Publications

Daniel Nüst, Dirk Eddelbuettel, Dom Bennett, Robrecht Cannoodt, Dav Clark, Gergely Daroczi, Mark Edmondson, Colin Fay, Ellis Hughes, Lars Kjeldgaard, Sean Lopp, Ben Marwick, Heather Nolis, Jacqueline Nolis, Hong Ooi, Karthik Ram, Noam Ross, Lori Shepherd, Péter Sólymos, Tyson Lee Swetnam, Nitesh Turaga, Charlotte Van Petegem, Jason Williams, Craig Willis, Nan Xiao (2020). The Rockerverse: Packages and Applications for Containerisation with R. The R Journal.

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Helena Todorov, Robrecht Cannoodt, Wouter Saelens, Yvan Saeys (2020). TinGa: fast and flexible trajectory inference with Growing Neural Gas. Bioinformatics.

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Bram Van de Sande, Christopher Flerin, Kristofer Davie, Maxime De Waegeneer, Gert Hulselmans, Sara Aibar, Ruth Seurinck, Wouter Saelens, Robrecht Cannoodt, Quentin Rouchon, Toni Verbeiren, Dries De Maeyer, Joke Reumers, Yvan Saeys, Stein Aerts (2020). A scalable SCENIC workflow for single-cell gene regulatory network analysis. Nature Protocols.

DOI

Koen Van den Berge, Hector Roux de Bézieux, Kelly Street, Wouter Saelens, Robrecht Cannoodt, Yvan Saeys, Sandrine Dudoit, Lieven Clement (2020). Flexible inference of both within-lineage and between-lineage differential expression.. Nature Communications.

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Robrecht Cannoodt, Wouter Saelens, Louise Deconinck, Yvan Saeys (2020). dyngen: a multi-modal simulator for spearheading new single-cell omics analyses. bioRxiv.

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Daniel Nüst, Dirk Eddelbuettel, Dom Bennett, Robrecht Cannoodt, Dav Clark, Gergely Daroczi, Mark Edmondson, Colin Fay, Ellis Hughes, Sean Lopp, Ben Marwick, Heather Nolis, Jacqueline Nolis, Hong Ooi, Karthik Ram, Noam Ross, Lori Shepherd, Nitesh Turaga, Craig Willis, Nan Xiao, Charlotte Van Petegem (2020). The Rockerverse: Packages and Applications for Containerization with R. arXiv.

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Lucia Lorenzi, Hua-Sheng Chiu, Francisco Avila Cobos, Stephen Gross, Pieter-Jan Volders, Robrecht Cannoodt, Justine Nuytens, Katrien Vanderheyden, Jasper Anckaert, Steve Lefever, Tine Goovaerts, Thomas Birkballe Hansen, Scott Kuersten, Nele Nijs, Tom Taghon, Karim Vermaelen, Ken R. Bracke, Yvan Saeys, Tim De Meyer, Nandan Deshpande, Govardhan Anande, Ting-Wen Chen, Marc R. Wilkins, Ashwin Unnikrishnan, Katleen De Preter, Jørgen Kjems, Jan Koster, Gary P. Schroth, Jo Vandesompele, Pavel Sumazin, Pieter Mestdagh (2019). The RNA Atlas, a single nucleotide resolution map of the human transcriptome. bioRxiv.

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Lukas M. Weber, Wouter Saelens, Robrecht Cannoodt, Charlotte Soneson, Alexander Hapfelmeier, Paul P. Gardner, Anne-Laure Boulesteix, Yvan Saeys, Mark D. Robinson (2019). Essential guidelines for computational method benchmarking. Genome Biology.

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Koen Van den Berge, Hector Roux de Bézieux, Kelly Street, Wouter Saelens, Robrecht Cannoodt, Yvan Saeys, Sandrine Dudoit, Lieven Clement (2019). Trajectory-based differential expression analysis for single-cell sequencing data. bioRxiv.

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Wouter Saelens, Robrecht Cannoodt, Helena Todorov, Yvan Saeys (2019). A comparison of single-cell trajectory inference methods. Nature Biotechnology.

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Helena Todorov, Robrecht Cannoodt, Wouter Saelens, Yvan Saeys (2018). Network Inference from Single-Cell Transcriptomic Data. Methods in Molecular Biology.

