Publications

BioRχiv

• Mol, F.N., & Vlijm, R. Automated STED nanoscopy for high-throughput imaging of cellular structures. bioRxiv, 2022, doi: https://doi.org/10.1101/2022.09.29.510126

Peer reviewed

• Jansen, R.L.M. et al., Overexpression of PEX14 results in mistargeting to mitochondria, accompanied by organelle fragmentation and clustering in human embryonic kidney cells. Biochim Biophys Acta Mol Cell Res. 2024, 1871(6):119754. DOI: 10.1016/j.bbamcr.2024.119754.
• de Lange, E.M.F. et al., STED super-resolution microscopy unveils the dynamics of Atg30 on yeast Pex3-labeled peroxisomes. iScience, 2024. 8;27(8):110481. DOI:10.1016/j.isci.2024.110481
• Richards, F. et al., Rapid internalization of nanoparticles by human cells at the single particle level. ACS Nano, 2023. DOI: 10.1021/acsnano.3c01124
• Hurtig, F. et al., The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances, 2023. 9(11), DOI: 10.1126/sciadv.ade5224
• Burgers, T.C.Q. & Vlijm, R., Fluorescence-based super-resolution-microscopy strategies for chromatin studies. Chromosoma, 2023. https://doi.org/10.1007/s00412-023-00792-9
• Stempels, F.C. et al., Giant worm-shaped ESCRT-scaffolds surround actin-independent integrin clusters. Journal of Cell Biology, 2023, 222 (7): e202205130. DOI: 10.1083/jcb.202205130
• Hemmatpour, H., et al., Temperature-responsive and biocompatible nanocarriers based on clay nanotubes for controlled anti-cancer drug release. Nanoscale, 2023. DOI: 10.1039/D2NR06801J
• de Lange, E.M.F. & Vlijm, R., Super-resolution imaging of peroxisomal proteins using STED nanoscopy. Methods in Molecular Biology, Springer Nature, 2023. 2643(65-84). DOI: 10.1007/978-1-0716-3048-8_5
• Iyer, A., et al., Chemogenetic Tags with Probe Exchange for Live-Cell Fluorescence Microscopy. ACS Chem. Biol., 2021. https://doi.org/10.1021/acschembio.1c00100
• Erdel, F., et al., Mouse Heterochromatin Adopts Digital Compaction States without Showing Hallmarks of HP1-Driven Liquid-Liquid Phase Separation. Molecular Cell, 2020. DOI: https://doi.org/10.1016/j.molcel.2020.02.005
• Vlijm, R., et al., STED nanoscopy of the centrosome linker reveals a CEP68-organized, periodic rootletin network anchored to a C-Nap1 ring at centrioles. Proc Natl Acad Sci U S A , 2018. 115(10): p. E2246 - E2253.

• Vlijm, R., et al., The supercoiling state of DNA determines the handedness of both H3 and CENP-A nucleosomes. Nanoscale, 2017. 9(5): p. 1862-1870.

• Butkevich, A.N., et al., Hydroxylated Fluorescent Dyes for Live-Cell Labeling: Synthesis, Spectra and Super-Resolution STED. Chemistry, 2017. 23(50): p. 12114-12119.

• Kim, S.H., et al., CENP-A and H3 Nucleosomes Display a Similar Stability to Force-Mediated Disassembly. PLoS One, 2016. 11(11): p. e0165078.

• Vlijm, R., et al., Experimental phase diagram of negatively supercoiled DNA measured by magnetic tweezers and fluorescence. Nanoscale, 2015. 7(7): p. 3205-16.

• Vlijm, R., et al., Comparing the Assembly and Handedness Dynamics of (H3.3-H4)2 Tetrasomes to Canonical Tetrasomes. PLoS One, 2015. 10(10): p. e0141267.

• Vlijm, R., et al., Nucleosome assembly dynamics involve spontaneous fluctuations in the handedness of tetrasomes. Cell Rep, 2015. 10(2): p. 216-25.

