NicheNet: modeling intercellular communication by linking ligands to target genes

By Robin Browaeys, Wouter Saelens, Yvan Saeys. Nature Methods, 2019

1,738 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/6e8f733034701bcc1e958d3705b5e27fde18ed3e

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

Gene regulatory network inference in the era of single-cell multi-omics (2023, methodology): “In particular, we envision the integration of GRNs with intracellular and intercellular communication processes 195–197 into spatially aware models 198,199 .”
Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma (2020, methodology): “For NicheNet (Browaeys et al., 2019) analysis, we derived TME cell type signatures by taking the top 100 differentially expressed genes in cells isolated from tumors or normal skin, including B cells, endothelial cells, fibroblasts, Langerhans cells, plasmacytoid DCs, CD1C DCs, CLEC9A DCs, T cells, ”
Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches (2022, neutral): “Cell 185, 1–18.e1–e27, January 20, 2022 e25 ll OPEN ACCESS Please cite this article in press as: Guilliams et al., Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches, Cell (2022), https://doi.org/10.1016/j.cell.2021.12.018 Resource For the mouse analyses, ”
Best practices for single-cell analysis across modalities (2023, neutral): “3).”
The technological landscape and applications of single-cell multi-omics (2023, background): “The aforementioned single-cell multi-omics methods require dissociation of cells from their tissue and thus lose information about physical interactions within and between cells, despite several computational efforts made to infer cell–cell interactions 96,97 .”
Pan-cancer single-cell landscape of tumor-infiltrating T cells (2021, methodology): “Using those overlapped signature genes and the NicheNet algorithm (41) to find shared ligands, we found that RORC and other type17 response-related genes were potentially induced in both TH17 and Tc17 by ligands such as IL23A and IL15 (fig.”
Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution (2022, methodology): “Many analytical tools have been developed for this task, such as SpaOTsc 21 , Giotto 71 , CellChat 72 , NicheNet 73 , ICELLNET 74 , and SingleCellSignalR 75 .”
Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis (2020, neutral): “Results We used four major types of resources: (1) molecular interactions, (2) enzyme-PTM relationships, (3) protein complexes and (4) molecule annotations about function, localization and other attributes (Figure 1a).”