An introduction to spatial transcriptomics for biomedical research

CG Williams, HJ Lee, T Asatsuma, R Vento-Tormo… - Genome Medicine, 2022 - Springer
Single-cell transcriptomics (scRNA-seq) has become essential for biomedical research over
the past decade, particularly in developmental biology, cancer, immunology, and …

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 …

Advances in spatial transcriptomics and related data analysis strategies

J Du, YC Yang, ZJ An, MH Zhang, XH Fu… - Journal of Translational …, 2023 - Springer
Spatial transcriptomics technologies developed in recent years can provide various
information including tissue heterogeneity, which is fundamental in biological and medical …

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 …

SpaGE: spatial gene enhancement using scRNA-seq

T Abdelaal, S Mourragui, A Mahfouz… - Nucleic acids …, 2020 - academic.oup.com
Single-cell technologies are emerging fast due to their ability to unravel the heterogeneity of
biological systems. While scRNA-seq is a powerful tool that measures whole-transcriptome …

ST Pipeline: an automated pipeline for spatial mapping of unique transcripts

JF Navarro, J Sjöstrand, F Salmén, J Lundeberg… - …, 2017 - academic.oup.com
Motivation In recent years we have witnessed an increase in novel RNA-seq based
techniques for transcriptomics analysis. Spatial transcriptomics is a novel RNA-seq based …

Spatially resolved transcriptomics adds a new dimension to genomics

L Larsson, J Frisén, J Lundeberg - Nature methods, 2021 - nature.com
As single-cell omics continue to advance, the field of spatially resolved transcriptomics has
emerged with a set of experimental and computational methods to map out the positions of …

Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics

SK Longo, MG Guo, AL Ji, PA Khavari - Nature Reviews Genetics, 2021 - nature.com
Single-cell RNA sequencing (scRNA-seq) identifies cell subpopulations within tissue but
does not capture their spatial distribution nor reveal local networks of intercellular …

SPASCER: spatial transcriptomics annotation at single-cell resolution

Z Fan, Y Luo, H Lu, T Wang, YZ Feng… - Nucleic Acids …, 2023 - academic.oup.com
In recent years, the explosive growth of spatial technologies has enabled the
characterization of spatial heterogeneity of tissue architectures. Compared to traditional …

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 …