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

S Jin, MV Plikus, Q Nie - Nature Protocols, 2024 - 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 …

Single‐cell RNA sequencing technologies and applications: A brief overview

D Jovic, X Liang, H Zeng, L Lin, F Xu… - Clinical and …, 2022 - Wiley Online Library
Single‐cell RNA sequencing (scRNA‐seq) technology has become the state‐of‐the‐art
approach for unravelling the heterogeneity and complexity of RNA transcripts within …

Applications of single-cell RNA sequencing in drug discovery and development

B Van de Sande, JS Lee, E Mutasa-Gottgens… - Nature Reviews Drug …, 2023 - nature.com
Single-cell technologies, particularly single-cell RNA sequencing (scRNA-seq) methods,
together with associated computational tools and the growing availability of public data …

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 …

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 …

Deciphering cell–cell interactions and communication from gene expression

E Armingol, A Officer, O Harismendy… - Nature Reviews …, 2021 - nature.com
Cell–cell interactions orchestrate organismal development, homeostasis and single-cell
functions. When cells do not properly interact or improperly decode molecular messages …

Inference and analysis of cell-cell communication using CellChat

S Jin, CF Guerrero-Juarez, L Zhang, I Chang… - Nature …, 2021 - nature.com
Understanding global communications among cells requires accurate representation of cell-
cell signaling links and effective systems-level analyses of those links. We construct a …

A comparison of single-cell trajectory inference methods

W Saelens, R Cannoodt, H Todorov, Y Saeys - Nature biotechnology, 2019 - nature.com
Trajectory inference approaches analyze genome-wide omics data from thousands of single
cells and computationally infer the order of these cells along developmental trajectories …

CellCall: integrating paired ligand–receptor and transcription factor activities for cell–cell communication

Y Zhang, T Liu, X Hu, M Wang, J Wang… - Nucleic acids …, 2021 - academic.oup.com
With the dramatic development of single-cell RNA sequencing (scRNA-seq) technologies,
the systematic decoding of cell-cell communication has received great research interest. To …