Publications

Milan Malfait, Jeroen Gilis, Koen Van den Berge, Alemu Takele Assefa, Bie Verbist, Lieven Clement (2024). Strategies for addressing pseudoreplication in multi-patient scRNA-seq data. bioRXiv.

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Alexandre Segers, Jeroen Gilis, Mattias Van Heetvelde, Elfride De Baere, Lieven Clement (2023). Juggling offsets unlocks RNA-seq tools for fast scalable differential usage, aberrant splicing and expression analyses. bioRXiv.

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Jeroen Gilis, Laura Perin, Milan Malfait, Koen Van den Berge, Alemu Takele Assefa, Bie Verbist, Davide Risso, Lieven Clement (2023). Differential detection workflows for multi-sample single-cell RNA-seq data. bioRXiv.

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Robin Browaeys, Jeroen Gilis, Chananchida Sang-Aram, Pieter De Bleser, Levi Hoste, Simon J. Tavernier, Diether Lambrechts, Ruth Seurinck, Yvan Saeys (2023). MultiNicheNet; a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data. bioRXiv.

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Anthony Sonrel, Almut Luetge, Charlotte Soneson, Izaskun Mallona Gonzalez, Pierre-Luc Germain, Sergey Knyazev, Jeroen Gilis, Reto Gerber, Ruth Seurinck, Dominique Paul, Emanuel Sonder, Helena L Crowell, Imran Fanaswala, Ahmad Al Ajami, Elyas Heidari, Stephan Schmeing, Stefan Milosavljevic, Yvan Saeys, Serghei Mangul, Mark D Robinson (2023). Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability. Genome Biology.

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Jeroen Gilis, Kristoffer Vitting-Seerup, Koen Van den Berge, Lieven Clement (2022). satuRn; Scalable analysis of differential transcript usage for bulk and single-cell RNA-sequencing applications. F1000Research.

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Jeroen Gilis, Steff Taelman, Lucas Davey, Lennart Martens, Lieven Clement (2020). Pitfalls in re-analysis of observational omics studies; a post-mortem of the human pathology atlas. bioRXiv.

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