Publications

Stephen J. Clark, Ricard Argelaguet, Tim Lohoff, Felix Krueger, Deborah Drage, Berthold Göttgens, John C. Marioni, Jennifer Nichols, Wolf Reik (2022). Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during mouse early organogenesis. Genome Biology.
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Leah U. Rosen, L. Carine Stapel, Ricard Argelaguet, Charlie George Barker, Andrian Yang, Wolf Reik, John C. Marioni (2022). Inter-gastruloid heterogeneity revealed by single cell transcriptomics time course: implications for organoid based perturbation studies. bioRxiv.
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Britta Velten, Jana M. Braunger, Ricard Argelaguet, Damien Arnol, Jakob Wirbel, Danila Bredikhin, Georg Zeller, Oliver Stegle (2022). Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO. Nature Methods.
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Ricard Argelaguet, Tim Lohoff, Jingyu Gavin Li, Asif Nakhuda, Deborah Drage, Felix Krueger, Lars Velten, Stephen J. Clark, Wolf Reik (2022). Decoding gene regulation in the mouse embryo using single-cell multi-omics. bioRxiv.
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Chantriolnt-Andreas Kapourani, Ricard Argelaguet, Guido Sanguinetti, Catalina a Vallejos (2021). scMET: Bayesian modeling of DNA methylation heterogeneity at single-cell resolution. Genome Biology.
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Bastiaan W. Haak, Ricard Argelaguet, Cormac M. Kinsella, Robert F. J. Kullberg, Jacqueline M. Lankelma, Martin Deijs, Michelle Klein, Maarten F. Jebbink, Floor Hugenholtz, Sarantos Kostidis, Martin Giera, Theodorus B. M. Hakvoort, Wouter J. De Jonge, Marcus J. Schultz, Tom Van Gool, Tom Van Der Poll, Willem M. De Vos, Lia M. Van Der Hoek, W. Joost Wiersinga (2021). Integrative Transkingdom Analysis of the Gut Microbiome in Antibiotic Perturbation and Critical Illness. mSystems.
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Ricard Argelaguet, Damien Arnol, Danila Bredikhin, Yonatan Deloro, Britta Velten, John C. Marioni, Oliver Stegle (2020). MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data. Genome Biology.
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Ricard Argelaguet, Stephen J. Clark, Hisham Mohammed, L. Carine Stapel, Christel Krueger, Chantriolnt-Andreas Kapourani, Ivan Imaz-Rosshandler, Tim Lohoff, Yunlong Xiang, Courtney W. Hanna, Sebastien Smallwood, Ximena Ibarra-Soria, Florian Buettner, Guido Sanguinetti, Wei Xie, Felix Krueger, Berthold Gottgens, Peter J. Rugg-Gunn, Gavin Kelsey, Wendy Dean, Jennifer Nichols, Oliver Stegle, John C. Marioni, Wolf Reik (2019). Multi-omics profiling of mouse gastrulation at single-cell resolution. Nature.
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Stephen J. Clark, Ricard Argelaguet, Chantriolnt-Andreas Kapourani, Thomas M. Stubbs, Heather J. Lee, Celia Alda-Catalinas, Felix Krueger, Guido Sanguinetti, Gavin Kelsey, John C. Marioni, Oliver Stegle, Wolf Reik (2018). scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells. Nature Communications.
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R. Argelaguet, B. Velten, D. Arnol, S. Dietrich, T. Zenz, J. C. Marioni, F. Buettner, W. Huber, O. Stegle (2018). Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets. Mol Syst Biol.
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