The diversification of methods for studying cell–cell interactions and communication

E Armingol, HM Baghdassarian, NE Lewis - Nature Reviews Genetics, 2024 - nature.com
No cell lives in a vacuum, and the molecular interactions between cells define most
phenotypes. Transcriptomics provides rich information to infer cell–cell interactions and …

[HTML][HTML] Spatially resolved transcriptomics: a comprehensive review of their technological advances, applications, and challenges

M Cheng, Y Jiang, J Xu, AFA Mentis, S Wang… - Journal of Genetics and …, 2023 - Elsevier
The ability to explore life kingdoms is largely driven by innovations and breakthroughs in
technology, from the invention of the microscope 350 years ago to the recent emergence of …

Single-cell multi-omic and spatial profiling of human kidneys implicates the fibrotic microenvironment in kidney disease progression

A Abedini, J Levinsohn, KA Klötzer, B Dumoulin, Z Ma… - Nature Genetics, 2024 - nature.com
Kidneys are intricate three-dimensional structures in the body, yet the spatial and molecular
principles of kidney health and disease remain inadequately understood. We generated …

Deciphering cell–cell communication at single-cell resolution for spatial transcriptomics with subgraph-based graph attention network

W Yang, P Wang, S Xu, T Wang, M Luo, Y Cai… - Nature …, 2024 - nature.com
The inference of cell–cell communication (CCC) is crucial for a better understanding of
complex cellular dynamics and regulatory mechanisms in biological systems. However …

Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy

JH Chen, LT Nieman, M Spurrell, V Jorgji… - Nature …, 2024 - nature.com
The organization of immune cells in human tumors is not well understood. Immunogenic
tumors harbor spatially localized multicellular 'immunity hubs' defined by expression of the T …

Optimal transport for single-cell and spatial omics

C Bunne, G Schiebinger, A Krause, A Regev… - Nature Reviews …, 2024 - nature.com
High-throughput single-cell profiling provides an unprecedented ability to uncover the
molecular states of millions of cells. These technologies are, however, destructive to cells …

A review of single-cell RNA-Seq annotation, integration, and cell–cell communication

C Cheng, W Chen, H Jin, X Chen - Cells, 2023 - mdpi.com
Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for investigating
cellular biology at an unprecedented resolution, enabling the characterization of cellular …

Enablers and challenges of spatial omics, a melting pot of technologies

T Alexandrov, J Saez‐Rodriguez… - Molecular Systems …, 2023 - embopress.org
Spatial omics has emerged as a rapidly growing and fruitful field with hundreds of
publications presenting novel methods for obtaining spatially resolved information for any …

ESICCC as a systematic computational framework for evaluation, selection, and integration of cell-cell communication inference methods

J Luo, M Deng, X Zhang, X Sun - Genome Research, 2023 - genome.cshlp.org
Cell-cell communication (CCC) is critical for determining cell fates and functions in
multicellular organisms. With the advent of single-cell RNA-sequencing (scRNA-seq) and …

Spatially resolved analysis of pancreatic cancer identifies therapy-associated remodeling of the tumor microenvironment

C Shiau, J Cao, D Gong, MT Gregory, NJ Caldwell… - Nature Genetics, 2024 - nature.com
In combination with cell-intrinsic properties, interactions in the tumor microenvironment
modulate therapeutic response. We leveraged single-cell spatial transcriptomics to dissect …