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

Project Information

IntScOmics

Grant agreement ID: 742225

DOI 10.3030/742225

Project closed

EC signature date 12 September 2017

Start date 1 January 2018

End date 31 December 2022

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost € 2 500 000,00

EU contribution € 2 500 000,00

Coordinated by

KONINKLIJKE NEDERLANDSE AKADEMIE VAN WETENSCHAPPEN - KNAW
Netherlands

Publications

Peer reviewed articles (15)

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

Author(s): 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.
Published in: Nature Communications, Issue 12, 2023, Page(s) 1286, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-21532-6

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

Author(s): 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.
Published in: Cell Genomics, Issue 2, 2022, Page(s) 100094, ISSN 2666-979X
Publisher: Elsevier
DOI: 10.1016/j.xgen.2022.100096

Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids

Author(s): 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
Published in: Nature, Issue 582/7812, 2020, Page(s) 405-409, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-020-2024-3

Cell Type Purification by Single-Cell Transcriptome-Trained Sorting

Author(s): Chloé S. Baron, Aditya Barve, Mauro J. Muraro, Reinier van der Linden, Gitanjali Dharmadhikari, Anna Lyubimova, Eelco J.P. de Koning, Alexander van Oudenaarden
Published in: Cell, Issue 179/2, 2019, Page(s) 527-542.e19, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2019.08.006

Sequencing metabolically labeled transcripts in single cells reveals mRNA turnover strategies

Author(s): Nico Battich, Joep Beumer, Buys de Barbanson, Lenno Krenning, Chloé S. Baron, Marvin E. Tanenbaum, Hans Clevers, Alexander van Oudenaarden
Published in: Science, Issue 367/6482, 2020, Page(s) 1151-1156, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aax3072

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

Author(s): J. Yeung, M. Florescu, P. Zeller, B.A. de Barbanson, M.D. Wellenstein, A. van Oudenaarden.
Published in: Nature Biotechnology, 2023, ISSN 1087-0156
Publisher: 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

Author(s): W. van Leeuwen, M. VanInsberghe, N. Battich, F. Salmén, A. van Oudenaarden, C. Rabouille.
Published in: Cell Rep Methods, Issue 2, 2022, Page(s) 100235, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1016/j.crmeth.2022.100235

Whole-organism clone tracing using single-cell sequencing

Author(s): Anna Alemany, Maria Florescu, Chloé S. Baron, Josi Peterson-Maduro, Alexander van Oudenaarden
Published in: Nature, Issue 556/7699, 2018, Page(s) 108-112, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/nature25969

Single-Cell Transcriptomics Meets Lineage Tracing

Author(s): Lennart Kester, Alexander van Oudenaarden
Published in: Cell Stem Cell, Issue 23/2, 2018, Page(s) 166-179, ISSN 1934-5909
Publisher: Cell Press
DOI: 10.1016/j.stem.2018.04.014

Mapping the physical network of cellular interactions

Author(s): Jean-Charles Boisset, Judith Vivié, Dominic Grün, Mauro J. Muraro, Anna Lyubimova, Alexander van Oudenaarden
Published in: Nature Methods, Issue 15/7, 2018, Page(s) 547-553, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-018-0009-z

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

Author(s): Andrea Attardi, Timothy Fulton, Maria Florescu, Gopi Shah, Leila Muresan, Martin O. Lenz, Courtney Lancaster, Jan Huisken, Alexander van Oudenaarden, Benjamin Steventon
Published in: Development, Issue 145/21, 2018, Page(s) dev166728, ISSN 0950-1991
Publisher: The Company of Biologists Ltd.
DOI: 10.1242/dev.166728

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

Author(s): 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
Published in: Nature Biotechnology. Nature Publishing Group, Issue 1, 2022, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.17863/cam.91785

Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis

Author(s): P. Zeller, J. Yeung, H. Viñas Gaza, B.A. de Barbanson, V. Bhardwaj, M. Florescu, R. van der Linden, A. van Oudenaarden.
Published in: Nature Genetics, Issue 55, 2023, Page(s) 333-345, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-022-01260-3

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

Author(s): M. VanInsberghe, J. van den Berg, A. Andersson-Rolf, H. Clevers, A. van Oudenaarden.
Published in: Nature, Issue 597, 2021, Page(s) 561-565, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-021-03887-4

An in vitro model of early anteroposterior organization during human development

Author(s): Naomi Moris, Kerim Anlas, Susanne C. van den Brink, Anna Alemany, Julia Schröder, Sabitri Ghimire, Tina Balayo, Alexander van Oudenaarden, Alfonso Martinez Arias
Published in: Nature, Issue 582/7812, 2020, Page(s) 410-415, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-020-2383-9