The dawn of spatial omics

D Bressan, G Battistoni, GJ Hannon - Science, 2023 - science.org
Spatial omics has been widely heralded as the new frontier in life sciences. This term
encompasses a wide range of techniques that promise to transform many areas of biology …

The expanding vistas of spatial transcriptomics

L Tian, F Chen, EZ Macosko - Nature Biotechnology, 2023 - nature.com
The formation and maintenance of tissue integrity requires complex, coordinated activities
by thousands of genes and their encoded products. Until recently, transcript levels could …

The emerging landscape of spatial profiling technologies

JR Moffitt, E Lundberg, H Heyn - Nature Reviews Genetics, 2022 - nature.com
Improved scale, multiplexing and resolution are establishing spatial nucleic acid and protein
profiling methods as a major pillar for cellular atlas building of complex samples, from …

[HTML][HTML] What is a cell type and how to define it?

H Zeng - Cell, 2022 - cell.com
Cell types are the basic functional units of an organism. Cell types exhibit diverse
phenotypic properties at multiple levels, making them challenging to define, categorize, 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 …

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 …

Single-cell multiregion dissection of Alzheimer's disease

H Mathys, CA Boix, LA Akay, Z Xia, J Davila-Velderrain… - Nature, 2024 - nature.com
Alzheimer's disease is the leading cause of dementia worldwide, but the cellular pathways
that underlie its pathological progression across brain regions remain poorly understood …

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 …

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 …

DestVI identifies continuums of cell types in spatial transcriptomics data

R Lopez, B Li, H Keren-Shaul, P Boyeau… - Nature …, 2022 - nature.com
Most spatial transcriptomics technologies are limited by their resolution, with spot sizes
larger than that of a single cell. Although joint analysis with single-cell RNA sequencing can …