Pe'er received her bachelor's degree in mathematics in 1995, her master's degree in 1999 and her PhD in computer science in 2003, all from the Hebrew University of Jerusalem.
Pe'er has won several prestigious awards including a Burroughs Wellcome Fund Career Award, a NSF CAREER award and a Stand Up To Cancer Innovative Research Grant. She was awarded an NIH Directors New Innovator Award in 2007 in order to investigate how genetic variations can cause changes throughout the whole body which can lead to autoimmune disease and cancer. Pe'er was awarded a Packard Fellowship in Science and Engineering in 2009. She was awarded the ISCB Overton Prize in 2014 for her significant contribution to research, particularly in using computational methods to understand the organization and function of molecular networks in cells. Her husband, Itsik Pe'er, is also a computational biologist at Columbia University.