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 …

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 …

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 …

Spatial components of molecular tissue biology

G Palla, DS Fischer, A Regev, FJ Theis - Nature Biotechnology, 2022 - nature.com
Methods for profiling RNA and protein expression in a spatially resolved manner are rapidly
evolving, making it possible to comprehensively characterize cells and tissues in health and …

Spatial biology of cancer evolution

Z Seferbekova, A Lomakin, LR Yates… - Nature Reviews …, 2023 - nature.com
The natural history of cancers can be understood through the lens of evolution given that the
driving forces of cancer development are mutation and selection of fitter clones. Cancer …

Squidpy: a scalable framework for spatial omics analysis

G Palla, H Spitzer, M Klein, D Fischer, AC Schaar… - Nature …, 2022 - nature.com
Spatial omics data are advancing the study of tissue organization and cellular
communication at an unprecedented scale. Flexible tools are required to store, integrate and …

Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder

K Dong, S Zhang - Nature communications, 2022 - nature.com
Recent advances in spatially resolved transcriptomics have enabled comprehensive
measurements of gene expression patterns while retaining the spatial context of the tissue …

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 …

The dawn of spatial omics

D Bressan, G Battistoni, GJ Hannon - Science, 2023 - science.org
Spatial omics has been widely heralded as the new frontier in life sciences. This term
encompasses a wide range of techniques that promise to transform many areas of biology …

Scalable in situ single-cell profiling by electrophoretic capture of mRNA using EEL FISH

LE Borm, A Mossi Albiach, CCA Mannens… - Nature …, 2023 - nature.com
Methods to spatially profile the transcriptome are dominated by a trade-off between
resolution and throughput. Here we develop a method named Enhanced ELectric …