Publications

  1. 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. doi: 10.1038/ismej.2015.66. Epub 2015 Apr 28. PubMed PMID: 25918833.
  2. 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 Feb 1;2015:875784. doi: 10.1155/2015/875784. eCollection 2015. PubMed PMID: 25709557; PubMed Central PMCID: PMC4330952.
  3. 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. 2015 Jan 7;5:749. doi: 10.3389/fmicb.2014.00749. eCollection 2014. PubMed PMID: 25610434; PubMed Central PMCID: PMC4285802.
  4. 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). pii: e01172-14. doi: 10.1128/genomeA.01172-14. PubMed PMID: 25395641; PubMed Central PMCID: PMC4241667.
  5. 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. doi: 10.1038/nchembio.1564. Epub 2014 Jun 29. PubMed PMID: 24974229; PubMed Central PMCID: PMC4104138.
  6. 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 24;12(6):e1001889. doi: 10.1371/journal.pbio.1001889. eCollection 2014 Jun. PubMed PMID: 24959919; PubMed Central PMCID: PMC4068987.
  7. Gilbert JA, Dick GJ, Jenkins B, Heidelberg J, Allen EE, Mackey KRM, DeLong EF. (2014) Meeting report: Ocean 'omics science, technology and cyberinfrastructure: current challenges and future requirements (August 20-23, 2013). SIGS 9, doi:10.4056/574.
  8. Coates RC, Podell S, Korobeynikov A, Lapidus A, Pevzner P, Sherman DH, Allen EE, Gerwick L, Gerwick WH. (2014) Characterization of cyanobacterial hydrocarbon composition and distribution of biosynthetic pathways. PLoS One 9, e85140.
  9. Podell S, Emerson JB, Jones CM, Ugalde JA, Welch S, Heidelberg KB, Banfield JF, Allen EE. (2014) Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community. ISME J 8, 979.
  10. Ugalde JA, Narasingarao P, Kuo S, Podell S, Allen EE. (2013) Draft genome sequence of "Candidatus Halobonum tyrrellensis" strain G22, isolated from the hypersaline waters of Lake Tyrrell, Australia. Genome Announc 1, e1001-13.
  11. Kharbush JJ, Ugalde JA, Hogle SL, Allen EE, Aluwihare LI. (2013) Composite bacterial hopanoids and their microbial producers across oxygen gradients in the water column of the California Current. Appl Environ Microbiol 79, 7491.
  12. Ugalde JA, Gallardo MJ, Belmar C, Munoz P, Ruiz-Tagle N, Ferrada-Fuentes S, Espinoza C, Allen EE, Gallardo VA. (2013) Microbial life in a fjord: metagenomic analysis of a microbial mat in Chilean Patagonia. PLoS One 8, e71952.
  13. Summers MM, Katz S, Allen EE, Rouse GW. (2013) Association of rhizobia with a marine polychaete. Environ Microbiol Rep 5, 492.
  14. Emerson JB, Andrade K, Thomas BC, Norman A, Allen EE, Heidelberg KB, Banfield JF. (2013) Virus-host and CRISPR dynamics in Archaea-dominated hypersaline Lake Tyrrell, Victoria, Australia. Archaea 2013, Article ID 370871.
  15. Podell S, Ugalde JA, Narasingarao P, Banfield JF, Heidelberg KB, Allen EE. (2013) Assembly-driven metagenomics of a hypersaline microbial ecosystem. PLoS One 8, e61692.
  16. Emerson JB, Thomas BC, Andrade K, Allen EE, Heidelberg KB, Banfield JF. (2012) Metagenomic assembly reveals dynamic viral populations in hypersaline systems. Appl Environ Microbiol Published ahead of print 6 July 2012.
  17. Emerson JB, Thomas BC, Andrade K, Allen EE, Heidelberg KB, Banfield JF. (2012) Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly. Appl Environ Microbiol 78, 6309-6320.
  18. 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. (2012) PLoS One 7, e34064.
  19. Mosier AC, Allen EE, Kim M, Ferriera S, Francis CA. (2012) Genome sequence of a low-salinity ammonia oxidizing archaeon from the San Francisco Bay estuary, “Candidatus Nitrosoarchaeum limnia” BG20. J Bacteriol 194, 2119-2120.
  20. Mosier AC, Allen EE, Kim M, Ferriera S, Francis CA. (2012) Genome sequence of “Candidatus Nitrosopumilus salaria” BD31, an ammonia oxidizing archaeon enriched from the San Francisco Bay estuary. J Bacteriol 194, 2121-2122.
  21. Zeigler-Allen L, Allen EE, Badger J, McCrow JP, Paulson I, Elbourne LDH, Thiagrijan M, Nealson KH, Williamson SJ, Venter JC, Allen AE. (2012) Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic. ISME J 6, 1403-1414
  22. Narasingarao P, Podell S, Ugalde JA, Brochier-Armanet C, Emerson J, Brocks JJ, Heidelberg, KB, Banfield JF, Allen EE. (2012) De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J 6, 81-93
  23. Ugalde JA, Podell S, Narasingarao P, Allen EE. (2011) Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between Archaea and Bacteria. Biol Direct 6, 52.
  24. Shulse CN, Allen EE. (2011) Widespread occurence of secondary lipid biosynthesis potential in microbial lineages. PLoS One 6, e20146.
  25. 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. (2011) Going deeper: Metagenome of a hadopelagic microbial community. PLoS One 6, e20388.
