Ruud van der Breggen

This study links immune infiltration in chordomas to increased transcriptional activity and distinct metabolic profiles, but causality remains unclear.

This study compares immunogenic features between undifferentiated soft tissue sarcoma and myxofibrosarcoma, finding differences in T cell and macrophage infiltration and their prognostic significance.

This study examines how a lifestyle intervention affects the blood transcriptomic and metabolomic responses to a nutrient challenge in elderly individuals.

The paper develops interpretable neural networks for multi-omics data to predict smoking status, age, and LDL levels, showing improved performance and generalizability across cohorts.

The paper identifies 818 genes influencing DNA methylation in blood using genetic anchors and causal inference, revealing both transcription factors and non-DNA-binding proteins with regulatory roles.

The paper identifies 49 gene drivers of downstream transcriptional changes using population genomics data and RNA-sequencing from 3,072 individuals.

The paper identifies trans-meQTLs linking disease variants to methylation changes at transcription factor binding sites, revealing eight-fold more downstream effects than trans-eQTLs.