Eric Allen

TitleAssociate Researcher
InstitutionUniversity of California San Diego
DepartmentMarine Biology
Address9500 Gilman Drive #0202
La Jolla CA 92093
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    Collapse Research 
    Collapse Research Activities and Funding
    Phylogenetic Binning of Metagenomic Sequence Data
    NIH/NHGRI R21HG005107Aug 24, 2009 - Jul 31, 2012
    Role: Principal Investigator

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    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Minich JJ, Zhu Q, Xu ZZ, Amir A, Ngochera M, Simwaka M, Allen EE, Zidana H, Knight R. Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus). Microbiologyopen. 2018 Aug 31; e00716. PMID: 30168288.
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    2. Plominsky AM, Henríquez-Castillo C, Delherbe N, Podell S, Ramirez-Flandes S, Ugalde JA, Santibañez JF, van den Engh G, Hanselmann K, Ulloa O, De la Iglesia R, Allen EE, Trefault N. Distinctive Archaeal Composition of an Artisanal Crystallizer Pond and Functional Insights Into Salt-Saturated Hypersaline Environment Adaptation. Front Microbiol. 2018; 9:1800. PMID: 30154761.
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    3. Guillemette R, Kaneko R, Blanton J, Tan J, Witt M, Hamilton S, Allen EE, Medina M, Hamasaki K, Koch BP, Azam F. Bacterioplankton drawdown of coral mass-spawned organic matter. ISME J. 2018 Jun 08. PMID: 29884827.
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    4. Allemann MN, Allen EE. Characterization and Application of Marine Microbial Omega-3 Polyunsaturated Fatty Acid Synthesis. Methods Enzymol. 2018; 605:3-32. PMID: 29909829.
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    5. Peoples LM, Donaldson S, Osuntokun O, Xia Q, Nelson A, Blanton J, Allen EE, Church MJ, Bartlett DH. Vertically distinct microbial communities in the Mariana and Kermadec trenches. PLoS One. 2018; 13(4):e0195102. PMID: 29621268.
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    6. Plominsky AM, Trefault N, Podell S, Blanton JM, De la Iglesia R, Allen EE, von Dassow P, Ulloa O. Metabolic potential and in situ transcriptomic profiles of previously uncharacterized key microbial groups involved in coupled carbon, nitrogen and sulfur cycling in anoxic marine zones. Environ Microbiol. 2018 Mar 24. PMID: 29575531.
      View in: PubMed
    7. Minich JJ, Zhu Q, Janssen S, Hendrickson R, Amir A, Vetter R, Hyde J, Doty MM, Stillwell K, Benardini J, Kim JH, Allen EE, Venkateswaran K, Knight R. KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples. mSystems. 2018 May-Jun; 3(3). PMID: 29577086.
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    8. Agarwal V, Blanton JM, Podell S, Taton A, Schorn MA, Busch J, Lin Z, Schmidt EW, Jensen PR, Paul VJ, Biggs JS, Golden JW, Allen EE, Moore BS. Metagenomic discovery of polybrominated diphenyl ether biosynthesis by marine sponges. Nat Chem Biol. 2017 05; 13(5):537-543. PMID: 28319100.
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    9. Leao T, Castelão G, Korobeynikov A, Monroe EA, Podell S, Glukhov E, Allen EE, Gerwick WH, Gerwick L. Comparative genomics uncovers the prolific and distinctive metabolic potential of the cyanobacterial genus Moorea. Proc Natl Acad Sci U S A. 2017 03 21; 114(12):3198-3203. PMID: 28265051.
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    10. Demidenko A, Akberdin IR, Allemann M, Allen EE, Kalyuzhnaya MG. Fatty Acid Biosynthesis Pathways in Methylomicrobium buryatense 5G(B1). Front Microbiol. 2016; 7:2167. PMID: 28119683.
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    11. Paerl RW, Bouget FY, Lozano JC, Vergé V, Schatt P, Allen EE, Palenik B, Azam F. Use of plankton-derived vitamin B1 precursors, especially thiazole-related precursor, by key marine picoeukaryotic phytoplankton. ISME J. 2017 03; 11(3):753-765. PMID: 27935586.
