Dr. Eisen's research focuses on understanding the genomic basis for how microorganisms, for example bacteria, interact with other species to lead to new functions. We study this in many systems, from single microbes or communities of microbes living "symbiotically" inside a host, to communities of microbes in the environment. To study these topics Dr. Eisen makes use of high throughput DNA sequencing methods applied to microbes in the lab or to samples isolated directly from the environment. The Eisen Lab research focuses on understanding the genomic basis for the origin of novelty (new functions and processes) in microorganisms. For many years, studies in this area were of limited scope. However, the advent of genome sequencing has allowed one to study the origin of novelty on a more global level. 

The Eisen lab's main location is in the U. C. Davis Genome Center. Dr. Eisen has appointments in the Section of Evolution and Ecology and the Department of Medical Microbiology at U. C. Davis and an Adjunct Appointment at the Joint Genome Institute.

Dr. Eisen is also a strong proponent of the Open Access movement in scientific publishing and is Academic Editor in Chief of PLoS Biology. Dr. Eisen is also an active and award winning science blogger.