A comparison of single-cell trajectory inference methods
Saelens, Wouter, Cannoodt, Robrecht, Todorov, Helena, Saeys, Yvan
Published in Nature biotechnology (01.05.2019)
Published in Nature biotechnology (01.05.2019)
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Journal Article
Trajectory-based differential expression analysis for single-cell sequencing data
Van den Berge, Koen, Roux de Bézieux, Hector, Street, Kelly, Saelens, Wouter, Cannoodt, Robrecht, Saeys, Yvan, Dudoit, Sandrine, Clement, Lieven
Published in Nature communications (05.03.2020)
Published in Nature communications (05.03.2020)
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Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells
Cannoodt, Robrecht, Saelens, Wouter, Deconinck, Louise, Saeys, Yvan
Published in Nature communications (24.06.2021)
Published in Nature communications (24.06.2021)
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Journal Article
A scalable SCENIC workflow for single-cell gene regulatory network analysis
Van de Sande, Bram, Flerin, Christopher, Davie, Kristofer, De Waegeneer, Maxime, Hulselmans, Gert, Aibar, Sara, Seurinck, Ruth, Saelens, Wouter, Cannoodt, Robrecht, Rouchon, Quentin, Verbeiren, Toni, De Maeyer, Dries, Reumers, Joke, Saeys, Yvan, Aerts, Stein
Published in Nature protocols (01.07.2020)
Published in Nature protocols (01.07.2020)
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Journal Article
Computational methods for trajectory inference from single‐cell transcriptomics
Cannoodt, Robrecht, Saelens, Wouter, Saeys, Yvan
Published in European journal of immunology (01.11.2016)
Published in European journal of immunology (01.11.2016)
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Journal Article
Computational flow cytometry: helping to make sense of high-dimensional immunology data
Saeys, Yvan, Van Gassen, Sofie, Lambrecht, Bart N
Published in Nature reviews. Immunology (01.07.2016)
Published in Nature reviews. Immunology (01.07.2016)
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Journal Article
A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment
Van Hove, Hannah, Martens, Liesbet, Scheyltjens, Isabelle, De Vlaminck, Karen, Pombo Antunes, Ana Rita, De Prijck, Sofie, Vandamme, Niels, De Schepper, Sebastiaan, Van Isterdael, Gert, Scott, Charlotte L, Aerts, Jeroen, Berx, Geert, Boeckxstaens, Guy E, Vandenbroucke, Roosmarijn E, Vereecke, Lars, Moechars, Diederik, Guilliams, Martin, Van Ginderachter, Jo A, Saeys, Yvan, Movahedi, Kiavash
Published in Nature neuroscience (01.06.2019)
Published in Nature neuroscience (01.06.2019)
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Analyzing high-dimensional cytometry data using FlowSOM
Quintelier, Katrien, Couckuyt, Artuur, Emmaneel, Annelies, Aerts, Joachim, Saeys, Yvan, Van Gassen, Sofie
Published in Nature protocols (01.08.2021)
Published in Nature protocols (01.08.2021)
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Journal Article
Evolution and diversity of cadherins and catenins
Gul, Ismail Sahin, Hulpiau, Paco, Saeys, Yvan, van Roy, Frans
Published in Experimental cell research (01.09.2017)
Published in Experimental cell research (01.09.2017)
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Journal Article
Targeting ferroptosis protects against experimental (multi)organ dysfunction and death
