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 …

CellChat for systematic analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

S Jin, MV Plikus, Q Nie - BioRxiv, 2023 - biorxiv.org
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 the …

CellCommuNet: an atlas of cell–cell communication networks from single-cell RNA sequencing of human and mouse tissues in normal and disease states

Q Ma, Q Li, X Zheng, J Pan - Nucleic Acids Research, 2024 - academic.oup.com
Cell− cell communication, as a basic feature of multicellular organisms, is crucial for
maintaining the biological functions and microenvironmental homeostasis of cells, organs …

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 …

Identify, quantify and characterize cellular communication from single-cell RNA sequencing data with scSeqComm

G Baruzzo, G Cesaro, B Di Camillo - Bioinformatics, 2022 - academic.oup.com
Motivation Recently, single-cell RNA-seq (scRNA-seq) data have been used to study
cellular communication. Most bioinformatics methods infer only the intercellular signaling …

New avenues for systematically inferring cell-cell communication: through single-cell transcriptomics data

X Shao, X Lu, J Liao, H Chen, X Fan - Protein & cell, 2020 - academic.oup.com
For multicellular organisms, cell-cell communication is essential to numerous biological
processes. Drawing upon the latest development of single-cell RNA-sequencing (scRNA …

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

R Browaeys, J Gilis, C Sang-Aram, P De Bleser… - BioRxiv, 2023 - biorxiv.org
Dysregulated cell-cell communication is a hallmark of many disease phenotypes. Due to
recent advances in single-cell transcriptomics and computational approaches, it is now …

[HTML][HTML] 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 …

[HTML][HTML] Predicting cell-to-cell communication networks using NATMI

R Hou, E Denisenko, HT Ong, JA Ramilowski… - Nature …, 2020 - nature.com
Abstract Development of high throughput single-cell sequencing technologies has made it
cost-effective to profile thousands of cells from diverse samples containing multiple cell …

Deciphering ligand–receptor-mediated intercellular communication based on ensemble deep learning and the joint scoring strategy from single-cell transcriptomic …

L Peng, J Tan, W Xiong, L Zhang, Z Wang… - Computers in Biology …, 2023 - Elsevier
Background: Cell–cell communication in a tumor microenvironment is vital to tumorigenesis,
tumor progression and therapy. Intercellular communication inference helps understand …