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Charlotte L. Scott, Wouter T’Jonck, Liesbet Martens, Helena Todorov, Dorine Sichien, Bieke Soen, Johnny Bonnardel, Sofie De Prijck, Niels Vandamme, Robrecht Cannoodt, Wouter Saelens, Bavo Vanneste, Wendy Toussaint, Pieter De Bleser, Nozomi Takahashi, Peter Vandenabeele, Sandrine Henri, Clare Pridans, David A. Hume, Bart N. Lambrecht, Patrick De Baetselier, Simon W.F. Milling, Jo A. Van Ginderachter, Bernard Malissen, Geert Berx, Alain Beschin, Yvan Saeys, Martin Guilliams (2018). The Transcription Factor ZEB2 Is Required to Maintain the Tissue-Specific Identities of Macrophages. Immunity.

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Robrecht Cannoodt, Joeri Ruyssinck, Jan Ramon, Katleen De Preter, Yvan Saeys (2018). IncGraph: Incremental graphlet counting for topology optimisation. PLOS ONE.

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Wouter Saelens, Robrecht Cannoodt, Yvan Saeys (2018). A comprehensive evaluation of module detection methods for gene expression data. Nature Communications.

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Wouter Saelens, Robrecht Cannoodt, Helena Todorov, Yvan Saeys (2018). A comparison of single-cell trajectory inference methods: towards more accurate and robust tools. bioRxiv.

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Pauline Depuydt, Valentina Boeva, Toby D Hocking, Robrecht Cannoodt, Inge M Ambros, Peter F Ambros, Shahab Asgharzadeh, Edward F Attiyeh, Valérie Combaret, Raffaella Defferrari, Matthias Fischer, Barbara Hero, Michael D Hogarty, Meredith S Irwin, Jan Koster, Susan Kreissman, Ruth Ladenstein, Eve Lapouble, Geneviève Laureys, Wendy B London, Katia Mazzocco, Akira Nakagawara, Rosa Noguera, Miki Ohira, Julie R Park, Ulrike Pötschger, Jessica Theissen, Gian Paolo Tonini, Dominique Valteau-Couanet, Luigi Varesio, Rogier Versteeg, Frank Speleman, John M Maris, Gudrun Schleiermacher, Katleen De Preter (2018). Genomic Amplifications and Distal 6q Loss: Novel Markers for Poor Survival in High-risk Neuroblastoma Patients. JNCI: Journal of the National Cancer Institute.

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Shana Claeys, Geertrui Denecker, Robrecht Cannoodt, Candy Kumps, Kaat Durinck, Frank Speleman, Katleen De Preter (2017). Early and late effects of pharmacological ALK inhibition on the neuroblastoma transcriptome. Oncotarget.

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Robrecht Cannoodt, Wouter Saelens, Dorine Sichien, Simon Tavernier, Sophie Janssens, Martin Guilliams, Bart Lambrecht, Katleen De Preter, Yvan Saeys (2016). SCORPIUS improves trajectory inference and identifies novel modules in dendritic cell development. bioRxiv.

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Robrecht Cannoodt, Wouter Saelens, Yvan Saeys (2016). Computational methods for trajectory inference from single-cell transcriptomics. European Journal of Immunology.

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Caroline Van Cauwenbergh, Kristof Van Schil, Robrecht Cannoodt, Miriam Bauwens, Thalia Van Laethem, Sarah De Jaegere, Wouter Steyaert, Tom Sante, Björn Menten, Bart P. Leroy, Frauke Coppieters, Elfride De Baere (2016). arrEYE: a customized platform for high-resolution copy number analysis of coding and noncoding regions of known and candidate retinal dystrophy genes and retinal noncoding RNAs. Genetics in Medicine.

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Anneleen Decock, Maté Ongenaert, Robrecht Cannoodt, Kimberly Verniers, Bram De Wilde, Geneviève Laureys, Nadine Van Roy, Ana P. Berbegall, Julie Bienertova-Vasku, Nick Bown, Nathalie Clément, Valérie Combaret, Michelle Haber, Claire Hoyoux, Jayne Murray, Rosa Noguera, Gaelle Pierron, Gudrun Schleiermacher, Johannes H. Schulte, Ray L. Stallings, Deborah A. Tweddle, for the Children’s Cancer and Leukaemi Group, Katleen De Preter, Frank Speleman, Jo Vandesompele (2015). Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma. Oncotarget.

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