Denis Duboule's scientific contributions concern the molecular genetics of vertebrate development, with interfaces in medical genetics, evolutionary biology and transcription regulation. Since 1985, he has published several discoveries linked to the development and evolution of the vertebrate body plan, most notably concerning the Hox gene family. In 1986, his laboratory published the cloning and organization of the first large genomic cluster of Hox genes in the mouse. In 1988, in collaboration with Steve Gaunt, he described the collinear expression of Hox genes in mammals, thus extending the property discovered by Ed Lewis from Diptera to vertebrates and other deuterostomes. In 1989, he observed temporal colinearity(Hox clock), i.e. the same principle of colinearity but applied to gene activation times. In 1989, with Robb Krumlauf, his laboratory reported the conservation of the structure of the homeotic system between Drosophila flies and vertebrates ; a unique homeotic complex existed in animals at the origin of protostomes and deuterostomes. In 1989 and 1991, the same genetic system (Hox genes) was co-opted and recycled for the specification of several axial structures, in particular limbs and external genitalia. The extension of this work to birds, in collaboration with Cheryll Tickle and Lewis Wolpert, shows the high degree of conservation of the function and regulation of these genes in vertebrates. In 1991, he proposed the concept of " posterior prevalence ", which describes the functional hierarchy of Hox proteins.

In 1994, he proposed the concept of the " phylotypic egg-timer "(Developmental hourglass), suggesting that phenotypic landscapes are reduced during a short period of vertebrate development, the " philotypic progression ", during which the embryos of all vertebrates express common characteristics, resulting from the existence of maximum constraints. Also in 1994, he proposed that Hox genes act like a clock. Consequently, all animals developing according to an anteroposterior temporal progression " must " have at least one entire complex of Hox genes. In 1995, the description of Hox genes in zebrafish during fin development led to a model of the evolutionary transition from fin to limb in tetrapods, in which fingers are tetrapod innovations, with no homologous structures in fish.

Since 1997, Denis Duboule has approached the question of the mechanisms underlying the collinearity of Hox genes using mouse molecular genetics. These genes are controlled at a global level, taking into account their respective positions on the chromosome. His laboratory then developed the TAMERE and STRING techniques to produce a large allelic series at the HoxD locus, leading to the concepts of "  landscapes" or " d'archipels " of regulation that implement collinearity mechanisms during limb development. Denis Duboule has also studied in detail the Hox clock process during the formation of the main body axis. This clock is associated with a transition in chromatin structure, accompanied by the successive passage of each of the Hox genes from a negative to an active domain.

The importance and significance of these observations for our understanding of gene regulation during development and the mechanisms of morphological evolution are discussed in several generalist journals and books.