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 …

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 …

Deep learning in spatial transcriptomics: Learning from the next next-generation sequencing

AA Heydari, SS Sindi - BioRxiv, 2022 - biorxiv.org
Spatial transcriptomics (ST) technologies are rapidly becoming the extension of single-cell
RNA sequencing (scRNAseq), holding the potential of profiling gene expression at a single …

Deep learning in spatial transcriptomics: Learning from the next next-generation sequencing

AA Heydari, SS Sindi - Biophysics Reviews, 2023 - pubs.aip.org
Spatial transcriptomics (ST) technologies are rapidly becoming the extension of single-cell
RNA sequencing (scRNAseq), holding the potential of profiling gene expression at a single …

webSCST: an interactive web application for single-cell RNA-sequencing data and spatial transcriptomic data integration

Z Zhang, F Cui, W Su, L Dou, A Xu, C Cao… - Bioinformatics, 2022 - academic.oup.com
Integrative analysis of single-cell RNA-sequencing (scRNA-seq) data with spatial data for
the same species and organ would provide each cell sample with a predictive spatial …

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 …

SPANN: annotating single-cell resolution spatial transcriptome data with scRNA-seq data

M Yuan, H Wan, Z Wang, Q Guo… - Briefings in …, 2024 - academic.oup.com
Motivation The rapid development of spatial transcriptome technologies has enabled
researchers to acquire single-cell-level spatial data at an affordable price. However …

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 …

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 …

[HTML][HTML] Recent advances in spatially resolved transcriptomics: challenges and opportunities

J Lee, M Yoo, J Choi - BMB reports, 2022 - ncbi.nlm.nih.gov
Single-cell RNA sequencing (scRNA-seq) has greatly advanced our understanding of
cellular heterogeneity by profiling individual cell transcriptomes. However, cell dissociation …