Youssef Idaghdour is particularly interested in studying the role genetic and environmental factors play in shaping health-related phenotypes and how interactions between these effects trigger disease and modulate its outcome. He does most of his experimental research on mammalian systems and he focuses on metabolic traits and immune response to cancer and infection. To achieve these goals, his lab generates high-dimensional genomic datasets from single-cells, tissues, and cells, and use bioinformatics and statistical genetic approaches to analyze the data.

Youssef is also interested in the area of ecological genomics and he's actively involved in developing genetic tools to facilitate population genetic analysis of endangered marine and wildlife species including Houbara bustards and falcons.