  26. Jones AC, Monroe EA, Podell S, Hess WR, Klages S, Esquenazi E, Niessen S, Hoover H, Rothmann M, Lasken RS, Yate JR, Reinhardt R, Kube M, Burkart M, Allen EE, Dorrestein PC, Gerwick WH, Gerwick L (2011) Genomic insights into the physiology and ecology of the marine filamentous cyanbacterium Lyngbya majuscule. Proc Natl Acad Sci 108, 8815-8820.
  27. Shulse CN, Allen EE. (2010) Diversity and distribution of microbial long-chain fatty acid biosynthetic genes in the marine environment. Environ Microbiol 13, 684-695.
  28. Eloe EA, Shulse CN, Fadrosh DW, Williamson SJ, Allen EE, Bartlett DH. (2010) Compositional differences in particle-associated and free-living microbial assemblages from an extreme deep ocean environment. Environ Microbiol Reports 3 (4), 449-458.
  29. Sun S, Chen J, Li W, Altinitas I, Lin A, Peltier S, Stocks K, Allen EE, Ellisman M, Grethe J, Wooley J. (2010) Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucl Acids Res 39, D546-551.
  30. Han S, Narasingarao P, Obraztsova A, Gieskes J, Hartmann A, Tebo BM, Allen EE, Deheyn DD. (2010) Mercury speciation in marine sediments under sulfate-limited conditions. Environ Sci Technol 44, 3752-3757.
  31. Morin PA, Archer FI, Foote AD, Vistrup 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. (2010) Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species. Genome Res 20, 908-916.
  32. Penn K, Jenkins C, Nett M, Udwary DW, Gontang EA, McGlinchey RP, Foster B, Lapidus A, Podell S, Allen EE, Moore BS, Jensen PR. (2009) Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria. ISME J 3, 1193-1203.
  33. Podell S, Gaasterland T, Allen EE (2008) A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm. BMC Bioinformatics 9, 419.
  34. Robidart JC, Bench SR, Feldman Ra, Novoradovsky A, Podell SB, Gaasterland T, Allen EE, Felbeck H. (2008) Metabolic versatility of the Riftia pachyptila endosymbiont revealed through metagenomics. Environ Microbiol 10, 727-737.
  35. Lo I, Denef V, VerBerkmoes NC, Shah M, Goltsman D, DiBartolo G, Tyson GW, Allen EE, Ram RJ, Detter JC, Richardson P, Thelen MP, Hettich RL, Banfield JF. (2007) Strain-resolved community proteomics reveals that recombination shapes the genomes of acidophilic bacteria. Nature 446, 537-541.
  36. Allen EE, Tyson GW, Whitaker RJ, Detter JC, Richardson PM, Banfield JF. (2007) Genome dynamics in a natural archaeal population. Proc Natl Acad Sci USA 104, 1883-1888.
  37. Baker BJ, Tyson GW, Webb RI, Flanagan J, Hugenholtz P, Allen EE, Banfield JF. (2006) Lineages of acidophilic archaea revealed by community genomic analysis. Science 314, 1933-1935.
  38. Banfield JF, Tyson GW, Allen EE, Whitaker RJ. (2005) The search for a molecular-level understanding of the processes that underpin the Earth’s biogeochemical cycles. (2005) Rev Mineral Geochem 59, 1-7.
  39. Tyson GW, Lo I, Baker BJ, Allen EE, Hugenholtz P, Banfield JF. (2005) Genome-directed isolation of the key nitrogen fixer, Leptospirillum ferrodiazotrophum sp. nov., from an acidophilic microbial community. Appl Environ Microbiol 71, 6319-6324.
  40. Allen EE, Banfield JF. (2005) Community genomics in microbial ecology and evolution. Nature Rev Microbiol 3, 489-498.
  41. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram R, Richardson P, Solovyev V, Rokshar D, Banfield JF. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37-43.
  42. Palenik B, Brahamsha B, Larimer FW, Land M, Hauser L, Chain P, Lamerdin J, Regala W, Allen EE, McCarren J, Paulsen I, Dufresne A, Partensky F, Webb EA, Waterbury J. (2003) The genome of a motile marine Synechococcus. Nature 424, 1037-1042.
  43. Allen EE (2002) Piezophysiology of membrane-based adaptations in the deep-sea bacterium Photobacterium profundum strain SS9. Dissertation, University of California, San Diego.
  44. Allen EE, Bartlett DH. (2002) 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.
  45. Allen EE, Bartlett DH. (2002) Piezophiles: microbial adaptation to the deep-sea environment. In ‘Extremophiles’, UNESCO Encyclopedia for Life Support Systems. EOLSS Publishers, Oxford, UK.
  46. Allen EE, Bartlett DH. (2000) 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.
  47. Kato C, Nogi Y, Komatsu T, Sato TI, Miura T, Allen EE, Lauro F, Kurino S, Noguchi S. (2000) Report of Japan Trench Microbial Investigation Cruise on YK99-05, leg 4. JAMSTEC J Deep Sea Res 17, 23-28.
  48. Allen EE, Facciotti D, Bartlett DH. (1999) 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.
  49. Bartlett DH, Allen EE. (1998) Role of unsaturated fatty acids in growth at high pressure and low temperature in the deep-sea bacterium Photobacterium profundum strain SS9. p. 32-37. In High Pressure Biology and Medicine (P.B,. Bennett, I. Demchenko, and R. R. Marquis, ed.), University of Rochester Press, Rochester, N.Y.