Jasper Zuallaert

The paper presents the E. coli PeptideAtlas build, a comprehensive pan-proteome resource covering 4,755 proteins and over 10,000 PTM sites from 40 datasets.

The paper evaluates AlphaFold models' ability to predict phosphorylation-induced structural changes in proteins using experimentally derived conformational ensembles.

The paper uses deep learning to predict ABA-responsive gene regulation in Arabidopsis by analyzing promoter sequences and identifies motifs beyond canonical ABF binding sites.

This study evaluates PTM predictors using protein language models, revealing a training bias from proteomics data that overestimates prediction accuracy and suggests a solution through negative sample filtering.

The paper develops SECRiFY, a method to assess secretability of protein fragments in yeast, revealing intrinsic disorder and flexibility as key factors.