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 transcriptome analysis in plants: advances and challenges

R Shaw, X Tian, J Xu - Molecular Plant, 2021 - cell.com
The rapid and enthusiastic adoption of single-cell RNA sequencing (scRNA-seq) has
demonstrated that this technology is far more than just another way to perform transcriptome …

Spatially informed cell-type deconvolution for spatial transcriptomics

Y Ma, X Zhou - Nature biotechnology, 2022 - nature.com
Many spatially resolved transcriptomic technologies do not have single-cell resolution but
measure the average gene expression for each spot from a mixture of cells of potentially …

Spatiotemporal immune landscape of colorectal cancer liver metastasis at single-cell level

Y Wu, S Yang, J Ma, Z Chen, G Song, D Rao, Y Cheng… - Cancer discovery, 2022 - AACR
Liver metastasis, the leading cause of colorectal cancer mortality, exhibits a highly
heterogeneous and suppressive immune microenvironment. Here, we sequenced 97 …

[HTML][HTML] Spatial transcriptomics and in situ sequencing to study Alzheimer's disease

WT Chen, A Lu, K Craessaerts, B Pavie, CS Frigerio… - Cell, 2020 - cell.com
Although complex inflammatory-like alterations are observed around the amyloid plaques of
Alzheimer's disease (AD), little is known about the molecular changes and cellular …

Robust decomposition of cell type mixtures in spatial transcriptomics

DM Cable, E Murray, LS Zou, A Goeva… - Nature …, 2022 - nature.com
A limitation of spatial transcriptomics technologies is that individual measurements may
contain contributions from multiple cells, hindering the discovery of cell-type-specific spatial …

Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram

T Biancalani, G Scalia, L Buffoni, R Avasthi, Z Lu… - Nature …, 2021 - nature.com
Charting an organs' biological atlas requires us to spatially resolve the entire single-cell
transcriptome, and to relate such cellular features to the anatomical scale. Single-cell and …

Spatially aware dimension reduction for spatial transcriptomics

L Shang, X Zhou - Nature communications, 2022 - nature.com
Spatial transcriptomics are a collection of genomic technologies that have enabled
transcriptomic profiling on tissues with spatial localization information. Analyzing spatial …

DSTG: deconvoluting spatial transcriptomics data through graph-based artificial intelligence

Q Song, J Su - Briefings in bioinformatics, 2021 - academic.oup.com
Recent development of spatial transcriptomics (ST) is capable of associating spatial
information at different spots in the tissue section with RNA abundance of cells within each …

NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport

N Moriel, E Senel, N Friedman, N Rajewsky… - Nature protocols, 2021 - nature.com
Single-cell RNA-sequencing (scRNA-seq) technologies have revolutionized modern
biomedical sciences. A fundamental challenge is to incorporate spatial information to study …