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
- 2022–2025: Clarivate Highly Cited Researcher (Top 1%)
- 2022: Elected Member of the American Academy of Arts and Sciences
- 2021: ERC Advanced Grant
- 2017: NWO Spinoza Prize
- 2017: ERC Advanced Grant
- 2017: Elected Member of the European Molecular Biology Organization (EMBO)
- 2014: Elected Member of the Royal Netherlands Academy of Arts and Sciences (KNAW)
- 2012: ERC Advanced Grant
- 2012: NWO Vici Grant
- 2008: Guggenheim Fellowship
- 2008: NIH Director's Pioneer Award
Key Publications
- 2026 | Tumour-reactive heterotypic CD8 T cell clusters from clinical samples | Nature | View publication
- 2025 | Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance | Christoph Geisenberger et al. | Nature Methods | View publication
- 2025 | Sequencing technologies to measure translation in single cells | Michael VanInsberghe et al. | Nature Reviews Molecular Cell Biology | View publication
- 2025 | Cytidine diphosphate diacylglycerol synthase 2 is a synthetic lethal target in mesenchymal-like cancers | Nature Genetics | View publication
- 2024 | Multimodal stimulation screens reveal unique and shared genes limiting T cell fitness | Cancer Cell | View publication
- 2022 | RNF31 inhibition sensitizes tumors to bystander killing by innate and adaptive immune cells | Cell Reports Medicine | View publication
- 2019 | Augmenting Immunotherapy Impact by Lowering Tumor TNF Cytotoxicity Threshold | Cell | View publication
- 2018 | Cooperative targeting of melanoma heterogeneity with an AXL antibody-drug conjugate and BRAF/MEK inhibitors | Nature Medicine | View publication
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 |