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 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 …

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 …

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 …

Robust mapping of spatiotemporal trajectories and cell–cell interactions in healthy and diseased tissues

D Pham, X Tan, B Balderson, J Xu, LF Grice… - Nature …, 2023 - nature.com
Spatial transcriptomics (ST) technologies generate multiple data types from biological
samples, namely gene expression, physical distance between data points, and/or tissue …

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 …

Screening cell–cell communication in spatial transcriptomics via collective optimal transport

Z Cang, Y Zhao, AA Almet, A Stabell, R Ramos… - Nature …, 2023 - nature.com
Spatial transcriptomic technologies and spatially annotated single-cell RNA sequencing
datasets provide unprecedented opportunities to dissect cell–cell communication (CCC) …

Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics

SK Longo, MG Guo, AL Ji, PA Khavari - Nature Reviews Genetics, 2021 - nature.com
Single-cell RNA sequencing (scRNA-seq) identifies cell subpopulations within tissue but
does not capture their spatial distribution nor reveal local networks of intercellular …

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 …