An introduction to spatial transcriptomics for biomedical research

CG Williams, HJ Lee, T Asatsuma, R Vento-Tormo… - Genome Medicine, 2022 - Springer
Single-cell transcriptomics (scRNA-seq) has become essential for biomedical research over
the past decade, particularly in developmental biology, cancer, immunology, and …

[HTML][HTML] Exploring tissue architecture using spatial transcriptomics

A Rao, D Barkley, GS França, I Yanai - Nature, 2021 - nature.com
Deciphering the principles and mechanisms by which gene activity orchestrates complex
cellular arrangements in multicellular organisms has far-reaching implications for research …

High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis

A Janesick, R Shelansky, AD Gottscho… - Nature …, 2023 - nature.com
Single-cell and spatial technologies that profile gene expression across a whole tissue are
revolutionizing the resolution of molecular states in clinical samples. Current commercially …

[HTML][HTML] Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution

B Li, W Zhang, C Guo, H Xu, L Li, M Fang, Y Hu… - Nature …, 2022 - nature.com
Spatial transcriptomics approaches have substantially advanced our capacity to detect the
spatial distribution of RNA transcripts in tissues, yet it remains challenging to characterize …

Robust mapping of spatiotemporal trajectories and cell–cell interactions in healthy and diseased tissues

D Pham, X Tan, B Balderson, J Xu, LF Grice… - Nature …, 2023 - nature.com
Spatial transcriptomics (ST) technologies generate multiple data types from biological
samples, namely gene expression, physical distance between data points, and/or tissue …

Spatial transcriptomics of dorsal root ganglia identifies molecular signatures of human nociceptors

D Tavares-Ferreira, S Shiers, PR Ray… - Science translational …, 2022 - science.org
Nociceptors are specialized sensory neurons that detect damaging or potentially damaging
stimuli and are found in the dorsal root ganglia (DRG) and trigeminal ganglia. These …

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 …

[HTML][HTML] Astrocytes and oligodendrocytes undergo subtype-specific transcriptional changes in Alzheimer's disease

JS Sadick, MR O'Dea, P Hasel, T Dykstra, A Faustin… - Neuron, 2022 - cell.com
Resolving glial contributions to Alzheimer's disease (AD) is necessary because changes in
neuronal function, such as reduced synaptic density, altered electrophysiological properties …

[HTML][HTML] Spatial transcriptomics at subspot resolution with BayesSpace

E Zhao, MR Stone, X Ren, J Guenthoer… - Nature …, 2021 - nature.com
Recent spatial gene expression technologies enable comprehensive measurement of
transcriptomic profiles while retaining spatial context. However, existing analysis methods …

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 …