A single-cell genomics approach integrating gene expression, lineage, and physical interactions

Publicaciones

Strand-specific single-cell methylomics reveals distinct modes of DNA demethylation dynamics during early mammalian development

Autores: M. Sen, D. Mooijman, A. Chialastri, J.C. Boisset, M. Popovic, B. Heindryckx, S.M. Chuva de Sousa Lopes , S.S. Dey, A. van Oudenaarden.
Publicado en: Nature Communications, Edición 12, 2023, Página(s) 1286, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-021-21532-6

Integration of multiple lineage measurements from the same cell reconstructs parallel tumor evolution

Autores: L. Kester, B. de Barbanson, A. Lyubimova, L.T. Chen, V. van der Schrier, A. Alemany, D. Mooijman, J. Peterson-Maduro, J. Drost, J. de Ridder, A. van Oudenaarden.
Publicado en: Cell Genomics, Edición 2, 2022, Página(s) 100094, ISSN 2666-979X
Editor: Elsevier
DOI: 10.1016/j.xgen.2022.100096

Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids

Autores: Susanne C. van den Brink, Anna Alemany, Vincent van Batenburg, Naomi Moris, Marloes Blotenburg, Judith Vivié, Peter Baillie-Johnson, Jennifer Nichols, Katharina F. Sonnen, Alfonso Martinez Arias, Alexander van Oudenaarden
Publicado en: Nature, Edición 582/7812, 2020, Página(s) 405-409, ISSN 0028-0836
Editor: Nature Publishing Group
DOI: 10.1038/s41586-020-2024-3

Cell Type Purification by Single-Cell Transcriptome-Trained Sorting

Autores: Chloé S. Baron, Aditya Barve, Mauro J. Muraro, Reinier van der Linden, Gitanjali Dharmadhikari, Anna Lyubimova, Eelco J.P. de Koning, Alexander van Oudenaarden
Publicado en: Cell, Edición 179/2, 2019, Página(s) 527-542.e19, ISSN 0092-8674
Editor: Cell Press
DOI: 10.1016/j.cell.2019.08.006

Sequencing metabolically labeled transcripts in single cells reveals mRNA turnover strategies

Autores: Nico Battich, Joep Beumer, Buys de Barbanson, Lenno Krenning, Chloé S. Baron, Marvin E. Tanenbaum, Hans Clevers, Alexander van Oudenaarden
Publicado en: Science, Edición 367/6482, 2020, Página(s) 1151-1156, ISSN 0036-8075
Editor: American Association for the Advancement of Science
DOI: 10.1126/science.aax3072

scChIX-seq infers dynamic relationships between histone modifications in single cells

Autores: J. Yeung, M. Florescu, P. Zeller, B.A. de Barbanson, M.D. Wellenstein, A. van Oudenaarden.
Publicado en: Nature Biotechnology, 2023, ISSN 1087-0156
Editor: Nature Publishing Group
DOI: 10.1038/s41587-022-01560-3

Identification of the stress granule transcriptome via RNA-editing in single cells and in vivo

Autores: W. van Leeuwen, M. VanInsberghe, N. Battich, F. Salmén, A. van Oudenaarden, C. Rabouille.
Publicado en: Cell Rep Methods, Edición 2, 2022, Página(s) 100235, ISSN 1087-0156
Editor: Nature Publishing Group
DOI: 10.1016/j.crmeth.2022.100235

Whole-organism clone tracing using single-cell sequencing

Autores: Anna Alemany, Maria Florescu, Chloé S. Baron, Josi Peterson-Maduro, Alexander van Oudenaarden
Publicado en: Nature, Edición 556/7699, 2018, Página(s) 108-112, ISSN 0028-0836
Editor: Nature Publishing Group
DOI: 10.1038/nature25969

Single-Cell Transcriptomics Meets Lineage Tracing

Autores: Lennart Kester, Alexander van Oudenaarden
Publicado en: Cell Stem Cell, Edición 23/2, 2018, Página(s) 166-179, ISSN 1934-5909
Editor: Cell Press
DOI: 10.1016/j.stem.2018.04.014

Mapping the physical network of cellular interactions

Autores: Jean-Charles Boisset, Judith Vivié, Dominic Grün, Mauro J. Muraro, Anna Lyubimova, Alexander van Oudenaarden
Publicado en: Nature Methods, Edición 15/7, 2018, Página(s) 547-553, ISSN 1548-7091
Editor: Nature Publishing Group
DOI: 10.1038/s41592-018-0009-z

Neuromesodermal progenitors are a conserved source of spinal cord with divergent growth dynamics

Autores: Andrea Attardi, Timothy Fulton, Maria Florescu, Gopi Shah, Leila Muresan, Martin O. Lenz, Courtney Lancaster, Jan Huisken, Alexander van Oudenaarden, Benjamin Steventon
Publicado en: Development, Edición 145/21, 2018, Página(s) dev166728, ISSN 0950-1991
Editor: The Company of Biologists Ltd.
DOI: 10.1242/dev.166728

High-throughput total RNA sequencing in single cells using VASA-seq

Autores: Fredrik Salmen; Joachim De Jonghe; Tomasz S. Kaminski; Anna Alemany; Guillermo E. Parada; Joe Verity-Legg; Ayaka Yanagida; Timo N. Kohler; Nicholas Battich; Floris van den Brekel; Anna L. Ellermann; Alfonso Martinez Arias; Jennifer Nichols; Martin Hemberg; Florian Hollfelder; Alexander van Oudenaarden
Publicado en: Nature Biotechnology. Nature Publishing Group, Edición 1, 2022, ISSN 1087-0156
Editor: Nature Publishing Group
DOI: 10.17863/cam.91785

Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis

Autores: P. Zeller, J. Yeung, H. Viñas Gaza, B.A. de Barbanson, V. Bhardwaj, M. Florescu, R. van der Linden, A. van Oudenaarden.
Publicado en: Nature Genetics, Edición 55, 2023, Página(s) 333-345, ISSN 1061-4036
Editor: Nature Publishing Group
DOI: 10.1038/s41588-022-01260-3

Single-cell Ribo-seq reveals cell cycle-dependent translational pausing

Autores: M. VanInsberghe, J. van den Berg, A. Andersson-Rolf, H. Clevers, A. van Oudenaarden.
Publicado en: Nature, Edición 597, 2021, Página(s) 561-565, ISSN 0028-0836
Editor: Nature Publishing Group
DOI: 10.1038/s41586-021-03887-4

An in vitro model of early anteroposterior organization during human development

Autores: Naomi Moris, Kerim Anlas, Susanne C. van den Brink, Anna Alemany, Julia Schröder, Sabitri Ghimire, Tina Balayo, Alexander van Oudenaarden, Alfonso Martinez Arias
Publicado en: Nature, Edición 582/7812, 2020, Página(s) 410-415, ISSN 0028-0836
Editor: Nature Publishing Group
DOI: 10.1038/s41586-020-2383-9

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