Research Explorer

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Researcher

Wouter Saelens

Publications & Research Data

Awards & Distinctions

35 Results

2026

Innate type 2 lymphocytes trigger an inflammatory switch in alveolar macrophages

Stijn VerwaerdeJean-François HastirSjoerd SchettersUrsula SmoleLeen SeysAntonio Pires da Silva BaptistaKieran EnglishMartijn SchuijsHelena Catharine AegerterKarel Van Damme et al.

A1 Journal Article in IMMUNITY

2025

ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning

Wouter SaelensOlga PushkarevBart Deplancke

A1 Journal Article in NATURE COMMUNICATIONS

Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq

Wangjie LiuWouter SaelensPernille RainerMarjan BiocaninVincent GardeuxAntoni Jakub GralakGuido van MierloAngelika GebhartJulie RusseilTingdang Liu et al.

A1 Journal Article in NATURE GENETICS

funkyheatmap : visualising data frames with mixed data types

Robrecht CannoodtLouise DeconinckArtuur CouckuytNikolay S. Markov*Luke ZappiaMalte D. LueckenMarta InterlandiYvan SaeysWouter Saelens

A2 Journal Article in JOURNAL OF OPEN SOURCE SOFTWARE

Spatially restricted and ontogenically distinct hepatic macrophages are required for tissue repair

Federico Francesco De PontiAnna BujkoZhuangzhuang LiuPaul CollinsSara SchuermansChristian MaueröderSeraja AmstelveenTinne THONELiesbet MartensJohn McKendrick et al.

A1 Journal Article in IMMUNITY

2024

A human omentum-specific mesothelial-like stromal population inhibits adipogenesis IGFBP2 secretion

Radiana FerreroPernille Yde RainerMarie RumplerJulie RusseilMagda ZacharaJoern PezoldtGuido van MierloVincent GardeuxWouter SaelensDaniel Alpern et al.

A1 Journal Article in CELL METABOLISM

Non-coding variants impact cis-regulatory coordination in a cell type-specific manner

Olga PushkarevGuido van MierloJudith Franziska KribelbauerWouter SaelensVincent GardeuxBart Deplancke

A1 Journal Article in GENOME BIOLOGY

SPArrOW : a flexible, interactive and scalable pipeline for spatial transcriptomics analysis

Lotte PollarisBavo VannesteBenjamin RombautArne DefauwFrank VernaillenJulien MortierWout VanhendenLiesbet MartensTinne ThonéJean-François Hastir et al.

The unfolded protein sensor IRE1a is essential for homeostatic dendritic cell maturation

Sophie JanssensVictor BosteelsSandra MaréchalEva ClootsLaurien Van HeddegemSimon TavernierSofie RennenClint De NolfSeraja AmstelveenJonathan Maelfait et al.

2023

Emergent dynamics of adult stem cell lineages from single nucleus and single cell RNA-Seq of Drosophila testes

Amelie A. RazGabriela S. VidaSarah R. SternSharvani MahadevarajuJaclyn M. FingerhutJennifer M. ViveirosSoumitra PalJasmine R. GreyMara R. GraceCameron W. Berry et al.

A1 Journal Article in ELIFE

2022

CD8 memory precursor cell generation is a continuous process

Helena TodorovMargaux PrieuxDaphne LaubretonMatteo BouvierShaoying WangSimon de BernardChristophe ArpinRobrecht CannoodtWouter SaelensArnaud Bonnaffoux et al.

A1 Journal Article in ISCIENCE

Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition

Johannes BuesMarjan BiocaninJoern PezoldtRiccardo DaineseAntonius ChrisnandySaba RezakhaniWouter SaelensVincent GardeuxRevant GuptaRita Sarkis et al.

A1 Journal Article in NATURE METHODS

Fly cell atlas : a single-nucleus transcriptomic atlas of the adult fruit fly

Hongjie LiJasper JanssensMaxime De WaegeneerSai Saroja KolluruKristofer DavieVincent GardeuxWouter SaelensFabrice DavidMaria BrbićKatina Spanier et al.

A1 Journal Article in SCIENCE

Live-seq enables temporal transcriptomic recording of single cells

Wanze ChenOrane Guillaume-GentilPernille Yde RainerChristoph G. GäbeleinWouter SaelensVincent GardeuxAmanda KlaegerRiccardo DaineseMagda ZacharaTomaso Zambelli et al.