Van Coillie, Samya, Van San, Emily, Goetschalckx, Ines, Wiernicki, Bartosz, Mukhopadhyay, Banibrata, Tonnus, Wulf, Choi, Sze Men, Roelandt, Ria, Dumitrascu, Catalina, Lamberts, Ludwig, Dams, Geert, Weyts, Wannes, Huysentruyt, Jelle, Hassannia, Behrouz, Ingold, Irina, Lele, Suhas, Meyer, Evelyne, Berg, Maya, Seurinck, Ruth, Saeys, Yvan, Vermeulen, An, van Nuijs, Alexander L N, Conrad, Marcus, Linkermann, Andreas, Rajapurkar, Mohan, Vandenabeele, Peter, Hoste, Eric, Augustyns, Koen, Vanden Berghe, Tom
Published in Nature communications (24.02.2022)
Published in Nature communications (24.02.2022)
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches
Guilliams, Martin, Bonnardel, Johnny, Haest, Birthe, Vanderborght, Bart, Wagner, Camille, Remmerie, Anneleen, Bujko, Anna, Martens, Liesbet, Thoné, Tinne, Browaeys, Robin, De Ponti, Federico F., Vanneste, Bavo, Zwicker, Christian, Svedberg, Freya R., Vanhalewyn, Tineke, Gonçalves, Amanda, Lippens, Saskia, Devriendt, Bert, Cox, Eric, Ferrero, Giuliano, Wittamer, Valerie, Willaert, Andy, Kaptein, Suzanne J.F., Neyts, Johan, Dallmeier, Kai, Geldhof, Peter, Casaert, Stijn, Deplancke, Bart, ten Dijke, Peter, Hoorens, Anne, Vanlander, Aude, Berrevoet, Frederik, Van Nieuwenhove, Yves, Saeys, Yvan, Saelens, Wouter, Van Vlierberghe, Hans, Devisscher, Lindsey, Scott, Charlotte L.
Published in Cell (20.01.2022)
Published in Cell (20.01.2022)
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Profiling peripheral nerve macrophages reveals two macrophage subsets with distinct localization, transcriptome and response to injury
Ydens, Elke, Amann, Lukas, Asselbergh, Bob, Scott, Charlotte L, Martens, Liesbet, Sichien, Dorine, Mossad, Omar, Blank, Thomas, De Prijck, Sofie, Low, Donovan, Masuda, Takahiro, Saeys, Yvan, Timmerman, Vincent, Stumm, Ralf, Ginhoux, Florent, Prinz, Marco, Janssens, Sophie, Guilliams, Martin
Published in Nature neuroscience (01.05.2020)
Published in Nature neuroscience (01.05.2020)
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Journal Article
Spotless, a reproducible pipeline for benchmarking cell type deconvolution in spatial transcriptomics
Sang-Aram, Chananchida, Browaeys, Robin, Seurinck, Ruth, Saeys, Yvan
Published in eLife (24.05.2024)
Published in eLife (24.05.2024)
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Journal Article
Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver
Remmerie, Anneleen, Martens, Liesbet, Thoné, Tinne, Castoldi, Angela, Seurinck, Ruth, Pavie, Benjamin, Roels, Joris, Vanneste, Bavo, De Prijck, Sofie, Vanhockerhout, Mathias, Binte Abdul Latib, Mushida, Devisscher, Lindsey, Hoorens, Anne, Bonnardel, Johnny, Vandamme, Niels, Kremer, Anna, Borghgraef, Peter, Van Vlierberghe, Hans, Lippens, Saskia, Pearce, Edward, Saeys, Yvan, Scott, Charlotte L.
Published in Immunity (Cambridge, Mass.) (15.09.2020)
Published in Immunity (Cambridge, Mass.) (15.09.2020)
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SpliceRover: interpretable convolutional neural networks for improved splice site prediction
Zuallaert, Jasper, Godin, Fréderic, Kim, Mijung, Soete, Arne, Saeys, Yvan, De Neve, Wesley
Published in Bioinformatics (15.12.2018)
Published in Bioinformatics (15.12.2018)
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Journal Article
Advances and Opportunities in Single-Cell Transcriptomics for Plant Research
Seyfferth, Carolin, Renema, Jim, Wendrich, Jos R, Eekhout, Thomas, Seurinck, Ruth, Vandamme, Niels, Blob, Bernhard, Saeys, Yvan, Helariutta, Yrjo, Birnbaum, Kenneth D, De Rybel, Bert
Published in Annual review of plant biology (17.06.2021)
Published in Annual review of plant biology (17.06.2021)
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