She received the National Science Foundation Young Investigator Award in 1994, the David and Lucile Packard Foundation Award in Science and Engineering in 1996, a Radcliffe Institute Fellowship in 2006, and a Guggenheim Foundation Fellowship for 2011. She was elected a Fellow of the Association for Computing Machinery (ACM) in 2015, of the International Society for Computational Biology (ISCB) in 2017, and of the American Association for the Advancement of Science (AAAS) in 2021. She received the ISCB Senior Scientist Award in 2024.