Since 2001, he is the Director of the Swiss National Research Center "Frontiers in Genetics" and since 2017, he is also a professor at the Collège de France.

After questioning Karl Illmensee's claims of having cloned a mouse, Duboule departed to work as a post-doc and then a group leader at the University of Strasbourg, with Pierre Chambon.

In 1988, he became a group leader at the European Molecular Biology Laboratory in Heidelberg, Germany.

[3] In 2017, he was elected professor at the Collège de France, holding the international chair in genome evolution and development.

These genes have been a paradigm to understand embryonic patterning, in developmental, evolutionary and pathological contexts.