W Zhai, L Ma - Nature Communications, 2023‏ - nature.com
Recent advancements in spatial transcriptomic technologies have enabled the
measurement of whole transcriptome profiles with preserved spatial context. However …