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ALLEN, ERIC

Associate Professor of Marine Biology

and Molecular Biology (Biological Sciences)

Degrees:

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

Research Interests:

• Microbial genomics and metagenomics
• Microbial oceanography
• Genetic structure of microbial populations
• Molecular genetics and ecological physiology of microbial "secondary lipid" biosynthesis (e.g., omega-3 polyunsaturated fatty acids)

Courses Recently Taught:

• ESYS101: Environmental Biology
• SIO 278: Seminar in Ocean Biosciences
• SIO278: Seminar in Ocean Biosciences
• SIO297: Marine Biology Seminar

Honors and Awards:

• 2012 - 2017 NSF CAREER Award
• 2011 - 2012 Hellman Fellow

Mentoring:

• Pieper, Lindsey (Undergrad; 2013-)
• Quijano, Marissa (Undergrad; 2013-)
• Blanton, Jessica (Graduate; 2012-)
• Allemann, Marco (Graduate; 2011-)
• Guiza, Bridget (Undergrad; 2010-2011)
• Fernandez, Brittany (Masters; 2009-2011)
• Golder, Julian (Undergrad; 2009-2010)
• Hammer, Toby (Undergrad; 2008-2009)
• Prieto-Davo, Alejandra (Post Doc; 2008-2009)
• Ugalde, Juan (Graduate; 2008-)
• Narasingarao, Priya (Post Doc; 2007-2010)
• Podell, Sheila (Other; 2007-)
• Shulse, Christine (Graduate; 2007-2012)
• Subbarao, Gowtham (Post Doc; 2007-)

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2013. Podell S, Ugalde JA, Narasingarao P, Banfield JF, Heidelberg KB, Allen EE. Assembly-driven community genomics of a hypersaline microbial ecosystem. PLoS One in press

2013. Summers M, Katz S, Allen EE, Rouse GW. Association of rhizobia with a marine polychaete. Environ Microbiol Reports in press

2012. Emerson JB, Thomas BC, Andrade K, Allen EE, Heidelberg KB, Banfield JF. Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly. Environ Microbiol 78:6309-6320.

2012. Ziemert N, Podell S, Penn K, Badger JH, Allen EE, Jensen PR. The Natural Product Domain Seeker NaPDoS: A phylogeny based bioinformatic tool to classify secondary metabolite gene diversity. PLoS One 7:e34064.

2012. Mosier AC, Allen EE, Kim M, Ferriera S, Francis CA. Genome sequence of “Candidatus Nitrosopumilus salaria” BD31, an ammonia oxidizing archaeon enriched from the San Francisco Bay estuary. J Bacteriol 194:2121-2122.

2012. Mosier AC, Allen EE, Kim M, Ferriera S, Francis CA. Genome sequence of a low-salinity ammonia oxidizing archaeon from the San Francisco Bay estuary, “Candidatus Nitrosoarchaeum limnia” BG20. J Bacteriol 194:2119-2120.

2012. Zeigler-Allen L, Allen EE, Badger J, McCrow JP, Paulson I, Elbourne LDH, Thiagrijan M, Nealson KH, Williamson SJ, Venter JC, Allen AE. Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic. ISME J Advanced Online Publication, January 26, 2012; doi:10.1038/ismej.2011.201

2012. Narasingarao P, Podell S, Ugalde JA, Brochier-Armanet C, Emerson J, Brocks JJ, Heidelberg, KB, Banfield JF, Allen EE. De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J 6:81-93.

2011. Ugalde JA, Podell S, Narasingarao P, Allen EE. Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between Archaea and Bacteria. Biol Direct 6:52.

2011. Shulse CN, Allen EE. Widespread occurence of secondary lipid biosynthesis potential in microbial lineages. PLoS One 6:e20146.

2011. Eloe EA, Fadrosh DW, Novotny M, Zeigler Allen L, Kim M, Lombardo M-J, Yee-Greenbaum J, Yooseph S, Allen EE, Lasken R, Williamson SJ, Bartlett DH. Going deeper: Metagenome of a hadopelagic microbial community. PLoS One 6:e20388.

2011. Jones A, Monroe E, Podell S, Hess W, Klages S, Esquenazi E, Niessen S, Hoover H, Rothmann M, Lasken R, Yates III J, Reinhardt R, Kube M, Burkart M, Allen EE, Gerwick W, Gerwick L. Genomic insights into the physiology and ecology of the marine filamentous cyanbacterium Lyngbya majuscule. Proc Natl Acad Sci USA 108:8815-8820.

2011. Shulse CN, Allen EE. Diversity and distribution of microbial long-chain fatty acid biosynthetic genes in the marine environment. Environ Microbiol 13:684-695.

2010. Eloe EA, Shulse CN, Fadrosh DW, Williamson SJ, Allen EE, Bartlett DH. Compositional differences in particle-associated and free-living microbial assemblages from an extreme deep ocean environment. Environ Microbiol Reports (first published online : 24 NOV 2010), DOI: 10.1111/j.1758-2229.2010.00223.

2010. Sun S, Chen J, Li W, Altintas I, Lin A, Peltier S, Stocks K, Allen EE, Ellisman M, Grethe J, Wooley J. Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucl Acids Res 39:D546-551.

2010. Han S, Narasingarao P, Obraztsova A, Gieskes J, Hartmann AC, Tebo BM, Allen EE, Deheyn DD. Mercury speciation in marine sediments under sulfate-limited conditions. Env Sci Technol 44:3752-3757.

2010. Morin PA, Archer FI, Foote AD, Vilstrup J, Allen EE, Wade P, Durban J, Parsons K, Pitman R, Li L, Bouffard P, Abel Nielsen SC, Rasmussen M, Willerslev E, Gilbert MTP, Harkins T. Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species. Genome Res 20:908-916.

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 3:1193-1203.

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.

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.

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.

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

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.

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.

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

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.

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.

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.

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.

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.

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.