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 …

Methods and applications for single-cell and spatial multi-omics

K Vandereyken, A Sifrim, B Thienpont… - Nature Reviews Genetics, 2023 - nature.com
The joint analysis of the genome, epigenome, transcriptome, proteome and/or metabolome
from single cells is transforming our understanding of cell biology in health and disease. In …

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 …

The expanding vistas of spatial transcriptomics

L Tian, F Chen, EZ Macosko - Nature Biotechnology, 2023 - nature.com
The formation and maintenance of tissue integrity requires complex, coordinated activities
by thousands of genes and their encoded products. Until recently, transcript levels could …

Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution

B Li, W Zhang, C Guo, H Xu, L Li, M Fang, Y Hu… - Nature …, 2022 - nature.com
Spatial transcriptomics approaches have substantially advanced our capacity to detect the
spatial distribution of RNA transcripts in tissues, yet it remains challenging to characterize …

Impact of the Human Cell Atlas on medicine

JE Rood, A Maartens, A Hupalowska, SA Teichmann… - Nature medicine, 2022 - nature.com
Single-cell atlases promise to provide a 'missing link'between genes, diseases and
therapies. By identifying the specific cell types, states, programs and contexts where disease …

Spatially informed cell-type deconvolution for spatial transcriptomics

Y Ma, X Zhou - Nature biotechnology, 2022 - nature.com
Many spatially resolved transcriptomic technologies do not have single-cell resolution but
measure the average gene expression for each spot from a mixture of cells of potentially …

[HTML][HTML] Spatial profiling of chromatin accessibility in mouse and human tissues

Y Deng, M Bartosovic, S Ma, D Zhang, P Kukanja… - Nature, 2022 - nature.com
Cellular function in tissue is dependent on the local environment, requiring new methods for
spatial map** of biomolecules and cells in the tissue context. The emergence of spatial …

Exploring tissue architecture using spatial transcriptomics

A Rao, D Barkley, GS França, I Yanai - Nature, 2021 - nature.com
Deciphering the principles and mechanisms by which gene activity orchestrates complex
cellular arrangements in multicellular organisms has far-reaching implications for research …

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 …