University of California, Davis
UC Davis Genome Center, the School of Medicine 
and the College of Biological Sciences.


 Dr. Eisen’s research focuses on communities of microbes and how they provide new functions - to each other or to a host. His study systems have included boiling acid pools, surface ocean waters, agents of many diseases, and the microbial ecosystems in and on plants and animals. He is also coordinating the largest microbial sequencing project to date – a Genomic Encyclopedia – being done at the DOE Joint Genome Institute where he holds an Adjunct Appointment.

His overarching goal in his research is to create a “Field Guide to the Microbes” much as exists for birds or trees. In addition to his research, Dr. Eisen is a vocal advocate for “open scholarship” especially "open access" to publications. He is also an active and award-winning blogger (e.g., http://phylogenomics.blogspot.com) and science communicator (e.g., http://www.ted.com/talks/jonathan_eisen_meet_your_microbes) and an elected member of the American Academy of Microbiology. Prior to working at UC Davis he was on the faculty of The Institute for Genomic Research and held an Adjunct Appointment at the Johns Hopkins University. He earned a Ph.D. in Biological Sciences from Stanford University and an A.B. in Biology from Harvard College.



  • Wilbanks EG, Jaekel U, Salman V, Humphrey PT, Eisen JA, Faccioti MT, Buckley DH, Zinder SH, Druschel GK, Fike DA, Orphan VJ. 2014. Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh. Environmental Microbiology doi: 10.1111/1462-2920.12388.
  • Eisen JA, Ganley E, MacCallum CJ. 2014. Open Science and Reporting Animal Studies: Who’s Accountable? PLOS Biology 12(1): e1001757. doi:10.1371/journal.pbio.1001757
  • Darling AE; Jospin G, Lowe E, Matsen FA, Bik HM, Eisen JA. 2014. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2:e243. http://dx.doi.org/10.7717/peerj.243.
  • Kyrpides N, Woyke T, Eisen JA, Garrity G, Lilburn T, Beck B, Whitman W, Hugenholtz P, & Klenk HP. 2014. Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project. Standards in Genomic Sciences, 9(3). doi:10.4056/506

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