Quantitative biology of development & stem cells
Our Focus
Living systems are built from individual cells, yet no two cells are truly identical. Even within genetically identical populations, cells differ in their molecular states, histories, and responses to their environment. This intrinsic heterogeneity underlies fundamental biological phenomena, from developmental decisions and tissue homeostasis to disease progression and treatment resistance.
Understanding biology therefore requires measurements that resolve processes at the level at which they occur: the single cell.
The van Oudenaarden lab focuses on developing novel sequencing technologies to read out biological processes in individual cells. We are interested in a wide range of mechanisms spanning the entire central dogma, including genome replication, transcription, and translation. By moving beyond population-averaged measurements, our work enables direct observation of variability, dynamics, and regulation that would otherwise remain hidden.
Our lab develops both experimental protocols and computational pipelines that make such measurements possible. By inventing new technologies and analytical frameworks, we empower researchers to perform single-cell experiments that were previously inaccessible, providing quantitative insights into how molecular processes give rise to cellular diversity and biological function.
About Alexander van Oudenaarden
Alexander van Oudenaarden
My Research
Prof. dr. ir. Alexander van Oudenaarden is director and group leader at the Hubrecht Institute (KNAW) and professor of quantitative biology of gene regulation at the Faculty of Science and the Faculty of Medicine at Utrecht University. His research group works with advanced (light) microscopy and sequencing technologies in order to study individual cells. Van Oudenaarden studied materials science and physics at Delft, where he also obtained his PhD in solid state physics. As a postdoc he worked at Stanford University collaborating with Steven Boxer and Julie Theriot. He was professor of physics and biology at the Massachusetts Institute of Technology (MIT). In 2012 he moved to the Hubrecht Institute after 15 years in the USA. His group combines techniques – in part developed by themselves – from developmental biology, molecular biology, physics, mathematics and computer science. He was awarded the 2011 and 2016 ERC Advanced Investigator grant and in 2017 van Oudenaarden won the Spinoza Award.
Awards
2017 Spinoza Award
2021, 2017,2012 ERC Advanced Grant
2022-2025 Clarivate Highly Cited Researcher (top 1%)
2022 Member of the American Academy of Arts and Sciences
2017 EMBO member
2014 KNAW member
2012 NWO VICI award
2008 Guggenheim Fellow
2008 NIH Pioneer Award
Key Publications
- 2026 Tumour-reactive heterotypic CD8 T cell clusters from clinical samples Nature 10.1038/s41586-025-09754-w
- 2025 Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance Nat Methods. 2025 Oct;22(10):2042-2051. 10.1038/s41592-025-02847-4.
- 2025 Sequencing technologies to measure translation in single cells. Nat Rev Mol Cell Biol. 2025 May;26(5):337-346 10.1038/s41580-024-00822-z
- 2025 Cytidine diphosphate diacylglycerol synthase 2 is a synthetic lethal target in mesenchymal-like cancers Nat Genet. 10.1038/s41588-025-02221-2
- 2024 Multimodal stimulation screens reveal unique and shared genes limiting T cell fitness Cancer Cell 10.1016/j.ccell.2024.02.016
- 2022 RNF31 inhibition sensitizes tumors to bystander killing by innate and adaptive immune cells Cell Rep Med. 10.1016/j.xcrm.2022.100655
- 2019 Augmenting Immunotherapy Impact by Lowering Tumor TNF Cytotoxicity Threshold Cell 10.1016/j.cell.2019.06.014
- 2018 Cooperative targeting of melanoma heterogeneity with an AXL antibody-drug conjugate and BRAF/MEK inhibitors Nat Med. 10.1038/nm.4472
Members
| Alexander van Oudenaarden Group leader | Alberto Griffa Phd Student | Amir Giladi PostDoc |
| Anna van Oudenaarden Senior researcher | Bert Jan Korte PhD Student | Björn van Sambeek Phd Student |
| Cansu Koyunlar PostDoc | Cas Blaauw Phd Student | Chih-Yao Chung PostDoc |
| Euan Joly-Smith PostDoc | Eugenio Marinelli Phd Student | Floris Leenders Technician |
| Helena Viñas Gaza PhD student | Jeroen van den Berg Postdoc | Josi Peterson Technician |
| Kseniia Sarieva PostDoc | Mees van der Ent PhD Student | Michael Vaninsberghe Post Doc |
| Nune Schelling Phd student | Widad Mammer Bouhou Technician | Alejandro Asensio López Postdoctoral Researcher |