Author

W. Vanderlinden

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 12

Signature Assays, Organisms & Methods

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Approach:experimental assay· 11 Assay:DNA methylation· 4 Research Focus:chromatin & epigenetic regulation· 3 Approach:statistical model· 3 Research Focus:cell type annotation· 2 Research Focus:clustering· 1 Approach:comparative / phylogenetic analysis· 1 Approach:deep learning· 1

Frequent Co-Authors

J. Lipfert· 11 shared P. J. Kolbeck· 7 shared T. Brouns· 3 shared Y.-Y. Lin· 3 shared M. de Jager· 2 shared S. De Feyter· 2 shared S. F. Konrad· 2 shared W. Frederickx· 2 shared

Activity by Year

2018-2024 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 26 mutual co-author links

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11 shared papersBiophysics

J. Lipfert

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12 papers

Recent·Most cited

Exploring protein-mediated compaction of DNA by coarse-grained simulations and unsupervised learning

M. de Jager, P. J. Kolbeck, W. Vanderlinden, J. Lipfert, L. Filion

The paper uses coarse-grained simulations and unsupervised learning to study protein-mediated DNA compaction, finding that protein-protein interactions are critical for forming looped structures observed experimentally.

bioRxiv · Mar 28, 2024Biophysics

HIV integrase compacts viral DNA into biphasic condensates

P. J. Kolbeck, M. de Jager, M. Gallano, T. Brouns, B. Bekaert, W. Frederickx, S. F. Konrad, S. Van Belle, F. Christ, S. De Feyter, Z. Debyser, L. C. Filion, J. Lipfert, W. Vanderlinden

This study shows HIV integrase compacts viral DNA into biphasic condensates, with the core susceptible to inhibitors and the outer layer resistant.

bioRxiv · Mar 15, 2024 · PreprintBiophysics

Epigenetic histone modifications H3K36me3 and H4K5/8/12/16ac induce open polynucleosome conformations via different mechanisms

Y.-Y. Lin, P. Muller, E. Karagianni, W. Vanderlinden, J. Lipfert

This study examines how H3K36me3 and H4K5/8/12/16ac histone modifications affect nucleosome structure and interactions in tri-nucleosome arrays, revealing distinct mechanisms for inducing open conformations.

bioRxiv · Feb 19, 2024Biophysics

Single-Molecule Morphology of Topologically Digested Olympic Networks

S. Ramakrishnan, Z. Chen, D. Michieletto, N. Savill, A. Schnaufer, L. Tubiana, Y. Fosado, W. Vanderlinden

The paper studies the structure and topology of kinetoplast DNA (kDNA) networks by sequencing and analyzing their morphology after partial digestion with restriction enzymes.

bioRxiv · Oct 18, 2023Biophysics

Topology-dependent DNA binding

P. J. Kolbeck, M. Tisma, B. T. Analikwu, W. Vanderlinden, C. Dekker, J. Lipfert

This study presents a quantitative model showing how DNA topology modulates binding, with experiments using fluorescent intercalators and psoralen to demonstrate topology-dependent effects.

bioRxiv · Jun 30, 2023Biophysics

High-yield, ligation-free assembly of DNA constructs with nucleosome positioning sequence repeats for single molecule manipulation assays

Y.-Y. Lin, T. Brouns, P. J. Kolbeck, W. Vanderlinden, J. Lipfert

This paper describes a method for high-yield DNA construct assembly with nucleosome positioning sequences for single-molecule manipulation assays, demonstrating stable tethers and proof-of-concept measurements on nucleosome dynamics.

bioRxiv · Jan 5, 2023Biophysics

A DNA origami fiducial for accurate 3D AFM imaging

P. J. Kolbeck, M. Dass, I. Martynenko, R. van Dijk-Moes, K. J. H. Brouwer, A. van Blaaderen, W. Vanderlinden, T. Liedl, J. Lipfert

This paper introduces a DNA origami fiducial to correct AFM image distortions by enabling accurate tip shape reconstruction and improving imaging precision.

bioRxiv · Nov 11, 2022 · PreprintBiophysics

DNA fluctuations reveal the size and dynamics of topological domains

W. Vanderlinden, E. Skoruppa, P. J. Kolbeck, E. Carlon, J. Lipfert

This paper develops a method to measure topological domain size and dynamics in supercoiled DNA using magnetic tweezers and simulations.

bioRxiv · Dec 21, 2021Biophysics

Twisting DNA by Salt

S. Cruz-León, W. Vanderlinden, P. Müller, T. Forster, G. Staudt, Y.-Y. Lin, J. Lipfert, N. Schwierz

This study investigates how DNA twist changes with ion concentration and identity using single-molecule experiments and simulations, revealing trends in cation-specific effects on DNA structure.

bioRxiv · Jul 14, 2021Biophysics

Intercalative DNA binding governs fluorescence enhancement of SYBR Gold

P. J. Kolbeck, W. Vanderlinden, T. Nicolaus, C. Gebhardt, T. Cordes, J. Lipfert

This study quantifies SYBR Gold binding to DNA using mechanical and spectroscopic methods, revealing intercalative binding and providing guidelines for quantitative DNA sensing.

bioRxiv · May 23, 2020 · PreprintBiophysics

High-throughput AFM analysis reveals unwrapping pathways of H3 and CENP-A nucleosomes

S. F. Konrad, W. Vanderlinden, W. Frederickx, T. Brouns, B. Menze, S. De Feyter, J. Lipfert

The paper uses high-throughput atomic force microscopy to analyze nucleosome unwrapping pathways, revealing differences between H3 and CENP-A nucleosomes.

bioRxiv · Apr 9, 2020Biophysics

The Dynamics and Energy Landscape of DNA Plectoneme Nucleation

P. U. Walker, W. Vanderlinden, J. Lipfert

The paper quantifies DNA buckling dynamics using magnetic tweezers and reconstructs energy landscapes revealing asymmetry and a bend transition state.

bioRxiv · Mar 13, 2018Biophysics