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 …

Cell segmentation in imaging-based spatial transcriptomics

V Petukhov, RJ Xu, RA Soldatov, P Cadinu… - Nature …, 2022 - nature.com
Single-molecule spatial transcriptomics protocols based on in situ sequencing or
multiplexed RNA fluorescent hybridization can reveal detailed tissue organization. However …

ClusterMap for multi-scale clustering analysis of spatial gene expression

Y He, X Tang, J Huang, J Ren, H Zhou, K Chen… - Nature …, 2021 - nature.com
Quantifying RNAs in their spatial context is crucial to understanding gene expression and
regulation in complex tissues. In situ transcriptomic methods generate spatially resolved …

Spatial charting of single-cell transcriptomes in tissues

R Wei, S He, S Bai, E Sei, M Hu, A Thompson… - Nature …, 2022 - nature.com
Single-cell RNA sequencing methods can profile the transcriptomes of single cells but
cannot preserve spatial information. Conversely, spatial transcriptomics assays can profile …

[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 …

Leveraging spatial transcriptomics data to recover cell locations in single-cell RNA-seq with CeLEry

Q Zhang, S Jiang, A Schroeder, J Hu, K Li… - Nature …, 2023 - nature.com
Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular
heterogeneity in health and disease. However, the lack of physical relationships among …

Integration of whole transcriptome spatial profiling with protein markers

N Ben-Chetrit, X Niu, AD Swett, J Sotelo, MS Jiao… - Nature …, 2023 - nature.com
Spatial transcriptomics and proteomics provide complementary information that
independently transformed our understanding of complex biological processes. However …

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

SG Rodriques, RR Stickels, A Goeva, CA Martin… - Science, 2019 - science.org
Spatial positions of cells in tissues strongly influence function, yet a high-throughput,
genome-wide readout of gene expression with cellular resolution is lacking. We developed …

Placing RNA in context and space–methods for spatially resolved transcriptomics

C Strell, MM Hilscher, N Laxman, J Svedlund… - The FEBS …, 2019 - Wiley Online Library
Single‐cell transcriptomics provides us with completely new insights into the molecular
diversity of different cell types and the different states they can adopt. The technique …

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 …