Boris Ephrussi studied fruit flies, yeast, and mouse genetics and development while working in France and the US during the twentieth century. In yeast, Ephrussi studied how mutations in the cytoplasm persisted across generations. In mice he studied the genetics of hybrids and the development of cancer. Working with George Wells Beadle on the causes of different eye colors in fruit flies, Ephrussi's research helped establish the one-gene-one-enzyme hypothesis. Ephrussi helped create new embryological techniques and contributed the theories of genetics and development.

Boris Ephrussi and George Wells Beadle developed a transplantation technique on flies, Drosophila melanogaster, which they described in their 1936 article A Technique of Transplantation for Drosophila. The technique of injecting a tissue from one fly larva into another fly larva, using a micropipette, to grow that tissue in the second larvae, was a means for investigating development of Drosophila. Through this technique, Beadle and Ephrussi studied the role of genes in embryological processes. Beadle and Ephrussi were the first to apply the transplantation method, which had previously been used in the study of larger insects, to the smaller sized Drosophila. Beadle and Ephrussi used this method of transplantation to determine if parts of the optic disc, the section of a larvae that later become the eye buds in the adult, could be extracted from one larva and transplanted into another. They later built upon this research to relate the production of molecules in cells to gene function.