Alexander van Oudenaarden Group

Quantitative biology of development & stem cells

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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

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
  1. 2026  Tumour-reactive heterotypic CD8 T cell clusters from clinical samples  Nature  10.1038/s41586-025-09754-w  
  2. 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.
  3. 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  
  4. 2025  Cytidine diphosphate diacylglycerol synthase 2 is a synthetic lethal target in mesenchymal-like cancers  Nat Genet.  10.1038/s41588-025-02221-2  
  5. 2024  Multimodal stimulation screens reveal unique and shared genes limiting T cell fitness  Cancer Cell  10.1016/j.ccell.2024.02.016 
  6. 2022  RNF31 inhibition sensitizes tumors to bystander killing by innate and adaptive immune cells  Cell Rep Med.  10.1016/j.xcrm.2022.100655  
  7. 2019  Augmenting Immunotherapy Impact by Lowering Tumor TNF Cytotoxicity Threshold  Cell  10.1016/j.cell.2019.06.014  
  8. 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