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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Jasmin Taubenschmid-Stowers, Maria Rostovskaya, Fátima Santos, Sebastian Ljung, Ricard Argelaguet, Felix Krueger, Jennifer Nichols, Wolf Reik (2022). 8C-like cells capture the human zygotic genome activation program in vitro.. Cell stem cell.

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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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Kelly B. Eckenrode, Dario Righelli, Marcel Ramos, Ricard Argelaguet, Christophe Vanderaa, Ludwig Geistlinger, Aedin Culhane, Laurent Gatto, Vincent Carey, Martin Morgan, Davide Risso, Levi Waldron (2021). Curated Single Cell Multimodal Landmark Datasets for R/Bioconductor. bioRxiv.

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Ricard Argelaguet, Anna S E Cuomo, Oliver Stegle, John C Marioni (2021). Computational principles and challenges in single-cell data integration. Nature Biotechnology.

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Kim-Anh Lê Cao, Al J Abadi, Emily F Davis-Marcisak, Lauren Hsu, Arshi Arora, Alexis Coullomb, Atul Deshpande, Yuzhou Feng, Pratheepa Jeganathan, Melanie Loth, Chen Meng, Wancen Mu, Vera Pancaldi, Kris Sankaran, Dario Righelli, Amrit Singh, Joshua S Sodicoff, Genevieve L Stein-O'Brien, Ayshwarya Subramanian, Joshua D Welch, Yue You, Ricard Argelaguet, Vincent J Carey, Ruben Dries, Casey S Greene, Susan Holmes, Michael I Love, Matthew E Ritchie, Guo-Cheng Yuan, Aedin C Culhane, Elana Fertig (2021). Community-wide hackathons to identify central themes in single-cell multi-omics.. Genome biology.

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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 Göttgens, 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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