NicheNet: Modeling Intercellular Communication by Linking Ligands to Target Genes

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2019 Dec 11

PMID 31819264

Citations 712

Authors

Robin Browaeys

Wouter Saelens

Yvan Saeys

Affiliations

Soon will be listed here.

Abstract

Computational methods that model how gene expression of a cell is influenced by interacting cells are lacking. We present NicheNet (https://github.com/saeyslab/nichenetr), a method that predicts ligand-target links between interacting cells by combining their expression data with prior knowledge on signaling and gene regulatory networks. We applied NicheNet to tumor and immune cell microenvironment data and demonstrate that NicheNet can infer active ligands and their gene regulatory effects on interacting cells.

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