I am currently researching the spatio-temporal organizing principles of megabase chromosomes as a PhD candidate in the group of Cees Dekker at the Department of Bionanoscience at the Kavli Institute of Nanoscience in Delft. I conduct experiments with bacterial DNA in microfabricated compartments that shed light on how tiny proteins and enzymes control its organization and how this, in turn, results in patterns of gene expression. By understanding different ways how a particular protein influences expression of genes, we gain information that can be used to for example develop new antibiotic compounds and build functional synthetic chromosomes from the bottom up.

We have various open student projects for bachelor and master students (including exchange) who want to do experimental wotk at the interface of biophysics, molecular biology, synthetic biology, and microfludics and nanoscience. We can further offer image analysis projects for students with previous experience in Python. Please drop me an e-mail if you are interested, I am happy to discuss and tailor project to your interests!



  • Hösli, L., Binini, N., Ferrari, K.D., Thieren, L., Looser, Z.J., Zuend, M., Zanker, H.S., Berry, S., Holub, M., Möbius, W. and Ruhwedel, T., 2022. Decoupling astrocytes in adult mice impairs synaptic plasticity and spatial learning. Cell Reports, 38(10), p.110484. (link)
  • Holub, M., Adobes-Vidal, M., Frutiger, A., Gschwend, P. M., Pratsinis, S. E., & Momotenko, D. (2020). Single-nanoparticle thermometry with a nanopipette. ACS nano, 14(6), 7358-7369. (link)
  • Fisch, P., Holub M., and Zenobi-Wong, M. “Improved Accuracy and Precision of Bioprinting through Progressive Cavity Pump-Controlled Extrusion.” Preprint. Bioengineering, January 24, 2020. (link)
  • Barrett, M., Ferrari, K., Stobart, J., Holub, M., & Weber, B. (2017). CHIPS: An Extensible Toolbox for Cellular and Hemodynamic Two-Photon Image Analysis. Neuroinformatics, Neuroinformatics, 04 October 2017. (link)
  • Hrdy, R.; Kynclova, H.; Klepacova, I.; Bartosik, M.; Neuzil, P. Portable Lock-in Amplifier-Based Electrochemical Method to Measure an Array of 64 Sensors for Point-of-Care Applications. ANALYTICAL CHEMISTRY, 2017, 86(17), 8731-8737. (link)
    • Contributed to the publication as an undergraduate researcher at CEITEC (Central European Institute of Technology)
  • Esipova T.V., Barrett M.J.P., Erlebach E., Masunov A.E., Weber B., Vinogradov S., 2019, Oxyphor 2P: A High-Performance Probe for Deep-Tissue Longitudinal Oxygen Imaging. Cell Metabolism, 29:1-9 (link)
    • Contributed to the publication as research assistant, carrying out in-vitro calibration

conference posters & talks

  • Fisch, P., Holub, M., Zenobi-Wong, M. (2017). Comparison of Printing Accuracy of Screw- vs. Press-Driven Extrusion of Bioinks. International conference on biofabrication, Beijing: 2017
  • Jedelský, J.; Malý, M.; Holub, M.; Jícha, M. (2015). Some Aspects of Disintegration of Annular Liquid Sheet in Pressure- Swirl Atomization. In Conference on Modelling Fluid Flow. Budapest: 2015. s. 1-8. ISBN: 978-963-313-190- 9.


  • Holub, M. (2019) Scanning Nanopipette Thermometry; Master thesis; ETH Zürich, Switzerland
  • Holub, M. (2017) A Novel Extrusion System for Bioprinting; Semester project, ETH Zürich, Switzerland
  • Holub, M. (2016). Cavitation in Microfluidics (link); Bachelor thesis; BUT, Brno, Czech Republic