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prof. dr. ir. A. van Oudenaarden

prof. dr. ir. A. van Oudenaarden

Full Professor
  • Molecular Cancer Research

Research Programs

Cancer

Side Activities

  • Director of the Hubrecht Institute
  • Professor of Quantitative Biology of Gene Regulations at the University Medical Center Utrecht and at Utrecht University
  • Member of the Koninklijke Hollandsche Maatschappij der Wetenschappen (KHMW)
  • Member of the Royal Netherlands Academy of Arts and Sciences (KNAW)
  • Member of the organizing committee of Single Cell Genomics (yearly conference)
  • Member of the advisory board of Single Cell Discoveries B.V.
  • Member of the national scientific advisory board of The Netherlands Cancer Institute (NKI)
  • Member of the advisory editorial board of Molecular Systems Biology
  • Member of the scientific advisory board at the Whitehead Institute for Biomedical Research
  • Member of the American Academy of Arts and Sciences as from 2022

Research Output (126)

SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors

Liu Ning Qing, Paassen Irene, Custers Lars, Zeller Peter, Teunissen Hans, Ayyildiz Dilara, He Jiayou, Buhl Juliane Laura, Hoving Eelco Wieger, van Oudenaarden Alexander, de Wit Elzo, Drost Jarno Dec 2023, In: Nature Communications. 14 14 p.

Embryo-uterine interaction coordinates mouse embryogenesis during implantation

Bondarenko Vladyslav, Nikolaev Mikhail, Kromm Dimitri, Belousov Roman, Wolny Adrian, Blotenburg Marloes, Zeller Peter, Rezakhani Saba, Hugger Johannes, Uhlmann Virginie, Hufnagel Lars, Kreshuk Anna, Ellenberg Jan, van Oudenaarden Alexander, Erzberger Anna, Lutolf Matthias P., Hiiragi Takashi 4 Sep 2023, In: EMBO Journal. 42 , p. 1-24 24 p.

Transcription factor induction of vascular blood stem cell niches in vivo

Hagedorn Elliott J., Perlin Julie R., Freeman Rebecca J., Wattrus Samuel J., Han Tianxiao, Mao Clara, Kim Ji Wook, Fernández-Maestre Inés, Daily Madeleine L., D'Amato Christopher, Fairchild Michael J., Riquelme Raquel, Li Brian, Ragoonanan Dana A.V.E., Enkhbayar Khaliun, Henault Emily L., Wang Helen G., Redfield Shelby E., Collins Samantha H., Lichtig Asher, Yang Song, Zhou Yi, Kunar Balvir, Gomez-Salinero Jesus Maria, Dinh Thanh T., Pan Junliang, Holler Karoline, Feldman Henry A., Butcher Eugene C., van Oudenaarden Alexander, Rafii Shahin, Junker J. Philipp, Zon Leonard I. 19 Jun 2023, In: Developmental Cell. 58 , p. 1037-1051.e4

Spatial transcriptomics unveils ZBTB11 as a regulator of cardiomyocyte degeneration in arrhythmogenic cardiomyopathy

Boogerd Cornelis J, Lacraz Grégory P A, Vértesy Ábel, van Kampen Sebastiaan J, Perini Ilaria, de Ruiter Hesther, Versteeg Danielle, Brodehl Andreas, van der Kraak Petra, Giacca Mauro, de Jonge Nicolaas, Junker Jan Philipp, van Oudenaarden Alexander, Vink Aryan, van Rooij Eva 31 Mar 2023, In: Cardiovascular research. 119 , p. 477-491 15 p.

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

Yeung Jake, Florescu Maria, Zeller Peter, de Barbanson Buys Anton, Wellenstein Max D., van Oudenaarden Alexander 2023, In: Nature Biotechnology. 41 , p. 813-823 11 p.

Epiblast inducers capture mouse trophectoderm stem cells in vitro and pattern blastoids for implantation in utero

Seong Jinwoo, Frias-Aldeguer Javier, Holzmann Viktoria, Kagawa Harunobu, Sestini Giovanni, Heidari Khoei Heidar, Scholte Op Reimer Yvonne, Kip Maarten, Pradhan Saurabh J., Verwegen Lucas, Vivié Judith, Li Linfeng, Alemany Anna, Korving Jeroen, Darmis Frank, van Oudenaarden Alexander, ten Berge Derk, Geijsen Niels, Rivron Nicolas C. 7 Jul 2022, In: Cell stem cell. 29 , p. 1102-1118.e8

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

van Leeuwen Wessel, VanInsberghe Michael, Battich Nico, Salmén Fredrik, van Oudenaarden Alexander, Rabouille Catherine 20 Jun 2022, In: Cell reports methods. 2

BMP gradient along the intestinal villus axis controls zonated enterocyte and goblet cell states

Beumer Joep, Puschhof Jens, Yengej Fjodor Yousef, Zhao Lianzheng, Martinez-Silgado Adriana, Blotenburg Marloes, Begthel Harry, Boot Charelle, van Oudenaarden Alexander, Chen Ye Guang, Clevers Hans 1 Mar 2022, In: Cell Reports. 38

Differential Survival and Therapy Benefit of Patients with Breast Cancer Are Characterized by Distinct Epithelial and Immune Cell Microenvironments

Kester Lennart, Seinstra Danielle, van Rossum Annelot G.J., Vennin Claire, Hoogstraat Marlous, van der Velden Daphne, Opdam Mark, van Werkhoven Erik, Hahn Kerstin, Nederlof Iris, Lips Ester H., Mandjes Ingrid A.M., van Leeuwen-Stok A. Elise, Canisius Sander, van Tinteren Harm, Imholz Alex L.T., Portielje Johanneke E.A., Bos Monique E.M.M., Bakker Sandra D., Rutgers Emiel J., Horlings Hugo M., Wesseling Jelle, Voest Emile E., Wessels Lodewyk F.A., Kok Marleen, Oosterkamp Hendrika M., van Oudenaarden Alexander, Linn Sabine C., van Rheenen Jacco 1 Mar 2022, In: Clinical Cancer Research. 28 , p. 960-971 12 p.

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

Salmen Fredrik, De Jonghe Joachim, Kaminski Tomasz S., Alemany Anna, Parada Guillermo E., Verity-Legg Joe, Yanagida Ayaka, Kohler Timo N., Battich Nicholas, van den Brekel Floris, Ellermann Anna L., Arias Alfonso Martinez, Nichols Jennifer, Hemberg Martin, Hollfelder Florian, van Oudenaarden Alexander 2022, In: Nature Biotechnology. 40 , p. 1780-1793 14 p.

All research output

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