Publications by authors named "Wouter Saelens"

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Innate type 2 lymphocytes trigger an inflammatory switch in alveolar macrophages.
Stijn Verwaerde, Jean-François Hastir, Sjoerd T T Schetters, Ursula Smole, Leen Seys, Wouter Saelens

Immunity· December 2025

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Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq.
Wangjie Liu, Wouter Saelens, Pernille Rainer, Marjan Biočanin, Vincent Gardeux

Nat Genet· October 2025

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Spatially restricted and ontogenically distinct hepatic macrophages are required for tissue repair.
Federico F De Ponti, Anna Bujko, Zhuangzhuang Liu, Paul J Collins, Sara Schuermans, Wouter Saelens

Immunity· July 2025

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Spatially restricted and ontogenically distinct hepatic macrophages are required for tissue repair.
Federico F De Ponti, Anna Bujko, Zhuangzhuang Liu, Paul J Collins, Sara Schuermans, Wouter Saelens

Immunity· February 2025

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ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning.
Wouter Saelens, Olga Pushkarev, Bart Deplancke

Nat Commun· January 2025

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A human omentum-specific mesothelial-like stromal population inhibits adipogenesis through IGFBP2 secretion.
Radiana Ferrero, Pernille Yde Rainer, Marie Rumpler, Julie Russeil, Magda Zachara, Wouter Saelens

Cell Metab· July 2024

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Non-coding variants impact cis-regulatory coordination in a cell type-specific manner.
Olga Pushkarev, Guido van Mierlo, Judith Franziska Kribelbauer, Wouter Saelens, Vincent Gardeux

Genome Biol· July 2024

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Emergent dynamics of adult stem cell lineages from single nucleus and single cell RNA-Seq of testes.
Amelie A Raz, Gabriela S Vida, Sarah R Stern, Sharvani Mahadevaraju, Jaclyn M Fingerhut, Wouter Saelens

Elife· February 2023

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CD8 memory precursor cell generation is a continuous process.
Helena Todorov, Margaux Prieux, Daphne Laubreton, Matteo Bouvier, Shaoying Wang, Wouter Saelens

iScience· September 2022

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Live-seq enables temporal transcriptomic recording of single cells.
Wanze Chen, Orane Guillaume-Gentil, Pernille Yde Rainer, Christoph G Gäbelein, Wouter Saelens

Nature· August 2022

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Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition.
Johannes Bues, Marjan Biočanin, Joern Pezoldt, Riccardo Dainese, Antonius Chrisnandy, Wouter Saelens

Nat Methods· March 2022

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Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly.
Hongjie Li, Jasper Janssens, Maxime De Waegeneer, Sai Saroja Kolluru, Kristofer Davie, Wouter Saelens

Science· March 2022

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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
Martin Guilliams, Johnny Bonnardel, Birthe Haest, Bart Vanderborght, Camille Wagner, Wouter Saelens

Cell· January 2022

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Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells.
Robrecht Cannoodt, Wouter Saelens, Louise Deconinck, Yvan Saeys

Nat Commun· June 2021

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A scalable SCENIC workflow for single-cell gene regulatory network analysis.
Bram Van de Sande, Christopher Flerin, Kristofer Davie, Maxime De Waegeneer, Gert Hulselmans, Wouter Saelens

Nat Protoc· July 2020

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TinGa: fast and flexible trajectory inference with Growing Neural Gas.
Helena Todorov, Robrecht Cannoodt, Wouter Saelens, Yvan Saeys

Bioinformatics· July 2020

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Trajectory-based differential expression analysis for single-cell sequencing data.
Koen Van den Berge, Hector Roux de Bézieux, Kelly Street, Wouter Saelens, Robrecht Cannoodt

Nat Commun· March 2020

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NicheNet: modeling intercellular communication by linking ligands to target genes.
Robin Browaeys, Wouter Saelens, Yvan Saeys

Nat Methods· February 2020

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Network Inference from Single-Cell Transcriptomic Data.
Helena Todorov, Robrecht Cannoodt, Wouter Saelens, Yvan Saeys

Methods Mol Biol· June 2019

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Essential guidelines for computational method benchmarking.
Lukas M Weber, Wouter Saelens, Robrecht Cannoodt, Charlotte Soneson, Alexander Hapfelmeier

Genome Biol· June 2019

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A comparison of single-cell trajectory inference methods.
Wouter Saelens, Robrecht Cannoodt, Helena Todorov, Yvan Saeys

Nat Biotechnol· May 2019

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The Transcription Factor ZEB2 Is Required to Maintain the Tissue-Specific Identities of Macrophages.
Charlotte L Scott, Wouter T'Jonck, Liesbet Martens, Helena Todorov, Dorine Sichien, Wouter Saelens

Immunity· August 2018

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A comprehensive evaluation of module detection methods for gene expression data.
Wouter Saelens, Robrecht Cannoodt, Yvan Saeys

Nat Commun· March 2018

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Computational methods for trajectory inference from single-cell transcriptomics.
Robrecht Cannoodt, Wouter Saelens, Yvan Saeys

Eur J Immunol· November 2016

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The transcription factor Zeb2 regulates development of conventional and plasmacytoid DCs by repressing Id2.
Charlotte L Scott, Bieke Soen, Liesbet Martens, Nicolas Skrypek, Wouter Saelens

J Exp Med· May 2016

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