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    12. Traller JC, Cokus SJ, Lopez DA, Gaidarenko O, Smith SR, McCrow JP, Gallaher SD, Podell S, Thompson M, Cook O, Morselli M, Jaroszewicz A, Allen EE, Allen AE, Merchant SS, Pellegrini M, Hildebrand M. Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype. Biotechnol Biofuels. 2016; 9:258. PMID: 27933100.
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    13. Fuentes-Valdés JJ, Plominsky AM, Allen EE, Tamames J, Vásquez M. Complete Genome Sequence of a Cylindrospermopsin-Producing Cyanobacterium, Cylindrospermopsis raciborskii CS505, Containing a Circular Chromosome and a Single Extrachromosomal Element. Genome Announc. 2016 Aug 25; 4(4). PMID: 27563040; PMCID: PMC5000824.
    14. Andrade K, Logemann J, Heidelberg KB, Emerson JB, Comolli LR, Hug LA, Probst AJ, Keillar A, Thomas BC, Miller CS, Allen EE, Moreau JW, Brocks JJ, Banfield JF. Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem. ISME J. 2015 Dec; 9(12):2697-711. PMID: 25918833; PMCID: PMC4817636 [Available on 12/01/16].
    15. Tully BJ, Emerson JB, Andrade K, Brocks JJ, Allen EE, Banfield JF, Heidelberg KB. De novo sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, reveal a variable genomic landscape. Archaea. 2015; 2015:875784. PMID: 25709557; PMCID: PMC4330952.
    16. Marietou A, Nguyen AT, Allen EE, Bartlett DH. Adaptive laboratory evolution of Escherichia coli K-12 MG1655 for growth at high hydrostatic pressure. Front Microbiol. 2014; 5:749. PMID: 25610434; PMCID: PMC4285802.
    17. Plominsky AM, Delherbe N, Ugalde JA, Allen EE, Blanchet M, Ikeda P, Santibañez F, Hanselmann K, Ulloa O, De la Iglesia R, von Dassow P, Astorga M, Gálvez MJ, González ML, Henríquez-Castillo C, Vaulot D, Lopes do Santos A, van den Engh G, Gimpel C, Bertoglio F, Delgado Y, Docmac F, Elizondo-Patrone C, Narváez S, Sorroche F, Rojas-Herrera M, Trefault N. Metagenome sequencing of the microbial community of a solar saltern crystallizer pond at cáhuil lagoon, chile. Genome Announc. 2014 Nov 13; 2(6). PMID: 25395641; PMCID: PMC4241667.
    18. Agarwal V, El Gamal AA, Yamanaka K, Poth D, Kersten RD, Schorn M, Allen EE, Moore BS. Biosynthesis of polybrominated aromatic organic compounds by marine bacteria. Nat Chem Biol. 2014 Aug; 10(8):640-7. PMID: 24974229; PMCID: PMC4104138.
    19. Keeling PJ, Burki F, Wilcox HM, Allam B, Allen EE, Amaral-Zettler LA, Armbrust EV, Archibald JM, Bharti AK, Bell CJ, Beszteri B, Bidle KD, Cameron CT, Campbell L, Caron DA, Cattolico RA, Collier JL, Coyne K, Davy SK, Deschamps P, Dyhrman ST, Edvardsen B, Gates RD, Gobler CJ, Greenwood SJ, Guida SM, Jacobi JL, Jakobsen KS, James ER, Jenkins B, John U, Johnson MD, Juhl AR, Kamp A, Katz LA, Kiene R, Kudryavtsev A, Leander BS, Lin S, Lovejoy C, Lynn D, Marchetti A, McManus G, Nedelcu AM, Menden-Deuer S, Miceli C, Mock T, Montresor M, Moran MA, Murray S, Nadathur G, Nagai S, Ngam PB, Palenik B, Pawlowski J, Petroni G, Piganeau G, Posewitz MC, Rengefors K, Romano G, Rumpho ME, Rynearson T, Schilling KB, Schroeder DC, Simpson AG, Slamovits CH, Smith DR, Smith GJ, Smith SR, Sosik HM, Stief P, Theriot E, Twary SN, Umale PE, Vaulot D, Wawrik B, Wheeler GL, Wilson WH, Xu Y, Zingone A, Worden AZ. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol. 2014 Jun; 12(6):e1001889. PMID: 24959919; PMCID: PMC4068987.
