Wim J. de Jonge

This paper uses spatial multi-omics to identify immunosuppressive interactions between AML, macrophages, and T cells in bone marrow, highlighting the Galectin-9 - CD44/TIM-3 axis as a therapeutic target.

This study directly visualizes eukaryotic transcription factor target search in living cells and finds that efficient localization occurs near the diffusion limit without requiring facilitated diffusion, instead relying on cooperative self-interactions mediated by intrinsically disordered regions.

The paper generates a single-cell multi-omics atlas of pediatric bone marrow, revealing age-related shifts in lineage differentiation linked to stromal cell heterogeneity.

This study investigates how TF clustering affects gene expression by analyzing Gal4 in budding yeast, finding that clustering aids target search but does not contribute to activation.

This study identifies Gcr2 as a Cdk8 substrate, showing its phosphorylation is critical for activating glycolysis genes.

The paper measures genome-wide off-rates of the yeast transcription factor Abf1 and shows how these dynamics relate to functional outcomes like transcriptional dependency and RNA polymerase II roadblocking.

The paper optimizes a ChIP protocol to improve quantitative comparability and reproducibility across samples.

The paper shows that RSC remodeler and pioneer factors work independently to position the +1 nucleosome at yeast promoters, facilitating transcription initiation through DNA sequence-directed action.