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 emerging landscape of spatial profiling technologies

JR Moffitt, E Lundberg, H Heyn - Nature Reviews Genetics, 2022 - nature.com
Improved scale, multiplexing and resolution are establishing spatial nucleic acid and protein
profiling methods as a major pillar for cellular atlas building of complex samples, from …

Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data

D Dimitrov, D Türei, M Garrido-Rodriguez… - Nature …, 2022 - nature.com
The growing availability of single-cell data, especially transcriptomics, has sparked an
increased interest in the inference of cell-cell communication. Many computational tools …

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 …

Cell2location maps fine-grained cell types in spatial transcriptomics

V Kleshchevnikov, A Shmatko, E Dann… - Nature …, 2022 - nature.com
Spatial transcriptomic technologies promise to resolve cellular wiring diagrams of tissues in
health and disease, but comprehensive mapping of cell types in situ remains a challenge …

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] Non-cell-autonomous cancer progression from chromosomal instability

J Li, MJ Hubisz, EM Earlie, MA Duran, C Hong… - Nature, 2023 - nature.com
Chromosomal instability (CIN) is a driver of cancer metastasis,,–, yet the extent to which this
effect depends on the immune system remains unknown. Using ContactTracing—a newly …

The landscape of aging

Y Cai, W Song, J Li, Y Jing, C Liang, L Zhang… - Science China Life …, 2022 - Springer
Aging is characterized by a progressive deterioration of physiological integrity, leading to
impaired functional ability and ultimately increased susceptibility to death. It is a major risk …

Spatial profiling technologies illuminate the tumor microenvironment

O Elhanani, R Ben-Uri, L Keren - Cancer cell, 2023 - cell.com
The tumor microenvironment (TME) is composed of many different cellular and acellular
components that together drive tumor growth, invasion, metastasis, and response to …