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Jonathan Eisen, Ph.D.

Professor , University of California, Davis
Davis, California, United States

Research field: Biological Sciences - Microbiology
Evolution, genomics, DNA repair, symbioses, metagenomics, microbiology, halophiles, archaea, phylogeny, novelty, microbial communities, host-microbe interactions, phylogenetics, forensics, bioinformatics, computational biology, microbiomes, ecology, micr


Awards and Grants

  •  Apr 2012 
    Elected Fellow American Academy of Microbiology
  •  Apr 2011 
    Benjamin Franklin Award for Open Science

Biographical Information

My research focuses on the mechanisms underlying the origin of novelty (how new processes and functions originate). Most of my work involves the use of high throughput DNA sequencing methods to characterize microbes and then the use and development of computational methods to analyze this type of type. In particular, my computational work has focused on integrating evolutionary analysis with genome analysis – so called “phylogenomics.” Previously, I applied this phylogenomic approach to cultured organisms, such as those from extreme environments and those with key properties as they relate to evolution or global climate cycles. Currently we are using sequencing and phylogenomic methods to study microbes directly in their natural habitats (i.e., without culturing). In particular we focus on how communities of microbes interact with each other or with planbt and animal hosts to create new functions.

In addition to research, I is also a vocal advocate for "Open Access'" to scientific publications and is the Academic Editor in Chief of PLoS Biology. I am also a active and (occasionally) award winning blogger/microblogger (e.g.,

Prior to moving to U. C. Davis I was on the faculty of The Institute for Genomic Research (TIGR) in Rockville, MD. I earned my PhD in Biological Sciences from Stanford University where I worked on the evolution of DNA repair processes in the lab of Philip C. Hanawalt. I earned my AB in Biology from Harvard College where I worked with Prof. Colleen Cavanaugh and Prof. Fakhri Bazzaz.


Professional Experience

2006 - Present
Adjunct Scientist at DOE Joint Genome Institute
Walnut Creek, California, United States
2006 - Present
Professor at University of California, Davis
Davis, California, United States
Classes taught:
BIS002C: Biodiversity and the Tree of Life
EVE198: Microbial phylogenomics
Sep 2000 - Sep 2009
Adjunct Faculty at The Johns Hopkins University
Baltimore, Maryland, United States
Dec 1998 - May 2006
Investigator at The Institute for Genomic Research
Rockville, Maryland, United States
Jun 1991 - Sep 1991
Field Assistant at Rocky Mountain Biological Laboratory
Gothic, Colorado, United States
Jun 1988 - Sep 1988
Field Assistant at Rocky Mountain Biological Laboratory
Gothic, Colorado, United States
Jun 1987 - Sep 1987
Intern Investigator at Public Defender Service of the District of Columbia
Washington, District of Columbia, United States

Sep 1991 - Nov 1998
Stanford University in Stanford, California, United States
Ph.D., Biological Sciences
Sep 1986 - Jun 1990
Harvard College in Cambridge, Massachusetts, United States
A.B., Biology

Contact Information


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Davis, California, United States
Main City

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