Главный консультант, Зав. Лабораторией "Центр aлгоритмической биотехнологии"
- NSF Young Investigator Award, 1994
- Howard Hughes Medical Institute Professor Award, 2006
- UCSD Chancellor Associates Award for Excellence in Research, 2007
- Election as Association for Computing Machinery (ACM) Fellow, 2010
- Recipient of the Honorary Degree and the commencement speaker, Simon Fraser University, Vancouver, Canada, 2011
- Leading Scientist, Megagrant Program of Russian Government, 2011
- Jon Postel Distinguished Lecture, University of California, Los Angeles, 2011
- Election as International Society for Computational Biology (ISCB) Fellow, 2012
- RECOMB Test of Time Award, 2013
- Alberto Apostolico Memorial Lecture, Georgia Institute of Technology, 2015
- James Kelly Distinguished Lecture, Pennsylvania State University, 2015
- Margaret Dayhoff Lecture, 10th International Conference on Bioinformatics, Atlanta, 2015