Gerald Rubin received his B.S. degree in biology from MIT in 1971; as an undergraduate, he spent two summers working at Cold Spring Harbor Laboratory. He obtained his Ph.D. from the University of Cambridge in 1974 for work done at the Medical Research Council Laboratory of Molecular Biology. He began working on the fruit fly, Drosophila, as a postdoctoral fellow in the laboratory of David S. Hogness at Stanford University, where he participated in some of the earliest studies of gene organization using the newly developed recombinant DNA methods.
His research has included studies of the structure and biology of transposable elements and molecular mechanisms of cell fate determination during development of the Drosophila retina. In 1982, he and Allan Spradling developed methods for making transgenic Drosophila, the first successful germ-line genetic engineering of a multicellular animal. Rubin served as the leader of the publicly funded effort to sequence the Drosophila melanogaster genome, which included collaborating with Celera Genomics Inc. to demonstrate that the whole genome shotgun method could successfully sequence an animal genome.
Rubin held faculty positions at Harvard Medical School and the Carnegie Institution of Washington's Department of Embryology before moving to the University of California, Berkeley, in 1983 to assume the John D. MacArthur Professorship (held until 1999). He became a Howard Hughes Medical Institute investigator in 1987. Rubin served as HHMI's vice president for biomedical research (2000–2002) and vice president and director of planning for Janelia Farm Campus (2002), and he became vice president and director, Janelia Farm Research Campus in 2003.
Rubin has been a member of the National Academy of Sciences since 1987. He is also a member of the Institute of Medicine and the American Academy of Arts and Sciences and a foreign member of the Royal Society (U.K.). He has received numerous awards, including the American Chemical Society Eli Lilly Award in Biological Chemistry, the National Academy of Sciences U.S. Steel Foundation Award in Molecular Biology, and the Genetics Society of America Medal.