Dissecting the Impact of Transcription Factor Dose on Cell Reprogramming Heterogeneity Using scTF-seq.
Wangjie Liu^* , Wouter Saelens^* , Pernille Rainer^* , Marjan Biočanin , Vincent Gardeux , Antoni Jakub Gralak , Guido van Mierlo , Angelika Gebhart , Julie Russeil , Tingdang Liu , Wanze Chen and Bart Deplancke.
Nature Genetics, Oct 2025.

• A high-throughput technology to study the effect of transcription factor dose.
• Applied to reprogramming, it reveals how TF dose affects cell fate heterogeneity.

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Funkyheatmap: Visualising Data Frames with Mixed Data Types.
Robrecht Cannoodt^* , Louise Deconinck^* , Artuur Couckuyt^* , Nikolay S. Markov^* , Luke Zappia , Malte D. Luecken , Marta Interlandi , Yvan Saeys^† and Wouter Saelens^†
Journal of Open Source Software, April 2025.

• A clean and easy way to make complex heatmaps in Python, R and Javascript.

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ChromatinHD Connects Single-Cell DNA Accessibility and Conformation to Gene Expression through Scale-Adaptive Machine Learning.
Wouter Saelens , Olga Pushkarev and Bart Deplancke.
Nature Communications, Jan 2025.

• A scale-adaptive machine learning method to link single-cell chromatin accessibility to gene expression.
• Outperforms peak- and window-based methods by a large margin.

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Spatial Proteogenomics Reveals Distinct and Evolutionarily Conserved Hepatic Macrophage Niches.
Martin Guilliams, Johnny Bonnardel, Birthe Haest, Bart Vanderborght, Camille Wagner, Anneleen Remmerie, Anna Bujko, Liesbet Martens, Tinne Thoné, Robin Browaeys, Federico F. De Ponti, Bavo Vanneste, Christian Zwicker, Freya R. Svedberg, Tineke Vanhalewyn, Amanda Gonçalves, Saskia Lippens, Bert Devriendt, Eric Cox, Giuliano Ferrero, Valerie Wittamer, Andy Willaert, Suzanne J. F. Kaptein, Johan Neyts, Kai Dallmeier, Peter Geldhof, Stijn Casaert, Bart Deplancke, Peter Dijke, Anne Hoorens, Aude Vanlander, Frederik Berrevoet, Yves Van Nieuwenhove, Yvan Saeys, Wouter Saelens^†, Hans Van Vlierberghe^†, Lindsey Devisscher^†, and Charlotte L. Scott^†.
Cell, Jan 2022.

• One of the first comprehensive liver cell atlases combining single-cell and spatial transcriptomics with proteomics.
• Beside being a key resource, it reveals distinct macrophage niches conserved across species.

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Spearheading Future Omics Analyses Using Dyngen, a Multi-Modal Simulator of Single Cells.
Robrecht Cannoodt^* , Wouter Saelens^* , Louise Deconinck and Yvan Saeys.
Nature Communications, Jun 2021.

• A flexible simulator for single-cell multi-omics data, useful for benchmarking computational methods.
• Builds on a detailed model of gene regulation, splicing, and translation.

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NicheNet: Modeling Intercellular Communication by Linking Ligands to Target Genes.
Robin Browaeys , Wouter Saelens^† and Yvan Saeys^†.
Nature Methods, Feb 2020.

• A widely used method to predict cell-cell communication from single-cell data.
• It uniquely not only looks at ligand-receptor pairs, which is bound to contain false-positives, but also models downstream target gene regulation to ensure the signaling is actively sensed by the cell.

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A Comparison of Single-Cell Trajectory Inference Methods.
Wouter Saelens^* , Robrecht Cannoodt^* , Helena Todorov and Yvan Saeys.
Nature Biotechnology, May 2019.

• The reference benchmark paper for single-cell trajectory inference methods.
• People love them or hate them, but everyone uses them.

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A Comprehensive Evaluation of Module Detection Methods for Gene Expression Data.
Wouter Saelens , Robrecht Cannoodt and Yvan Saeys.
Nature Communications, Mar 2018.

• Not all module detection methods are created equal: decomposition methods work best - if you can handle the more complex interpretation.

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