[4] Aerts completed his postdoc training working on the genomics of gene regulation in the fruit fly model Drosophila melanogaster in the lab of Bassem Hassan at VIB in Leuven, including a research visit at the Developmental Biology Institute of Marseille, Luminy (IBDML), in France, with Denis Thierry and Carl Herrmann.

[19] In 2022, the consortium announced the completion of a single-nucleus transcriptomic atlas of the adult fruit fly,[20][21] which they hope will serve as a valuable resource for the research community and as a reference for studies of gene function at single-cell resolution.

[22] The generation of cell and tissue atlases help research to study biological processes, not only in flies but also for modeling human diseases at a whole-organism level with cell-type resolution.

Aerts is also part of a pan-European research consortium called LifeTime, which aims to track, understand and target human cells during the onset and progression of complex diseases, and to analyse their response to therapy at single-cell resolution.

[24] MendelCraft, a MineCraft mod developed by the Aerts lab, is a video game designed to teach children about DNA, genetics, and the laws of Mendel, by allowing them to cross and clone different breeds of virtual chickens.