[HTML][HTML] Spatially resolved transcriptomics: a comprehensive review of their technological advances, applications, and challenges

M Cheng, Y Jiang, J Xu, AFA Mentis, S Wang… - Journal of Genetics and …, 2023 - Elsevier
The ability to explore life kingdoms is largely driven by innovations and breakthroughs in
technology, from the invention of the microscope 350 years ago to the recent emergence of …

[HTML][HTML] A comprehensive overview of graph neural network-based approaches to clustering for spatial transcriptomics T. Liu et al. Overview of Spatial Transcriptomics …

T Liu, ZY Fang, Z Zhang, Y Yu, M Li, MZ Yin - Computational and Structural …, 2023 - Elsevier
Spatial transcriptomics technologies enable researchers to accurately quantify and localize
messenger ribonucleic acid (mRNA) transcripts at a high resolution while preserving their …

The covariance environment defines cellular niches for spatial inference

D Haviv, J Remšík, M Gatie, C Snopkowski… - Nature …, 2024 - nature.com
A key challenge of analyzing data from high-resolution spatial profiling technologies is to
suitably represent the features of cellular neighborhoods or niches. Here we introduce the …

Spatial transcriptomics data and analytical methods: an updated perspective

S Khan, JJ Kim - Drug Discovery Today, 2024 - Elsevier
Spatial transcriptomics (ST) is a newly emerging field that integrates high-resolution imaging
and transcriptomic data to enable the high-throughput analysis of the spatial localization of …

Spatial transcriptomics: emerging technologies in tissue gene expression profiling

A Robles-Remacho, RM Sanchez-Martin… - Analytical …, 2023 - ACS Publications
In this Perspective, we discuss the current status and advances in spatial transcriptomics
technologies, which allow high-resolution mapping of gene expression in intact cell and …

TissUUmaps 3: Improvements in interactive visualization, exploration, and quality assessment of large-scale spatial omics data

N Pielawski, A Andersson, C Avenel, A Behanova… - Heliyon, 2023 - cell.com
Background and objectives Spatially resolved techniques for exploring the molecular
landscape of tissue samples, such as spatial transcriptomics, often result in millions of data …

EAGS: efficient and adaptive Gaussian smoothing applied to high-resolved spatial transcriptomics

T Lv, Y Zhang, M Li, Q Kang, S Fang, Y Zhang… - …, 2024 - academic.oup.com
Background The emergence of high-resolved spatial transcriptomics (ST) has facilitated the
research of novel methods to investigate biological development, organism growth, and …

[HTML][HTML] VT3D: a visualization toolbox for 3D transcriptomic data

L Guo, Y Li, Y Qi, Z Huang, K Han, X Liu, X Liu… - Journal of Genetics and …, 2023 - Elsevier
Data visualization empowers researchers to communicate their results that support scientific
reasoning in an intuitive way. Three-dimension (3D) spatially resolved transcriptomic atlases …

Recent advances in understanding neuronal diversity and neural circuit complexity across different brain regions using single-cell sequencing

Y Xing, C Zan, L Liu - Frontiers in Neural Circuits, 2023 - frontiersin.org
Neural circuits are characterized as interconnecting neuron networks connected by
synapses. Some kinds of gene expression and/or functional changes of neurons and …

Spatial omics techniques and data analysis for cancer immunotherapy applications

Y Zhang, RY Lee, CW Tan, X Guo, WWY Yim… - Current Opinion in …, 2024 - Elsevier
Highlights•Spatial omics provide multi-layer molecular profiling of cancer with high
resolution.•mIHC/IF and spatial transcriptomics techniques are advancing immunotherapy.• …