Jef Boeke did foundational work on mechanistic and genomic aspects of DNA transposition. He develops new technologies in genetics, genomics and synthetic biology.  He elucidated a major form of transposition, based on reverse transcription of RNA.  He coined the term “retrotransposition” to describe this process, common to all eukaryotic genomes.

He uses yeast as a SynBio platform for construction of fully synthetic chromosomes for practical and theoretical studies and leads the international team synthesizing an engineered version of the yeast genome called Sc2.0. He founded and directs the Institute for Systems Genetics at NYU Langone Health.