CROST: a comprehensive repository of spatial transcriptomics

G Wang, S Wu, Z Xiong, H Qu, X Fang… - Nucleic Acids …, 2024 - academic.oup.com
The development of spatial transcriptome sequencing technology has revolutionized our
comprehension of complex tissues and propelled life and health sciences into an era of …

From tissues to cell types and back: single-cell gene expression analysis of tissue architecture

X Chen, SA Teichmann, KB Meyer - Annual Review of …, 2018 - annualreviews.org
With the recent transformative developments in single-cell genomics and, in particular,
single-cell gene expression analysis, it is now possible to study tissues at the single-cell …

Concordance of MERFISH spatial transcriptomics with bulk and single-cell RNA sequencing

J Liu, V Tran, VNP Vemuri, A Byrne… - Life science …, 2023 - life-science-alliance.org
Spatial transcriptomics extends single-cell RNA sequencing (scRNA-seq) by providing
spatial context for cell type identification and analysis. Imaging-based spatial technologies …

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 …

SPACEL: deep learning-based characterization of spatial transcriptome architectures

H Xu, S Wang, M Fang, S Luo, C Chen, S Wan… - Nature …, 2023 - nature.com
Spatial transcriptomics (ST) technologies detect mRNA expression in single cells/spots
while preserving their two-dimensional (2D) spatial coordinates, allowing researchers to …

Topological and geometric analysis of cell states in single-cell transcriptomic data

T Huynh, Z Cang - Briefings in Bioinformatics, 2024 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) enables dissecting cellular heterogeneity in
tissues, resulting in numerous biological discoveries. Various computational methods have …

STRIDE: accurately decomposing and integrating spatial transcriptomics using single-cell RNA sequencing

D Sun, Z Liu, T Li, Q Wu, C Wang - Nucleic Acids Research, 2022 - academic.oup.com
The recent advances in spatial transcriptomics have brought unprecedented opportunities to
understand the cellular heterogeneity in the spatial context. However, the current limitations …

GTAD: a graph-based approach for cell spatial composition inference from integrated scRNA-seq and ST-seq data

T Zhang, Z Zhang, L Li, B Dong, G Wang… - Briefings in …, 2024 - academic.oup.com
With the emergence of spatial transcriptome sequencing (ST-seq), research now heavily
relies on the joint analysis of ST-seq and single-cell RNA sequencing (scRNA-seq) data to …

Inferring spatial and signaling relationships between cells from single cell transcriptomic data

Z Cang, Q Nie - Nature communications, 2020 - nature.com
Single-cell RNA sequencing (scRNA-seq) provides details for individual cells; however,
crucial spatial information is often lost. We present SpaOTsc, a method relying on structured …

BayesSpace enables the robust characterization of spatial gene expression architecture in tissue sections at increased resolution

E Zhao, MR Stone, X Ren, T Pulliam, P Nghiem… - bioRxiv, 2020 - biorxiv.org
Recently developed spatial gene expression technologies such as the Spatial
Transcriptomics and Visium platforms allow for comprehensive measurement of …