Willem Vanderlinden

Irregular nucleosome positioning governs a crystalline to liquid-like phase transition and tunes chromatin accessibility

The paper shows that nucleosome positioning determines chromatin's physical state, with irregular positioning enabling accessibility for transcription while maintaining genome protection.

The Effects of DMSO on DNA Conformations and Mechanics

This paper investigates how DMSO affects DNA structure and mechanics using single-molecule techniques and simulations, finding that DMSO increases DNA flexibility and compaction up to 50% concentration.

Complex rheology of condensin in entangled DNA

This study investigates how yeast condensin affects the rheology and viscoelasticity of entangled DNA, showing it increases viscosity and elasticity even without ATP.

Chromatin Protection by the Chromosomal Passenger Complex

This study reveals how the chromosomal passenger complex (CPC) interacts with nucleosomes to protect centromeric chromatin, showing its non-catalytic role in maintaining chromatin stability.

Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling

This paper introduces NanoRCS, a method using nanopore sequencing and consensus calling to accurately estimate tumor fractions from cfDNA by analyzing SNVs, CNAs, and fragmentomics.

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

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.

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

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.

HIV integrase compacts viral DNA into biphasic condensates

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

Quantifying epigenetic modulation of nucleosome breathing by high-throughput AFM imaging

This study uses high-throughput AFM imaging to analyze how histone modifications affect nucleosome structure, finding that H3K36me3 increases unwrapping while others act through higher-order processes.