• Publications
• Awards
• Affiliations

ALLEN, ERIC

Assistant Professor of Marine Biology

and Molecular Biology (Biological Sciences)

Degrees:

• B.S., University of Oregon
• Ph.D., UCSD, Scripps Institution of Oceanography

Research Interests:

• Environmental genomics
• Microbial oceanography / ecology / evolution / biogeography
• Genetic structure of microbial populations
• Molecular genetics and ecological physiology of unique marine source lipids (e.g. microbial omega-3 polyunsaturated fatty acids)

Courses:

• BGGN297: Research Conference
• BGGN299: Thesis Research in Biology
• BIMM120: Bacteriology
• BISP194: Adv Topics in Modern Biology
• BISP196: Honors Thesis in Biology
• BISP199: Individual Research for Ugrads
• SIO299: Research

Mentoring:

• Golder, Julian (Undergrad; 2009-)
• Hammer, Toby (Undergrad; 2008-2009)
• Prieto-Davo, Alejandra (Post Doc; 2008-2009)
• Stratton, Taylor (Graduate; 2008-)
• Ugalde, Juan (Graduate; 2008-)
• Narasingarao, Priya (Post Doc; 2007-)
• Podell, Sheila (Other; 2007-)
• Shulse, Christine (Graduate; 2007-)
• Subbarao, Gowtham (Post Doc; 2007-)

1999. Allen EE, Facciotti D, Bartlett DH. Monounsaturated but not polyunsaturated fatty acids are required for growth of the deep-sea bacterium Photobacterium profundum SS9 at high pressure and low temperature. Appl. Environ. Microbiol. 65, 1710-1720.

2000. Allen EE, Bartlett DH. FabF is required for piezoregulation of cis-vaccenic acid levels and piezophilic growth of the deep-sea bacterium, Photobacterium profundum strain SS9. J. Bacteriol. 182, 1264-1271.

2002. Allen EE, Bartlett DH. Piezophiles: microbial adaptation to the deep-sea environment. In 'Extremophiles', UNESCO Encyclopedia for Life Support Systems. EOLSS Publishers, Oxford, UK.

2002. Allen EE, Bartlett DH. Structure and regulation of the omega-3 polyunsaturated fatty acid synthase genes from the deep-sea bacterium Photobacterium profundum strain SS9. Microbiology 148, 1903-1914.

2003. Palenik B, Brahamsha B, Larimer FW, Land L, Hauser L, Chain P, Lamerdin J, Regala W, Allen EE, McCarren J, Paulsen I, Dufresne A, Partensky F, Webb EA, Waterbury J. The genome of a motile marine Synechococcus. Nature 424, 1037-1042.

2004. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram R, Richardson P, Solovyev V, Rokhsar D, Banfield JF. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37-43.

2005. Allen EE, Banfield JF. Community genomics in microbial ecology and evolution. Nature Rev. Microbiol. 3, 489-498.

2005. Tyson GW, Lo I, Baker BJ, Allen EE, Hugenholtz P, Banfield JF. Genome-directed isolation of the key nitrogen fixer, Leptospirillum ferrodiazotrophum sp. nov., from an acidophilic microbial community. Appl. Environ. Microbiol. 71, 6319-6324.

2005. Banfield JF, Tyson GW, Allen EE, Whitaker RJ. The search for a molecular-level understanding of the processes that underpin the Earth's biogeochemical cycles. Rev. Mineral. Geochem. 59, 1-7.

2006. Baker BJ, Tyson GW, Webb RI, Flanagan J, Hugenholtz P, Allen EE, Banfield JF. Lineages of acidophilic archaea revealed by community genomic analysis. Science 314, 1933-1935.

2007. Allen EE, Tyson GW, Whitaker RJ, Detter JC, Richardson PM, Banfield JF. Genome dynamics in a natural archaeal population. Proc. Natl. Acad. Sci. U.S.A. 104, 1883-1888.

2007. Lo I, Denef V, VerBerkmoes NC, Shah M, Goltsman D, DiBartolo G, Tyson GW, Allen EE, Ram RJ, Detter C, Richardson P, Thelen MP, Hettich RL, Banfield JF. Strain-resolved community proteomics reveals that recombination shapes the genomes of acidophilic bacteria. Nature 446, 537-541.

2008. Robidart JC, Bench SR, Feldman RA, Novoradovsky A, Podell SB, Gaasterland T, Allen EE, Felbeck H. Metabolic versatility of the Riftia pachyptila endosymtiont revealed through metagenomics. Environ. Microbiol. 10, 727-737.

2008. Podell S, Gaasterland T, Allen EE. A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm. BMC Bioinformatics 9, 419.

2009. Penn, K, Jenkins C, Nett M, Udwary DW, Gontang EA, McGlinchey RP, Foster B, Lapidus A, Podell S, Allen EE, Moore BS, Jensen PR. Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria. ISME J. 1-11.