A1 Journal Article in NATURE

Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches

Martin GuilliamsJohnny BonnardelBirthe HaestBart VanderborghtCamille WagnerAnneleen RemmerieAnna BujkoLiesbet MartensTinne ThonéRobin Browaeys et al.

A1 Journal Article in CELL

2021

Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells

Robrecht CannoodtWouter SaelensLouise DeconinckYvan Saeys

A1 Journal Article in NATURE COMMUNICATIONS

2020

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

Bram van de SandeChristopher FlerinKristofer DavieMaxime De WaegeneerGert HulselmansSara AibarRuth SeurinckWouter SaelensRobrecht CannoodtQuentin Rouchon et al.

A1 Journal Article in NATURE PROTOCOLS

NicheNet : modeling intercellular communication by linking ligands to target genes

Robin BrowaeysWouter SaelensYvan Saeys

A1 Journal Article in NATURE METHODS

TinGa : fast and flexible trajectory inference with Growing Neural Gas

Helena TodorovRobrecht CannoodtWouter SaelensYvan Saeys

A1 Journal Article in BIOINFORMATICS

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

Koen Van den BergeHector Roux de BézieuxKelly StreetWouter SaelensRobrecht CannoodtYvan SaeysSandrine DudoitLieven Clement

A1 Journal Article in NATURE COMMUNICATIONS

2019

A comparison of single-cell trajectory inference methods

Wouter SaelensRobrecht CannoodtHelena TodorovYvan Saeys

A1 Journal Article in NATURE BIOTECHNOLOGY

Developing and benchmarking methods for analysing transcriptomics data

Wouter SaelensYvan SaeysBart Lambrecht

Dynbenchmark : accuracy, scalability, robustness and usability of single-cell trajectory inference methods

Robrecht CannoodtWouter SaelensHelena TodorovYvan Saeys

Essential guidelines for computational method benchmarking

Lukas M WeberWouter SaelensRobrecht CannoodtCharlotte SonesonAlexander HapfelmeierPaul P GardnerAnne-Laure BoulesteixYvan SaeysMark D Robinson

A1 Journal Article in GENOME BIOLOGY

Network inference from single-cell transcriptomic data

Helena TodorovRobrecht CannoodtWouter SaelensYvan Saeys

Bookchapter in Gene regulatory networks : methods and protocols

2018

A comprehensive evaluation of module detection methods for gene expression data

Wouter SaelensRobrecht CannoodtYvan Saeys

A1 Journal Article in NATURE COMMUNICATIONS

The transcription factor ZEB2 is required to maintain the tissue-specific identities of macrophages

Charlotte ScottWouter T'JonckLiesbet MartensHelena TodorovDorine SichienBieke SoenJohnny BonnardelSofie De PrijckNiels VandammeRobrecht Cannoodt et al.

A1 Journal Article in IMMUNITY

2016

Computational methods for trajectory inference from single-cell transcriptomics

Robrecht CannoodtWouter SaelensYvan Saeys

A1 Journal Article in EUROPEAN JOURNAL OF IMMUNOLOGY

Improving marker gene discovery from high-dimensional single-cell snapshot data

Robrecht CannoodtWouter SaelensKatleen De PreterYvan Saeys

The transcription factor Zeb2 regulates development of conventional and plasmacytoid DCs by repressing Id2

Charlotte ScottBieke SoenLiesbet MartensNicolas SkrypekWouter SaelensJoachim TaminauGillian BlanckeGert Van IsterdaelDanny HuylebroeckJody Haigh et al.

A1 Journal Article in JOURNAL OF EXPERIMENTAL MEDICINE

Unbiased modelling of dynamic processes with single-cell RNA-sequencing

Robrecht CannoodtWouter SaelensKatleen De PreterYvan Saeys

Unbiased modelling of dynamic processes with single-cell RNA-sequencing

Robrecht CannoodtWouter SaelensKatleen De PreterYvan Saeys

Unbiased modelling of dynamic processes with single-cell RNA-sequencing

Robrecht CannoodtWouter SaelensKatleen De PreterYvan Saeys

Yolk sac macrophages, fetal liver, and adult monocytes can colonize an empty niche and develop into functional tissue-resident macrophages

Lianne van de LaarWouter SaelensSofie De PrijckLiesbet MartensCharlotte ScottGert Van IsterdaelEik HoffmannRudi BeyaertYvan SaeysBart Lambrecht et al.

A1 Journal Article in IMMUNITY

2015

Inferring developmental chronologies from single cell RNA

Robrecht CannoodtWouter SaelensKatleen De PreterYvan Saeys