Radboud University

Radboud University

Our groups
Michiel Vermeulen Group

Proteomics & Chromatin biology

Radboud University
Kép

Our Focus

The main focus of our lab is to decipher (epi)genetic regulation of gene expression and cell fate in (differentiated) stem cells using integrative omics approaches. Furthermore, we use the same technology to study deregulation of gene expression in cancer. Our lab also develops new proteomics and genomics technology for cancer research, which we make available to the Oncode community.  

  

Current main research questions include:  

  

  • What are the molecular mechanisms of context-dependent oncogenes and tumour suppressors in CRC  
  • How do chromatin associated proteins synergize with transcription factors to regulate gene expression and cell fate?  

About Michiel Vermeulen

My Research

Michiel Vermeulen performed his doctoral work in the laboratory of Henk Stunnenberg at the University of Nijmegen in the Netherlands. In 2005 he joined the lab of Matthias Mann in Munich, Germany as a post-doctoral fellow. In 2009 he was appointed as assistant professor and in 2013 as associate professor at the University Medical Center Utrecht in The Netherlands. In February 2014 he was appointed as full professor at the Radboud University in Nijmegen, The Netherlands. Since February 2023 he also holds a part-time position as senior group leader at the Dutch Cancer Institute. The group currently consists of 8 PhD students, 5 post-docs and 3 technicians. Awarded grants include NWO-VIDI (2009), an ERC Starting Grant (2012), an ERC Consolidator Grant (2017) and an NWO-VICI (2021). He was elected as member of Academia Europeae in 2019 and an a member of EMBO in 2022.

Awards

  • 2008: Max Planck Institute for Biochemistry Junior Research Award.

  • 2000: Van Nieuwenhoven award for best undergraduate student in biology, University of Nijmegen

Key Publications

  1. Kliza KW, Liu Q, Roosenboom LWM, Jansen PWTC, Filippov DV, Vermeulen M. (2021) Reading ADP-ribosylation using chemical biology and interaction proteomics. Molecular cell, 81(21), 4552-4567.

  2. Santos-Barriopedro I, van Mierlo G, Vermeulen M (2021). Off-the-shelf proximity biotinylation for interaction proteomics. Nature Communications, 12(1):5015.

  3. Edupuganti RR, Geiger S, Lindeboom RGH, Shi H, Hsu PJ, Lu Z, Wang SY, Baltissen MPA, Jansen PWTC, Rossa M, Müller M, Stunnenberg HG, He C, Carell T, Vermeulen M. (2017) N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis. Nature Structural and Molecular Biology, 24(10):870-878.

  4. Zhang, X., Smits, A. H., van Tilburg, G. B., Jansen, P. W., Makowski, M. M., Ovaa, H., & Vermeulen, M. (2017). An interaction landscape of ubiquitin signaling. Molecular cell, 65(5), 941-955.

  5. Spruijt, C. G., Gnerlich, F., Smits, A. H., Pfaffeneder, T., Jansen, P. W., Bauer, C., ... & Eberl, H. C. (2013). Dynamic readers for 5-(hydroxy) methylcytosine and its oxidized derivatives. Cell, 152(5), 1146-1159.

Members

Michiel Vermeulen
Group leader		Aniek Martens      
Phd student		Aniek Verstappen    
Phd student
Balaji Srinivasan    
PostDoc		Inge De Krijger     
Postdoc		Lieke Lamers    
Technician
Margit Janssen    
PhD student		Maria-Teresa Alejo Vinogradova     
Phd student		Marijke Baltissen    
Technician
Martijn Hendriksen    
Research analyst		Suzan Stelloo    
Post Doc		 
Suzanne Weijers     
Phd student		Yunna Erika Strøm    
PhD student		 
   
Our groups
Maike Hansen Group

Single Cell Analysis, Cell Fate Decisions 

Radboud University
Kép

Our Focus

Cells are incredibly complex out-of-equilibrium systems that constantly react to changing environments in an efficient and strategic manner.  As a consequence, it is necessary for cells to make fast and accurate decisions about their functional roles to fit their needs both at short and long timescales.  Throughout the decision-making process fluctuations in protein levels– called noise– play a pivotal role.  A high amount of noise allows probabilistic decision-making and enhances fitness when cells find themselves in variable environments.  However, noise can be detrimental for commitment to cellular (fate-)decisions, requiring cells to implement strategies to minimize noise when it is unfavourable.  Due to the prevalence and importance of cellular-decision making in healthy and pathogenic cells, it is important to identify the molecular events that drive and modulate noise throughout the decision-making process.   

  

In our research, we aim to identify the molecular drivers of gene expression noise and regulatory topologies that modulate (i.e., enhance or suppress) noise.  By combining single-molecule imaging, single-cell sequencing, and time-lapse microscopy with mathematical models we aim to map the mechanisms that modulate noise and drive cellular decision-making.  We focus on the role of gene-expression noise in cell-fate decisions of embryonic stem cells and cancer cells.  

About Maike Hansen

Members

Maike Hansen
Oncode Investigator		Aafke Jonker    
Engineer		Frank Nelissen    
Engineer
Luca Wagner    
PhD Student		Martin Emmaneel    
Phd student		Meilin Yu    
PhD student
Merijn Koot    
PhD Student		Pieter Verhagen    
PhD student		Sue Griendt    
PhD Student
Xinyu Hu    
PostDoc		  
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