Jonathan A. Eisen
Professor
jaeisen@ucdavis.edu

UC Davis Genome Center
Evolution and Ecology
Medical Microbiology and Immunology
Adjunct Scientist, Joint Genome Institute

Office
GBSF 5311
530-752-3498


Picture of Jonathan Eisen, Jonathan A Eisen
 
Degrees:
1998 PhD Stanford University Biological Sciences
1990 A.B. Harvard College Biology
Research Interests:
Main Research Focus
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.


 Open Science
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.
Awards:
Esquire Magazine, "Best and Brightest Innovators", 2002
Department and Center Affiliations:
Department of Evolution and Ecology
Department of Medical Microbiology and Immunology
UC Davis Genome Center
UC Davis Center for Population Biology
CBS Graduate Group Affiliations:
Population Biology  
Graduate Groups not Housed in CBS:
Microbiology  
Publications: Last updated 11/22/2009
  • Eisen JA, MacCallum CJ. 2009. Genomics of emerging infectious disease: A PLoS collection. PLoS Biol. 7(10):e1000224.
  • Hartman AL, Lough DM, Barupal DK, Fiehn O, Fishbein T, Zasloff M, Eisen JA. 2009. Human gut microbiome adopts an alternative state following small bowel transplantation. Proc Natl Acad Sci U S A. 106(40):17187-92.
  • Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham J E.,. Bryant DA, Robb FT Colman AS,. Tallon L J, BadgerJH, Madupu R,. Ward NL, Eisen JA. 2009. Complete Genome Sequence of the Aerobic CO-Oxidizing Thermophile Thermomicrobium roseum. PLoS ONE 4(1) e4207.
  • Wu D, Hartman A, Ward N, Eisen JA. 2008. An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP). PLoS ONE 3(7): e2566.
  • Wu M, Eisen JA. 2008. A simple, fast, and accurate method of phylogenomic inference. Genome Biology 2008, 9:R151. PMID: 18851752.
  • Eisen JA. 2007. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biology 5(3): e82.
  • Wu D, Daugherty SC, Aken SE, Pai GH, Watkins KL, Khouri H, Tallon LJ, Zaborsky JM, Dunbar HE, Tran PL, Moran NA, and Eisen JA. Metabolic Complementarity and Genomics of the Dual Bacterial Symbiosis of Sharpshooters. PLoS Biol 2006 Jun 6; 4(6) e188.
  • Evolution (Textbook), Cold Spring Harbor Press, 2007. See Book Web Site
  • Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, et al. 2006. Macronuclear genome sequence of the ciliate Tetrahymena thermophila , a model eukaryote. PLoS Biol. 4(9):e286.
  • Wu M, Sun LV, Vamathevan J, Riegler M, Deboy R, Brownlie JC, McGraw EA, Martin W, Esser C, Ahmadinejad N, Wiegand C, Madupu R, Beanan MJ, Brinkac LM, Daugherty SC, Durkin AS, Kolonay JF, Nelson WC, Mohamoud Y, Lee P, Berry K, Young MB, Utterback T, Weidman J, Nierman WC, Paulsen IT, Nelson KE, Tettelin H, O'Neill SL, Eisen JA. 2004. Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol. 2(3):E69
  • Wu M, Sun LV, Vamathevan J, Riegler M, Deboy R, Brownlie JC, McGraw EA, Martin W, Esser C, Ahmadinejad N, Wiegand C, Madupu R, Beanan MJ, Brinkac LM, Daugherty SC, Durkin AS, Kolonay JF, Nelson WC, Mohamoud Y, Lee P, Berry K, Young MB, Utterback T, Weidman J, Nierman WC, Paulsen IT, Nelson KE, Tettelin H, O'Neill SL, Eisen JA. 2004. Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. Courses:
    BIS 002C Introduction to Biology
    EVE 298 Microbial phylogenomics Spring 2010