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 …

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 …

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 …

SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network

J Hu, X Li, K Coleman, A Schroeder, N Ma, DJ Irwin… - Nature …, 2021 - nature.com
Recent advances in spatially resolved transcriptomics (SRT) technologies have enabled
comprehensive characterization of gene expression patterns in the context of 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 …

[PDF][PDF] 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 …

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 …

Single-cell Stereo-seq reveals induced progenitor cells involved in axolotl brain regeneration

X Wei, S Fu, H Li, Y Liu, S Wang, W Feng, Y Yang… - Science, 2022 - science.org
The molecular mechanism underlying brain regeneration in vertebrates remains elusive. We
performed spatial enhanced resolution omics sequencing (Stereo-seq) to capture spatially …

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 …