John Quackenbush received his PhD in 1990 in theoretical physics from UCLA working on string theory models. Following two years as a postdoctoral fellow in physics, Dr. Quackenbush applied for and received a Special Emphasis Research Career Award from the National Center for Human Genome Research to work on the Human Genome Project. He spent two years at the Salk Institute and two years at Stanford University working at the interface of genomics and computational biology.

In 1997 he joined the faculty of The Institute for Genomic Research (TIGR) where his focus began to shift to understanding what was encoded within the human genome. Since joining the faculties of the Dana-Farber Cancer Institute and the Harvard School of Public Health in 2005, his work has focused on the use of genomic data to reconstruct the networks of genes that drive the development of diseases such as cancer and emphysema.