Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics

GS Gulati, JP D'Silva, Y Liu, L Wang… - … Reviews Molecular Cell …, 2024 - nature.com
Single-cell transcriptomics has broadened our understanding of cellular diversity and gene
expression dynamics in healthy and diseased tissues. Recently, spatial transcriptomics has …

Spatial transcriptomics: technical aspects of recent developments and their applications in neuroscience and cancer research

HE Park, SH Jo, RH Lee, CP Macks, T Ku… - Advanced …, 2023 - Wiley Online Library
Spatial transcriptomics is a newly emerging field that enables high‐throughput investigation
of the spatial localization of transcripts and related analyses in various applications for …

Integrating spatial and single-cell transcriptomics data using deep generative models with SpatialScope

X Wan, J Xiao, SST Tam, M Cai, R Sugimura… - Nature …, 2023 - nature.com
The rapid emergence of spatial transcriptomics (ST) technologies is revolutionizing our
understanding of tissue spatial architecture and biology. Although current ST methods …

High-sensitive spatially resolved T cell receptor sequencing with SPTCR-seq

JK Benotmane, J Kueckelhaus, P Will, J Zhang… - Nature …, 2023 - nature.com
Spatial resolution of the T cell repertoire is essential for deciphering cancer-associated
immune dysfunction. Current spatially resolved transcriptomic technologies are unable to …

Spatial transcriptomics deconvolution at single-cell resolution using Redeconve

Z Zhou, Y Zhong, Z Zhang, X Ren - Nature Communications, 2023 - nature.com
Computational deconvolution with single-cell RNA sequencing data as reference is pivotal
to interpreting spatial transcriptomics data, but the current methods are limited to cell-type …

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 …

A prognostic neural epigenetic signature in high-grade glioma

R Drexler, R Khatri, T Sauvigny, M Mohme, CL Maire… - Nature Medicine, 2024 - nature.com
Neural–tumor interactions drive glioma growth as evidenced in preclinical models, but
clinical validation is limited. We present an epigenetically defined neural signature of …

STellaris: a web server for accurate spatial mapping of single cells based on spatial transcriptomics data

X Li, C Xiao, J Qi, W Xue, X Xu, Z Mu… - Nucleic acids …, 2023 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) provides insights into gene expression
heterogeneities in diverse cell types underlying homeostasis, development and pathological …

Principled and interpretable alignability testing and integration of single-cell data

R Ma, ED Sun, D Donoho, J Zou - Proceedings of the …, 2024 - National Acad Sciences
Single-cell data integration can provide a comprehensive molecular view of cells, and many
algorithms have been developed to remove unwanted technical or biological variations and …

Spatial transcriptomics in development and disease

R Zhou, G Yang, Y Zhang, Y Wang - Molecular Biomedicine, 2023 - Springer
The proper functioning of diverse biological systems depends on the spatial organization of
their cells, a critical factor for biological processes like shaping intricate tissue functions and …