Jonathan A. Eisen
Professor
jaeisen@ucdavis.edu
http://twitter.com/phylogenomics
UC Davis Genome Center
Evolution and Ecology
Medical Microbiology and Immunology
Adjunct Scientist, Joint Genome Institute
Office
GBSF 5311
530-752-3498
Degrees:
1998
PhD
Stanford University
Biological Sciences
1990
A.B.
Harvard College
Biology
Research Contribution to Society:
My 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 we make use of high throughput DNA sequencing methods applied to microbes in the lab or to samples isolated directly from the environment.
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
Benjamin Franklin Award for contributions to Open Science, 2011
Elected Fellow of the American Academy of Microbiology, 2012
Elected Fellow of the American Academy of Microbiology, 2012
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 7/26/2012
Jonathan Eisen: Meet your microbes. TED Talks. April 2012.
Eisen JA. 2012. Badomics words and the power and peril of the ome-meme. Gigascience 1:6.
Langille MGI, Laird M, Hsiao W, Chiu T, Eisen JA, Brinkman F. 2012. MicrobeDB: a locally maintainable database of microbial genomic sequence. Bioinformatics doi: 10.1093/bioinformatics/bts273. PMID: 22576174.
Wu M, Chatterji S, Eisen JA. 2012. Accounting for alignment uncertainty in phylogenomics. PLoS ONE 7(1): e30288. PMID: 22272325. PDF.
Monier A, Welsh RM, Gentemann C, Weinstock G, Sodergren E, Armbrust EV, Eisen JA, Worden AZ. 2012. Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges. Environmental Microbiology 14(1): 162-76. PMID: 21914098. PDF.
Fass JN, Joshi NA, Couvillion MT, Bowen J, Gorovsky MA, Hamilton EP, Orias E, Hong K, Coyne RS, Eisen JA, Chalker DL, Lin D, Collins K. 2011. Genome-scale analysis of programmed DNA elimination sites in Tetrahymena thermophila. G3 1(6): 515-522. PMID: 22384362. PDF.
Chandler JA, Lang JM, Bhatnagar S, Eisen JA, Kopp A. 2011. Bacterial communities of diverse Drosophila species: Ecological context of a host-microbe model system. PLoS Genetics 7(9): e1002272. PMID: 21966276. PDF.
Darling A, Tritt A, Eisen JA, Facciotti M. 2011. Mauve assembly metrics. Bioinformatics, 10.1093/bioinformatics/btr451. PMID: 21810901. PDF.
Kembel S, Eisen JA, Pollard KS, Green JL. 2011. The phylogenetic diversity of metagenomes. PLoS ONE 6(8): e23214. PMID: 21912589. PDF.
Mindell DP, Fisher BL, Roopnarine P, Eisen JA, Mace GM, Page RDM, Pyle RL. 2011. Aggregating, tagging and integrating biodiversity research. PLoS ONE 6(8): e19491. PMCID: PMC3148223. PDF.
Martiny JBH, Eisen JA, Penn K, Allison SD, Horner-Devine MC. 2011. Drivers of bacterial β-diversity depend on spatial scale. Proc. Natl. Acad. Sci. USA. 108: 7850-7854. PMID: 21518859. PDF.
Wu D, Wu M, Halpern A, Rusch D, Yooseph S, Frazier M, Venter JC, Eisen JA. 2011.Stalking the fourth domain in metagenomic data: searching for and possible discovery of novel deep branches in phylogenetic trees. PLoS ONE 6(3): e18011. PMID: 21437252. PDF.
Sharpton TJ, Risenfeld S, Kembel SW, Ladau J, O’Dwyer J, Green JL, Eisen JA, Pollard KS. 2011. PhylOTU: A high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS Computational Biology 7(1): e1001061. PMID: 21283775. PDF.
Wu M, Eisen JA. 2011. Towards automated phylogenomic inference. In Frans J. de Bruijn, (ed), Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. Wiley Press.
Eisen JA. 2011. Environmental shotgun sequencing: Its potential and challenges for studying the hidden world of microbes. In Frans J. de Bruijn, (ed), Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. Wiley Press.
Spring S, Scheuner C, Lapidus A, Lucas S, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Chen F, Nolan M, Saunders E, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Lykidis A, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Goodwin L, Detter JC, Brettin T, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. 2010. The genome sequence of Methanohalophilus mahii SLP reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments. Archaea 2010: 690737. PMID: 21234345. PDF.
Hartman AL, Riddle S, McPhillips T, Ludäscher B, Eisen JA. 2010. Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences. BMC Bioinformatics 11: 317. PMID: 20540779. PDF.
Gilbert JA, Meyer F, Antonopoulos D, Balaji P, Brown CT, Brown CT, Desai N, Eisen JA, Evers D, Field D, Feng W, Huson D, Jansson J, Knight R, Knight J, Kolker E, Konstantindis K, Kostka J, Kyrpides N, Mackelprang R, McHardy A, Quince C, Raes J, Sczyrba A, Shade A, Stevens R. 2010. Meeting Report. The Terabase Metagenomics workshop and the vision of an Earth Microbiome Project. Standards in Genomic Sciences, 3(3): 243-248. PMID: 21304727. PDF.
Morgan JL, Darling A, Eisen JA. 2010. Metagenomic sequencing of an in vitro-simulated microbial community. PLoS ONE 5(4): e10209. PMID: 20419134. PDF.
Langille MGI, Eisen JA. 2010. BioTorrents: a file sharing service for scientific data. PLoS ONE 5(4): e10071. PMID: 20418944. PDF.
Hartman AL, Norais C, Badger JH, Delmas S, Haldenby S, Madupu R, Robinson J, Khouri H, Ren Q, Lowe TM, Maupin-Furlow J, Pohlschroder M, Daniels C, Pfeiffer F, Allers T, Eisen JA. 2010. The complete genome sequence of Haloferax volcanii DS2, a model archaeon. PLoS ONE 5(3): e9605. PMID: 20333302. PDF.
Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA. 2009. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462(7276):1056-60. . Also see New York Times article
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. PMID: 19805153. PDF.
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
Courses:
BIS
002C
Introduction to Biology
EVE
161
Microbial Phylogenomics