Julian van Gerwen

Capabilities, specificity gaps and training-data dependence of AlphaFold3 across diverse application areas

This paper evaluates AlphaFold3's performance across diverse structural biology tasks, finding uneven accuracy and strong dependence on training data.

Predicting cellular functions of human phosphosites

The paper develops predictors to functionally characterize human phosphosites using integrated data, revealing novel functions and connections to DNA repair and cell survival.

Mapping the functional importance of site-specific ubiquitination across the human proteome

The paper maps the functional importance of site-specific ubiquitination across the human proteome by analyzing conservation, perturbation, and machine learning scores.

Repurposing UBE2W for programmable protein ubiquitylation

This paper introduces UbyW, a platform for site-specific ubiquitylation using UBE2W, enabling efficient production of ubiquitylated proteins and identifying USP15 as a deubiquitylase for Ran K71 monoubiquitylation.

Site-specific metabolic labeling reveals proteome-wide phospho-dynamics

This study introduces PulsPhos, a method to quantify site-specific phosphorylation lifetimes in living cells and applies it to pharmacological perturbations.

The genetic and dietary landscape of the muscle insulin signalling network

This study uses phosphoproteomics to show how genetic background and diet influence insulin signalling in muscle, revealing key regulators of insulin responsiveness and glycolysis in insulin resistance.

Phosphoproteomics reveals rewiring of the insulin signaling network and multi-nodal defects in insulin resistance

This study uses phosphoproteomics to show that insulin resistance involves rewired signaling networks and widespread dysregulation of GSK3 activity.