Eugene studied biology at Northwestern University with the late Jon Widom and at ETH Zurich with Timothy J. Richmond. He received his PhD at the University of California, San Francisco under Jonathan S. Weissman. Here, he developed ribosome profiling for prokaryotes and investigated mechanisms of protein folding in vivo. He then trained under Michael Rape at the University of California, Berkeley, where he uncovered a novel role for the anaphase promoting complex in gene expression regulation. Eugene currently runs his own lab as a principal investigator at Massachusetts General Hospital in the Center for Cancer Research, where he focuses on various aspects of ubiquitin biology. He is also on the faculty at Harvard Medical School in the Department of Medicine.