    20. Coates RC, Podell S, Korobeynikov A, Lapidus A, Pevzner P, Sherman DH, Allen EE, Gerwick L, Gerwick WH. Characterization of cyanobacterial hydrocarbon composition and distribution of biosynthetic pathways. PLoS One. 2014; 9(1):e85140. PMID: 24475038.
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    21. Podell S, Emerson JB, Jones CM, Ugalde JA, Welch S, Heidelberg KB, Banfield JF, Allen EE. Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community. ISME J. 2014 May; 8(5):979-90. PMID: 24335829; PMCID: PMC3996697.
    22. Ugalde JA, Narasingarao P, Kuo S, Podell S, Allen EE. Draft Genome Sequence of "Candidatus Halobonum tyrrellensis" Strain G22, Isolated from the Hypersaline Waters of Lake Tyrrell, Australia. Genome Announc. 2013 Dec 12; 1(6). PMID: 24336364; PMCID: PMC3861417.
    23. Kharbush JJ, Ugalde JA, Hogle SL, Allen EE, Aluwihare LI. Composite bacterial hopanoids and their microbial producers across oxygen gradients in the water column of the California Current. Appl Environ Microbiol. 2013 Dec; 79(23):7491-501. PMID: 24077702; PMCID: PMC3837760.
    24. Ugalde JA, Gallardo MJ, Belmar C, Muñoz P, Ruiz-Tagle N, Ferrada-Fuentes S, Espinoza C, Allen EE, Gallardo VA. Microbial life in a fjord: metagenomic analysis of a microbial mat in Chilean patagonia. PLoS One. 2013; 8(8):e71952. PMID: 24015199.
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    25. Emerson JB, Andrade K, Thomas BC, Norman A, Allen EE, Heidelberg KB, Banfield JF. Virus-host and CRISPR dynamics in Archaea-dominated hypersaline Lake Tyrrell, Victoria, Australia. Archaea. 2013; 2013:370871. PMID: 23853523; PMCID: PMC3703381.
    26. Podell S, Ugalde JA, Narasingarao P, Banfield JF, Heidelberg KB, Allen EE. Assembly-driven community genomics of a hypersaline microbial ecosystem. PLoS One. 2013; 8(4):e61692. PMID: 23637883; PMCID: PMC3630111.
    27. Summers MM, Katz S, Allen EE, Rouse GW. Association of rhizobia with a marine polychaete. Environ Microbiol Rep. 2013 Aug; 5(4):492-8. PMID: 23864561.
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    28. Emerson JB, Thomas BC, Andrade K, Allen EE, Heidelberg KB, Banfield JF. Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly. Appl Environ Microbiol. 2012 Sep; 78(17):6309-20. PMID: 22773627; PMCID: PMC3416638.
    29. Mosier AC, Allen EE, Kim M, Ferriera S, Francis CA. Genome sequence of "Candidatus Nitrosopumilus salaria" BD31, an ammonia-oxidizing archaeon from the San Francisco Bay estuary. J Bacteriol. 2012 Apr; 194(8):2121-2. PMID: 22461555; PMCID: PMC3318490.
    30. Mosier AC, Allen EE, Kim M, Ferriera S, Francis CA. Genome sequence of "Candidatus Nitrosoarchaeum limnia" BG20, a low-salinity ammonia-oxidizing archaeon from the San Francisco Bay estuary. J Bacteriol. 2012 Apr; 194(8):2119-20. PMID: 22461554; PMCID: PMC3318456.
    31. Zeigler Allen L, Allen EE, Badger JH, McCrow JP, Paulsen IT, Elbourne LD, Thiagarajan M, Rusch DB, 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. 2012 Jul; 6(7):1403-14. PMID: 22278668; PMCID: PMC3379637.
