The technological landscape and applications of single-cell multi-omics

A Baysoy, Z Bai, R Satija, R Fan - Nature Reviews Molecular Cell …, 2023 - nature.com
Single-cell multi-omics technologies and methods characterize cell states and activities by
simultaneously integrating various single-modality omics methods that profile the …

Decoding the tumor microenvironment with spatial technologies

LA Walsh, DF Quail - Nature Immunology, 2023 - nature.com
Visualization of the cellular heterogeneity and spatial architecture of the tumor
microenvironment (TME) is becoming increasingly important to understand mechanisms of …

[HTML][HTML] Spatial epigenome–transcriptome co-profiling of mammalian tissues

D Zhang, Y Deng, P Kukanja, E Agirre, M Bartosovic… - Nature, 2023 - nature.com
Emerging spatial technologies, including spatial transcriptomics and spatial epigenomics,
are becoming powerful tools for profiling of cellular states in the tissue context,,,–. However …

High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq

Y Liu, M DiStasio, G Su, H Asashima, A Enninful… - Nature …, 2023 - nature.com
In this study, we extended co-indexing of transcriptomes and epitopes (CITE) to the spatial
dimension and demonstrated high-plex protein and whole transcriptome co-mapping. We …

CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity

M Varrone, D Tavernari, A Santamaria-Martínez… - Nature Genetics, 2024 - nature.com
Tissues are organized in cellular niches, the composition and interactions of which can be
investigated using spatial omics technologies. However, systematic analyses of tissue …

Spatial metatranscriptomics resolves host–bacteria–fungi interactomes

S Saarenpää, O Shalev, H Ashkenazy, V Carlos… - Nature …, 2023 - nature.com
The interactions of microorganisms among themselves and with their multicellular host take
place at the microscale, forming complex networks and spatial patterns. Existing technology …

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 …

Stgnnks: identifying cell types in spatial transcriptomics data based on graph neural network, denoising auto-encoder, and k-sums clustering

L Peng, X He, X Peng, Z Li, L Zhang - Computers in Biology and Medicine, 2023 - Elsevier
Background: Spatial transcriptomics technologies fully utilize spatial location information,
tissue morphological features, and transcriptional profiles. Integrating these data can greatly …

Decoder-seq enhances mRNA capture efficiency in spatial RNA sequencing

J Cao, Z Zheng, D Sun, X Chen, R Cheng, T Lv… - Nature …, 2024 - nature.com
Spatial transcriptomics technologies with high resolution often lack high sensitivity in mRNA
detection. Here we report a dendrimeric DNA coordinate barcoding design for spatial RNA …

Enablers and challenges of spatial omics, a melting pot of technologies

T Alexandrov, J Saez‐Rodriguez… - Molecular Systems …, 2023 - embopress.org
Spatial omics has emerged as a rapidly growing and fruitful field with hundreds of
publications presenting novel methods for obtaining spatially resolved information for any …