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Updated: Jan 2, 2026

Measuring Transcellular Interactions through Protein Aggregation in a Heterologous Cell System
Published on: May 22, 2020
NicheNet: modeling intercellular communication by linking ligands to target genes
Robin Browaeys1,2, Wouter Saelens1,2, Yvan Saeys3,4
1Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium.
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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