    32. Ugalde JA, Podell S, Narasingarao P, Allen EE. Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria. Biol Direct. 2011 Oct 10; 6:52. PMID: 21985229; PMCID: PMC3198991.
    33. Narasingarao P, Podell S, Ugalde JA, Brochier-Armanet C, Emerson JB, 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. 2012 Jan; 6(1):81-93. PMID: 21716304; PMCID: PMC3246234.
    34. Eloe EA, Fadrosh DW, Novotny M, Zeigler Allen L, Kim M, Lombardo MJ, Yee-Greenbaum J, Yooseph S, Allen EE, Lasken R, Williamson SJ, Bartlett DH. Going deeper: metagenome of a hadopelagic microbial community. PLoS One. 2011; 6(5):e20388. PMID: 21629664; PMCID: PMC3101246.
    35. Shulse CN, Allen EE. Widespread occurrence of secondary lipid biosynthesis potential in microbial lineages. PLoS One. 2011; 6(5):e20146. PMID: 21629834; PMCID: PMC3098273.
    36. Jones AC, Monroe EA, Podell S, Hess WR, Klages S, Esquenazi E, Niessen S, Hoover H, Rothmann M, Lasken RS, Yates JR, Reinhardt R, Kube M, Burkart MD, Allen EE, Dorrestein PC, Gerwick WH, Gerwick L. Genomic insights into the physiology and ecology of the marine filamentous cyanobacterium Lyngbya majuscula. Proc Natl Acad Sci U S A. 2011 May 24; 108(21):8815-20. PMID: 21555588; PMCID: PMC3102346.
    37. 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 Rep. 2011 Aug; 3(4):449-58. PMID: 23761307.
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    38. Shulse CN, Allen EE. Diversity and distribution of microbial long-chain fatty acid biosynthetic genes in the marine environment. Environ Microbiol. 2011 Mar; 13(3):684-95. PMID: 21105981.
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    39. 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. Nucleic Acids Res. 2011 Jan; 39(Database issue):D546-51. PMID: 21045053; PMCID: PMC3013694.
    40. 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. Environ Sci Technol. 2010 May 15; 44(10):3752-7. PMID: 20429556.
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    41. 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 MT, Harkins T. Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species. Genome Res. 2010 Jul; 20(7):908-16. PMID: 20413674; PMCID: PMC2892092.
    42. 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. 2009 Oct; 3(10):1193-203. PMID: 19474814; PMCID: PMC2749086.
    43. Podell S, Gaasterland T, Allen EE. A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm. BMC Bioinformatics. 2008 Oct 07; 9:419. PMID: 18840280; PMCID: PMC2573894.
    44. Robidart JC, Bench SR, Feldman RA, Novoradovsky A, Podell SB, Gaasterland T, Allen EE, Felbeck H. Metabolic versatility of the Riftia pachyptila endosymbiont revealed through metagenomics. Environ Microbiol. 2008 Mar; 10(3):727-37. PMID: 18237306.
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    45. Lo I, Denef VJ, Verberkmoes NC, Shah MB, Goltsman D, DiBartolo G, Tyson GW, Allen EE, Ram RJ, Detter JC, Richardson P, Thelen MP, Hettich RL, Banfield JF. Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature. 2007 Mar 29; 446(7135):537-41. PMID: 17344860.
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    46. 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. 2007 Feb 06; 104(6):1883-8. PMID: 17267615; PMCID: PMC1794283.
    47. Baker BJ, Tyson GW, Webb RI, Flanagan J, Hugenholtz P, Allen EE, Banfield JF. Lineages of acidophilic archaea revealed by community genomic analysis. Science. 2006 Dec 22; 314(5807):1933-5. PMID: 17185602.
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    48. 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. 2005 Oct; 71(10):6319-24. PMID: 16204553; PMCID: PMC1266007.
    49. Allen EE, Banfield JF. Community genomics in microbial ecology and evolution. Nat Rev Microbiol. 2005 Jun; 3(6):489-98. PMID: 15931167.
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    50. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature. 2004 Mar 04; 428(6978):37-43. PMID: 14961025.
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    51. 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. 2002 Jun; 148(Pt 6):1903-13. PMID: 12055309.
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