Best practices for single-cell analysis across modalities

L Heumos, AC Schaar, C Lance, A Litinetskaya… - Nature Reviews …, 2023 - nature.com
Recent advances in single-cell technologies have enabled high-throughput molecular
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …

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 …

Benchmarking spatial clustering methods with spatially resolved transcriptomics data

Z Yuan, F Zhao, S Lin, Y Zhao, J Yao, Y Cui… - Nature …, 2024 - nature.com
Spatial clustering, which shares an analogy with single-cell clustering, has expanded the
scope of tissue physiology studies from cell-centroid to structure-centroid with spatially …

Spatially resolved multiomics of human cardiac niches

K Kanemaru, J Cranley, D Muraro, AMA Miranda… - Nature, 2023 - nature.com
The function of a cell is defined by its intrinsic characteristics and its niche: the tissue
microenvironment in which it dwells. Here we combine single-cell and spatial …

High resolution map** of the tumor microenvironment using integrated single-cell, spatial and in situ analysis

A Janesick, R Shelansky, AD Gottscho… - Nature …, 2023 - nature.com
Single-cell and spatial technologies that profile gene expression across a whole tissue are
revolutionizing the resolution of molecular states in clinical samples. Current commercially …

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 …

The scverse project provides a computational ecosystem for single-cell omics data analysis

I Virshup, D Bredikhin, L Heumos, G Palla… - Nature …, 2023 - nature.com
Single-cell omics technologies have enabled the creation of comprehensive cell atlases
across tissues and species and delivered key insights into the biological mechanisms …

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 …

Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics

GS Gulati, JP D'Silva, Y Liu, L Wang… - … Reviews Molecular Cell …, 2024 - nature.com
Single-cell transcriptomics has broadened our understanding of cellular diversity and gene
expression dynamics in healthy and diseased tissues. Recently, spatial transcriptomics has …

Spatial transcriptomics reveals discrete tumour microenvironments and autocrine loops within ovarian cancer subclones

E Denisenko, L de Kock, A Tan, AB Beasley… - Nature …, 2024 - nature.com
High-grade serous ovarian carcinoma (HGSOC) is genetically unstable and characterised
by the presence of subclones with distinct genotypes. Intratumoural heterogeneity is linked …