Spatial mapping of cellular senescence: emerging challenges and opportunities

AU Gurkar, AA Gerencser, AL Mora, AC Nelson… - Nature aging, 2023 - nature.com
Cellular senescence is a well-established driver of aging and age-related diseases. There
are many challenges to mapping senescent cells in tissues such as the absence of specific …

Principles and challenges of modeling temporal and spatial omics data

B Velten, O Stegle - Nature Methods, 2023 - nature.com
Studies with temporal or spatial resolution are crucial to understand the molecular dynamics
and spatial dependencies underlying a biological process or system. With advances in high …

A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics

H Li, J Zhou, Z Li, S Chen, X Liao, B Zhang… - Nature …, 2023 - nature.com
Spatial transcriptomics technologies are used to profile transcriptomes while preserving
spatial information, which enables high-resolution characterization of transcriptional patterns …

Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST

Y Long, KS Ang, M Li, KLK Chong, R Sethi… - Nature …, 2023 - nature.com
Spatial transcriptomics technologies generate gene expression profiles with spatial context,
requiring spatially informed analysis tools for three key tasks, spatial clustering, multisample …

Inferring super-resolution tissue architecture by integrating spatial transcriptomics with histology

D Zhang, A Schroeder, H Yan, H Yang, J Hu… - Nature …, 2024 - nature.com
Spatial transcriptomics (ST) has demonstrated enormous potential for generating intricate
molecular maps of cells within tissues. Here we present iStar, a method based on …

scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics

D Song, Q Wang, G Yan, T Liu, T Sun, JJ Li - Nature Biotechnology, 2024 - nature.com
We present a statistical simulator, scDesign3, to generate realistic single-cell and spatial
omics data, including various cell states, experimental designs and feature modalities, by …

Origin, structure, and composition of the spider major ampullate silk fiber revealed by genomics, proteomics, and single-cell and spatial transcriptomics

S Sonavane, S Hassan, U Chatterjee, L Soler… - Science …, 2024 - science.org
Spiders produce nature's toughest fiber using renewable components at ambient
temperatures and with water as solvent, making it highly interesting to replicate for the …

Spatially aware dimension reduction for spatial transcriptomics

L Shang, X Zhou - Nature communications, 2022 - nature.com
Spatial transcriptomics are a collection of genomic technologies that have enabled
transcriptomic profiling on tissues with spatial localization information. Analyzing spatial …

Construction of a 3D whole organism spatial atlas by joint modelling of multiple slices with deep neural networks

G Wang, J Zhao, Y Yan, Y Wang, AR Wu… - Nature Machine …, 2023 - nature.com
Spatial transcriptomics (ST) technologies are revolutionizing the way to explore the spatial
architecture of tissues. Currently, ST data analysis is often restricted to a single two …

Tumour vasculature at single-cell resolution

X Pan, X Li, L Dong, T Liu, M Zhang, L Zhang, X Zhang… - Nature, 2024 - nature.com
Tumours can obtain nutrients and oxygen required to progress and metastasize through the
blood supply. Inducing angiogenesis involves the sprouting of established vessel beds and …