Jonathan Eisen, Ph.D.
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
Publications
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Journal Article (225)
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Andrew Tritt, Jonathan A Eisen, Marc T Facciotti et al. (2012) An integrated pipeline for de novo assembly of microbial genomes., e42304. In PloS one 7 (9).Download PDF (363.86 KB)
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Alex Copeland, Wei Gu, Montri Yasawong et al. (2012) Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1(T)) from a deep-sea hydrothermal vent chimney., 21-30. In Standards in genomic sciences 6 (1).Download PDF (3.67 MB)
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Alex Copeland, Xiaojing Zhang, Monica Misra et al. (2012) Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T))., 145-54. In Standards in genomic sciences 6 (2).Download PDF (3.6 MB)
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Marcel Huntemann, Hazuki Teshima, Alla Lapidus et al. (2012) Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1(T))., 185-93. In Standards in genomic sciences 6 (2).Download PDF (3.73 MB)
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Alex Copeland, Ahmet Zeytun, Montri Yassawong et al. (2012) Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRP(T))., 240-50. In Standards in genomic sciences 6 (2).Download PDF (4.16 MB)
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Cliff Han, Oleg Kotsyurbenko, Olga Chertkov et al. (2012) Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1(T))., 94-103. In Standards in genomic sciences 6 (1).Download PDF (2.84 MB)
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Birte Abt, Cliff Han, Carmen Scheuner et al. (2012) Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1(T)), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerocha, 194-209. In Standards in genomic sciences 6 (2).Download PDF (2.27 MB)
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Iain Anderson, Elizabeth Saunders, Alla Lapidus et al. (2012) Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812(T))., 155-64. In Standards in genomic sciences 6 (2).Download PDF (2.74 MB)
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Xingpeng Jiang, Morgan G I Langille, Russell Y Neches et al. (2012) Functional Biogeography of Ocean Microbes Revealed through Non-Negative Matrix Factorization., e43866. In PloS one 7 (9).Download PDF (605.1 KB)
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Bjorn A Traag, Antonia Pugliese, Jonathan A Eisen et al. (2012) Gene conservation among endospore-forming bacteria reveals additional sporulation genes in Bacillus subtilis.. In Journal of bacteriology.
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Book (2)
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T Connely, P Sharp, D Ausiello et al. (2009) A New Biology for the 21st Century, 112.Download PDF (4.47 MB)
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N Barton, DEG Briggs, JA Eisen et al. (2007) Evolution, 833. In COld Spring Harbor Laboratory Press.
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Book Section (2)
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Frank T Robb, Juan M Gonzalez, Tatyana Sokolova et al. (2005) Primary Energy Metabolism in Geothermal Environments: The Role of Carbon Monoxide, 163-170. In Geothermal biology and geochemistry in Yellowstone National Park..Download PDF (2.22 MB)
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Jonathan A. Eisen (1999) Mechanistic basis for microsatellite instability, 34–48. In Microsatellites—evolution and applications.Download PDF (3.26 MB)
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Conference Proceedings (1)
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Eisen JA Chatterji S, Yamazaki I, Bai Z (2008) CompostBin: a DNA composition-based algorithm for binning environmental shotgun reads, 17-28. In RECOMB 2008: Proceedings of the 12th annual international conference on Research in computational molecular biology.Download PDF (1.88 MB)
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Working Paper (1)
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Jonathan A. Eisen (2005) The Axis of Evol: Getting to the root of DNA repair with Philogeny.Download PDF (246.31 KB)
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Thesis (1)
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Jonathan A. Eisen (1998) Evolution of DNA repair genes, proteins and processes, 442..Download PDF (6.1 MB)
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Awards and Grants
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Apr 2012Elected Fellow American Academy of Microbiology
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Apr 2011Benjamin 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., http://phylogenomics.blogspot.com http://twitter.com/phylogenomics).
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.
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., http://phylogenomics.blogspot.com http://twitter.com/phylogenomics).
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.
CV
Professional Experience
2006 - Present
2006 - Present
Professor at University of California, Davis
Davis, California, United States
Classes taught:
BIS002C: Biodiversity and the Tree of Life
EVE198: Microbial phylogenomics
Davis, California, United States
Classes taught:
BIS002C: Biodiversity and the Tree of Life
EVE198: Microbial phylogenomics
Sep 2000 - Sep 2009
Dec 1998 - May 2006
Jun 1991 - Sep 1991
Jun 1988 - Sep 1988
Jun 1987 - Sep 1987
Intern Investigator at Public Defender Service of the District of Columbia
Washington, District of Columbia, United States
Washington, District of Columbia, United States
Education
Sep 1991 - Nov 1998
Sep 1986 - Jun 1990
Contact Information
| Webpage: | http://phylogenomics.blogspot.com |
Public Groups
Public groups Jonathan is a member of
Public groups Jonathan is following
Destinations
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