• Vlijm, R., V.D.T. J, and C. Dekker, Counterintuitive DNA Sequence Dependence in Supercoiling-Induced DNA Melting. PLoS One, 2015. 10(10): p. e0141576.

• Katan, A.J., et al., Dynamics of nucleosomal structures measured by high-speed atomic force microscopy. Small, 2015. 11(8): p. 976-84.

• Vlijm, R., et al., NAP1-assisted nucleosome assembly on DNA measured in real time by single-molecule magnetic tweezers. PLoS One, 2012. 7(9): p. e46306.

• Patil, A.V., et al., Fabrication and characterization of polymer insulated carbon nanotube modified electrochemical nanoprobes. Nanoscale, 2010. 2(5): p. 734-8.

Code

• Mol, F.N., & Vlijm, R. (2022). Ring-colocalization (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.7307223, as used in Hurtig et al.

Data sets

• Burgers, T.C.Q., Mol, F.N. & Vlijm, R., (2022), Dataset of ESCRT-III polymer rings (CdvB, CdvB1 and CdvB2) in wildtype archaea (Sacidocaldarius_DSM639) imaged by (dyMIN) STED nanoscopy, https://doi.org/10.34894/Q6BYSQ, DataverseNL, V1, as used in Hurtig et al..

Other (thesis / abstracts)

• Thesis: Vlijm, R., Assembling a single-molecule view on nucleosome dynamics, in Bionanoscience. 2014, Delft University of Technology: Delft. p. 164.
• Vlijm, R., et al., STED Nanoscopy of the Centrosome Linker Reveals a CEP68-Organized, Periodic Rootletin Network Anchored to a C-Nap1 Ring at Centrioles. Biophysical Journal, 2018. 114(3): p. 535a. https://doi.org/10.1016/j.bpj.2017.11.2926

• Ordu, O., et al., Investigating the Handedness Dynamics of Tetrasomes. Biophysical Journal, 2016. 110(3): p. 562a. https://doi.org/10.1016/j.bpj.2015.11.3007

• Hyun Kim, S., et al., The Handedness of Nucleosomes is Governed by the Supercoiling of DNA. Biophysical Journal, 2016. 110(3): p. 70a. https://doi.org/10.1016/j.bpj.2015.11.440

• Vlijm, R., et al., Nucleosome Assembly Dynamics Involve Spontaneous Fluctuations in the Handedness of Tetrasomes. Biophysical Journal, 2015. 108(2): p. 205a. https://doi.org/10.1016/j.bpj.2014.11.1132

• Vlijm, R., Y. Dalal, and C. Dekker, Torque Mediated Kinetics of CENP-A Nucleosomes Reveals Resilience to Tension. Biophysical Journal, 2015. 108(2): p. 539a. https://doi.org/10.1016/j.bpj.2014.11.2954

• Vlijm, R., et al., Nucleosome Dynamics Involve Spontaneous Fluctuations in the Handedness of Tetrasomes. Biophysical Journal, 2014. 106(2): p. 74a. https://doi.org/10.1016/j.bpj.2013.11.486

• Katan, A., et al., Dynamics of NAP1-Assisted Nucleosome Assembly Imaged with High-Speed Atomic Force Microscopy. Biophysical Journal, 2014. 106(2): p. 429a. https://doi.org/10.1016/j.bpj.2013.11.2416

• Vlijm, R., et al., NAP1-Assisted Nucleosome Assembly on DNA Measured in Real Time by Single-Molecule Magnetic Tweezers. Biophysical Journal, 2013. 104(2): p. 38a-39a. https://doi.org/10.1016/j.bpj.2012.11.250

• Vlijm, R., et al., Real Time Visualization of hRPA Binding to Torsionally Controlled Double-Stranded DNA. Biophysical Journal, 2013. 104(2): p. 73a. https://doi.org/10.1016/j.bpj.2012.11.442

• Soni, G., et al., Nucleosome Detection using Solid State Nanopores. Biophysical Journal, 2012. 102(3): p. 730a. https://doi.org/10.1016/j.bpj.2011.11.3960