International Society for Computational Biology (ISCB) – Accomplishment by a Senior Scientist Award, 2022.
Kadar Award for research excellence, Tel Aviv University, 2017.
RECOMB 2016 and 2011 “Test of Time” Awards
Fellow, the Association for Computing Machines, 2012.
Fellow, the International Society for Computational Biology, 2012.
Landau Prize in Bioinformatics, 2011