CellChat for systematic analysis of cell–cell communication from single-cell transcriptomics

S **, MV Plikus, Q Nie - Nature Protocols, 2025 - nature.com
Recent advances in single-cell sequencing technologies offer an opportunity to explore cell–
cell communication in tissues systematically and with reduced bias. A key challenge is …

Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics

GS Gulati, JP D'Silva, Y Liu, L Wang… - … Reviews Molecular Cell …, 2024 - nature.com
Single-cell transcriptomics has broadened our understanding of cellular diversity and gene
expression dynamics in healthy and diseased tissues. Recently, spatial transcriptomics has …

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 …, 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 …

Cell–cell communication: new insights and clinical implications

J Su, Y Song, Z Zhu, X Huang, J Fan, J Qiao… - Signal Transduction and …, 2024 - nature.com
Multicellular organisms are composed of diverse cell types that must coordinate their
behaviors through communication. Cell–cell communication (CCC) is essential for growth …

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 …

Spatiotemporal omics for biology and medicine

L Liu, A Chen, Y Li, J Mulder, H Heyn, X Xu - Cell, 2024 - cell.com
The completion of the Human Genome Project has provided a foundational blueprint for
understanding human life. Nonetheless, understanding the intricate mechanisms through …

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 …

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 …

LIANA+ provides an all-in-one framework for cell–cell communication inference

D Dimitrov, PSL Schäfer, E Farr, P Rodriguez-Mier… - Nature Cell …, 2024 - nature.com
The growing availability of single-cell and spatially resolved transcriptomics has led to the
development of many approaches to infer cell–cell communication, each capturing only a …

[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 …