After completing his M.S., Koren joined the J. Craig Venter Institute (JCVI) as a bioinformatics engineer under the supervision of Granger Sutton.

[1] In parallel, Koren worked under the supervision Mihai Pop at the University of Maryland, College Park, where he developed several tools for metagenome assembly and analysis.

[1] In 2010, Koren joined the National Biodefense Analysis and Countermeasures Center (NBACC) where he led genome assembly development and pioneered the use of single-molecule sequencing for the reconstruction of complete genomes.

[1] In 2022, he was one of the lead authors on the publication reporting the first complete female human genome.

[2] In 2023, the Partnership for Public Service named, Koren, Arang Rhie, Adam M. Phillippy and the Telomere-to-Telomere (T2T) Consortium as finalists for the Samuel J. Heyman Service to America Medal in the field of Science, Technology and Environment for "conducting the first complete assembly of the human genome".