Results 11 to 20 of about 13,173,007 (100)

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

Nature Methods, 2023
This work presents a computational framework, COMMOT, to spatially infer cell–cell communication from transcriptomics data based on a variant of optimal transport (OT).
Zixuan Cang, Yanxiang Zhao, Axel A. Almet, Adam R. Stabell, Raul Ramos, M. Plikus, Scott X. Atwood, Qing Nie   +7 more
semanticscholar   +1 more source

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

bioRxiv, 2023
Recent advances in single-cell sequencing technologies offer an opportunity to explore cell-cell communication in tissues systematically and with reduced bias.
Suoqin Jin, M. Plikus, Qing Nie
semanticscholar   +1 more source

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

bioRxiv, 2023
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 possible to study intercellular communication on a genome- and tissue-wide scale.
Robin Browaeys, Jeroen Gilis, Chananchida Sang-aram, Pieter De Bleser, L. Hoste, S. Tavernier, D. Lambrechts, R. Seurinck, Y. Saeys   +8 more
semanticscholar   +1 more source

A Review of Single-Cell RNA-Seq Annotation, Integration, and Cell–Cell Communication

Cells, 2023
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 heterogeneity, identification of rare but significant cell types, and ...
Changde Cheng, Wenan Chen, Hongjian Jin, Xiang Chen   +3 more
semanticscholar   +1 more source

Inference and analysis of cell-cell communication using CellChat

Nature Communications, 2020
Understanding global communications among cells requires accurate representation of cell-cell signaling links and effective systems-level analyses of those links.
Suoqin Jin, C. Guerrero-Juarez, Lihua Zhang, Ivan Chang, Raul Ramos, Chen-Hsiang Kuan, P. Myung, M. Plikus, Q. Nie   +8 more
semanticscholar   +1 more source

Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data

Nature Communications, 2022
The growing availability of single-cell data, especially transcriptomics, has sparked an increased interest in the inference of cell-cell communication. Many computational tools were developed for this purpose.
Daniel Dimitrov, D. Türei, Martín Garrido-Rodriguez, Paul L Burmedi, J. Nagai, Charlotte Boys, R. O. Ramirez Flores, Hyojin Kim, B. Szalai, I. Costa, Alberto Valdeolivas, Aurélien Dugourd, J. Saez-Rodriguez   +12 more
semanticscholar   +1 more source

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

Nature Protocols, 2020
Cell–cell communication mediated by ligand–receptor complexes is critical to coordinating diverse biological processes, such as development, differentiation and inflammation.
M. Efremova, Miquel Vento-Tormo, S. Teichmann, R. Vento-Tormo   +3 more
semanticscholar   +1 more source

Insight into Extracellular Vesicle-Cell Communication: From Cell Recognition to Intracellular Fate

Cells, 2022
Extracellular vesicles (EVs) are heterogamous lipid bilayer-enclosed membranous structures secreted by cells. They are comprised of apoptotic bodies, microvesicles, and exosomes, and carry a range of nucleic acids and proteins that are necessary for cell-
Lana Ginini, S. Billan, Eran Fridman, Z. Gil   +3 more
semanticscholar   +1 more source

Context-aware deconvolution of cell–cell communication with Tensor-cell2cell

Nature Communications, 2022
Cell interactions determine phenotypes, and intercellular communication is shaped by cellular contexts such as disease state, organismal life stage, and tissue microenvironment.
Erick Armingol, Hratch M. Baghdassarian, C. Martino, A. Perez-Lopez, Caitlin M. Aamodt, R. Knight, N. Lewis   +6 more
semanticscholar   +1 more source

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

Nucleic Acids Research, 2021
With the dramatic development of single-cell RNA sequencing (scRNA-seq) technologies, the systematic decoding of cell-cell communication has received great research interest.
Yang Zhang, Tianyuan Liu, Xuesong Hu, Mei Wang, Jing Wang, Bo Zou, Puwen Tan, Tianyu Cui, Yiying Dou, Lin Ning, Yan Huang, Shuan Rao, Dong Wang, Xiaoyang Zhao   +13 more
semanticscholar   +1 more source