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 …

Spatial components of molecular tissue biology

G Palla, DS Fischer, A Regev, FJ Theis - Nature Biotechnology, 2022 - nature.com
Methods for profiling RNA and protein expression in a spatially resolved manner are rapidly
evolving, making it possible to comprehensively characterize cells and tissues in health and …

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 …

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 …

Clinical and translational values of spatial transcriptomics

L Zhang, D Chen, D Song, X Liu, Y Zhang… - … and Targeted Therapy, 2022 - nature.com
The combination of spatial transcriptomics (ST) and single cell RNA sequencing (scRNA-
seq) acts as a pivotal component to bridge the pathological phenomes of human tissues with …

Deciphering cell–cell communication at single-cell resolution for spatial transcriptomics with subgraph-based graph attention network

W Yang, P Wang, S Xu, T Wang, M Luo, Y Cai… - Nature …, 2024 - nature.com
The inference of cell–cell communication (CCC) is crucial for a better understanding of
complex cellular dynamics and regulatory mechanisms in biological systems. However …

Advances in spatial transcriptomic data analysis

R Dries, J Chen, N Del Rossi, MM Khan… - Genome …, 2021 - genome.cshlp.org
Spatial transcriptomics is a rapidly growing field that promises to comprehensively
characterize tissue organization and architecture at the single-cell or subcellular resolution …

Unsupervised spatially embedded deep representation of spatial transcriptomics

H Xu, H Fu, Y Long, KS Ang, R Sethi, K Chong, M Li… - Genome Medicine, 2024 - Springer
Optimal integration of transcriptomics data and associated spatial information is essential
towards fully exploiting spatial transcriptomics to dissect tissue heterogeneity and map out …

Benchmarking and integration of methods for deconvoluting spatial transcriptomic data

L Yan, X Sun - Bioinformatics, 2023 - academic.oup.com
Motivation The rapid development of spatial transcriptomics (ST) approaches has provided
new insights into understanding tissue architecture and function. However, the gene …

A comprehensive comparison on cell-type composition inference for spatial transcriptomics data

J Chen, W Liu, T Luo, Z Yu, M Jiang… - Briefings in …, 2022 - academic.oup.com
Spatial transcriptomics (ST) technologies allow researchers to examine transcriptional
profiles along with maintained positional information. Such spatially resolved transcriptional …