Museum of spatial transcriptomics

L Moses, L Pachter - Nature methods, 2022 - nature.com
The function of many biological systems, such as embryos, liver lobules, intestinal villi, and
tumors, depends on the spatial organization of their cells. In the past decade, high …

Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics

GS Gulati, JP D'Silva, Y Liu, L Wang… - … Reviews Molecular Cell …, 2024 - nature.com
Single-cell transcriptomics has broadened our understanding of cellular diversity and gene
expression dynamics in healthy and diseased tissues. Recently, spatial transcriptomics has …

A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics

H Li, J Zhou, Z Li, S Chen, X Liao, B Zhang… - Nature …, 2023 - nature.com
Spatial transcriptomics technologies are used to profile transcriptomes while preserving
spatial information, which enables high-resolution characterization of transcriptional patterns …

STalign: Alignment of spatial transcriptomics data using diffeomorphic metric mapping

K Clifton, M Anant, G Aihara, L Atta, OK Aimiuwu… - Nature …, 2023 - nature.com
Spatial transcriptomics (ST) technologies enable high throughput gene expression
characterization within thin tissue sections. However, comparing spatial observations across …

Benchmarking and integration of methods for deconvoluting spatial transcriptomic data

L Yan, X Sun - Bioinformatics, 2023 - academic.oup.com
Motivation The rapid development of spatial transcriptomics (ST) approaches has provided
new insights into understanding tissue architecture and function. However, the gene …

[HTML][HTML] Computational solutions for spatial transcriptomics

I Kleino, P Frolovaitė, T Suomi, LL Elo - Computational and structural …, 2022 - Elsevier
Transcriptome level expression data connected to the spatial organization of the cells and
molecules would allow a comprehensive understanding of how gene expression is …

In silico tissue generation and power analysis for spatial omics

EAG Baker, D Schapiro, B Dumitrascu, S Vickovic… - Nature …, 2023 - nature.com
As spatially resolved multiplex profiling of RNA and proteins becomes more prominent, it is
increasingly important to understand the statistical power available to test specific …

BayesTME: an end-to-end method for multiscale spatial transcriptional profiling of the tissue microenvironment

H Zhang, MV Hunter, J Chou, JF Quinn, M Zhou… - Cell Systems, 2023 - cell.com
Spatial variation in cellular phenotypes underlies heterogeneity in immune recognition and
response to therapy in cancer and many other diseases. Spatial transcriptomics holds the …

Spatial transcriptomics technology in cancer research

Q Yu, M Jiang, L Wu - Frontiers in Oncology, 2022 - frontiersin.org
In recent years, spatial transcriptomics (ST) technologies have developed rapidly and have
been widely used in constructing spatial tissue atlases and characterizing spatiotemporal …

FICTURE: scalable segmentation-free analysis of submicron-resolution spatial transcriptomics

Y Si, CH Lee, Y Hwang, JH Yun, W Cheng, CS Cho… - Nature …, 2024 - nature.com
Spatial transcriptomics (ST) technologies have advanced to enable transcriptome-wide
gene expression analysis at submicron resolution over large areas. However, analysis of …