Eugene Viktorovich Koonin (Russian: Евге́ний Ви́кторович Ку́нин; born October 26, 1956) is a Russian-American biologist and Senior Investigator at the National Center for Biotechnology Information (NCBI).

[4] From 1985 until 1991, Koonin worked as a research scientist in computational biology in the Institutes of Poliomyelitis and Microbiology at the USSR Academy of Medical Sciences, studying virus biochemistry and bacterial genetics.

[4] Koonin's principal research goals include the comparative analysis of sequenced genomes and automatic methods for genome-scale annotation of gene functions.

[4][12] As of 2014, Koonin serves on the advisory editorial board of Trends in Genetics,[13] and is co-Editor-in-Chief of the open access journal Biology Direct.

[16][17] In 2016, Semantic Scholar AI program included Koonin on its list of top ten most influential biomedical researchers.