NicheNet: modeling intercellular communication by linking ligands to target genes

Robin Browaeys, Wouter Saelens, Yvan Saeys

Nature Methods

BiologySignal TransductionFunctional GenomicsModeling Intercellular CommunicationEngineering +11

A comparison of single-cell trajectory inference methods

Wouter Saelens, Robrecht Cannoodt, Helena Todorov, +1

Nature Biotechnology

A scalable SCENIC workflow for single-cell gene regulatory network analysis

Bram Van de Sande, Christopher Flerin, Kristofer Davie, +12

Nature Protocols

EngineeringGeneticsGene Regulatory NetworkTrajectory AnalysisSingle Cell Sequencing +14

Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches

Martin Guilliams, Johnny Bonnardel, Birthe Haest, +35

Cell

Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly

Hongjie Li, Jasper Janssens, Maxime De Waegeneer, +153

Science

Trajectory-based differential expression analysis for single-cell sequencing data

Koen Van den Berge, Hector Roux de Bézieux, Kelly Street, +5

Nature Communications

Yolk Sac Macrophages, Fetal Liver, and Adult Monocytes Can Colonize an Empty Niche and Develop into Functional Tissue-Resident Macrophages

Lianne van de Laar, Wouter Saelens, Sofie De Prijck, +8

Immunity

InflammationMacrophage BiologyCytokineDevelopmental BiologyGranulocyte +9

A comprehensive evaluation of module detection methods for gene expression data

Wouter Saelens, Robrecht Cannoodt, Yvan Saeys

Nature Communications

The Transcription Factor ZEB2 Is Required to Maintain the Tissue-Specific Identities of Macrophages

Charlotte L. Scott, Wouter T’Jonck, Liesbet Martens, +25

Immunity

Live-seq enables temporal transcriptomic recording of single cells

Wanze Chen, Orane Guillaume‐Gentil, Pernille Yde Rainer, +9

Nature