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Items: 1 to 50 of 83

1.

Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection.

Kolody BC, McCrow JP, Allen LZ, Aylward FO, Fontanez KM, Moustafa A, Moniruzzaman M, Chavez FP, Scholin CA, Allen EE, Worden AZ, Delong EF, Allen AE.

ISME J. 2019 Nov;13(11):2817-2833. doi: 10.1038/s41396-019-0472-2. Epub 2019 Jul 18.

2.

Comparative Genomics of Cyanobacterial Symbionts Reveals Distinct, Specialized Metabolism in Tropical Dysideidae Sponges.

Schorn MA, Jordan PA, Podell S, Blanton JM, Agarwal V, Biggs JS, Allen EE, Moore BS.

MBio. 2019 May 14;10(3). pii: e00821-19. doi: 10.1128/mBio.00821-19.

3.

Linkage of Marine Bacterial Polyunsaturated Fatty Acid and Long-Chain Hydrocarbon Biosynthesis.

Allemann MN, Shulse CN, Allen EE.

Front Microbiol. 2019 Apr 3;10:702. doi: 10.3389/fmicb.2019.00702. eCollection 2019.

4.

Microbial Community Diversity Within Sediments from Two Geographically Separated Hadal Trenches.

Peoples LM, Grammatopoulou E, Pombrol M, Xu X, Osuntokun O, Blanton J, Allen EE, Nunnally CC, Drazen JC, Mayor DJ, Bartlett DH.

Front Microbiol. 2019 Mar 15;10:347. doi: 10.3389/fmicb.2019.00347. eCollection 2019.

5.

Diversity and composition of intertidal gastropod microbiomes across a major marine biogeographic boundary.

Neu AT, Allen EE, Roy K.

Environ Microbiol Rep. 2019 Jun;11(3):434-447. doi: 10.1111/1758-2229.12743. Epub 2019 Mar 27.

PMID:
30834681
6.

High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity.

Minich JJ, Humphrey G, Benitez RAS, Sanders J, Swafford A, Allen EE, Knight R.

mSystems. 2018 Nov 6;3(6). pii: e00166-18. doi: 10.1128/mSystems.00166-18. eCollection 2018 Nov-Dec.

7.

Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles.

Podell S, Blanton JM, Neu A, Agarwal V, Biggs JS, Moore BS, Allen EE.

ISME J. 2019 Feb;13(2):468-481. doi: 10.1038/s41396-018-0292-9. Epub 2018 Oct 5.

PMID:
30291328
8.

Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus).

Minich JJ, Zhu Q, Xu ZZ, Amir A, Ngochera M, Simwaka M, Allen EE, Zidana H, Knight R.

Microbiologyopen. 2018 Dec;7(6):e00716. doi: 10.1002/mbo3.716. Epub 2018 Aug 31.

9.

Distinctive Archaeal Composition of an Artisanal Crystallizer Pond and Functional Insights Into Salt-Saturated Hypersaline Environment Adaptation.

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.

Front Microbiol. 2018 Aug 14;9:1800. doi: 10.3389/fmicb.2018.01800. eCollection 2018.

10.

Characterization and Application of Marine Microbial Omega-3 Polyunsaturated Fatty Acid Synthesis.

Allemann MN, Allen EE.

Methods Enzymol. 2018;605:3-32. doi: 10.1016/bs.mie.2018.02.018. Epub 2018 Apr 6.

PMID:
29909829
11.

Bacterioplankton drawdown of coral mass-spawned organic matter.

Guillemette R, Kaneko R, Blanton J, Tan J, Witt M, Hamilton S, Allen EE, Medina M, Hamasaki K, Koch BP, Azam F.

ISME J. 2018 Sep;12(9):2238-2251. doi: 10.1038/s41396-018-0197-7. Epub 2018 Jun 8.

12.

Vertically distinct microbial communities in the Mariana and Kermadec trenches.

Peoples LM, Donaldson S, Osuntokun O, Xia Q, Nelson A, Blanton J, Allen EE, Church MJ, Bartlett DH.

PLoS One. 2018 Apr 5;13(4):e0195102. doi: 10.1371/journal.pone.0195102. eCollection 2018.

13.

KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples.

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.

mSystems. 2018 Mar 13;3(3). pii: e00218-17. doi: 10.1128/mSystems.00218-17. eCollection 2018 May-Jun.

14.

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.

Plominsky AM, Trefault N, Podell S, Blanton JM, De la Iglesia R, Allen EE, von Dassow P, Ulloa O.

Environ Microbiol. 2018 Aug;20(8):2727-2742. doi: 10.1111/1462-2920.14109. Epub 2018 Apr 16.

PMID:
29575531
15.

Multicomponent Condensation Reactions via ortho-Quinone Methides.

Allen EE, Zhu C, Panek JS, Schaus SE.

Org Lett. 2017 Apr 7;19(7):1878-1881. doi: 10.1021/acs.orglett.7b00647. Epub 2017 Mar 30.

16.

Metagenomic discovery of polybrominated diphenyl ether biosynthesis by marine sponges.

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.

Nat Chem Biol. 2017 May;13(5):537-543. doi: 10.1038/nchembio.2330. Epub 2017 Mar 20.

17.

Comparative genomics uncovers the prolific and distinctive metabolic potential of the cyanobacterial genus Moorea.

Leao T, Castelão G, Korobeynikov A, Monroe EA, Podell S, Glukhov E, Allen EE, Gerwick WH, Gerwick L.

Proc Natl Acad Sci U S A. 2017 Mar 21;114(12):3198-3203. doi: 10.1073/pnas.1618556114. Epub 2017 Mar 6.

18.

Fatty Acid Biosynthesis Pathways in Methylomicrobium buryatense 5G(B1).

Demidenko A, Akberdin IR, Allemann M, Allen EE, Kalyuzhnaya MG.

Front Microbiol. 2017 Jan 10;7:2167. doi: 10.3389/fmicb.2016.02167. eCollection 2016.

19.

Use of plankton-derived vitamin B1 precursors, especially thiazole-related precursor, by key marine picoeukaryotic phytoplankton.

Paerl RW, Bouget FY, Lozano JC, Vergé V, Schatt P, Allen EE, Palenik B, Azam F.

ISME J. 2017 Mar;11(3):753-765. doi: 10.1038/ismej.2016.145. Epub 2016 Dec 9.

20.

Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype.

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.

Biotechnol Biofuels. 2016 Nov 25;9:258. eCollection 2016.

21.

Complete Genome Sequence of a Cylindrospermopsin-Producing Cyanobacterium, Cylindrospermopsis raciborskii CS505, Containing a Circular Chromosome and a Single Extrachromosomal Element.

Fuentes-Valdés JJ, Plominsky AM, Allen EE, Tamames J, Vásquez M.

Genome Announc. 2016 Aug 25;4(4). pii: e00823-16. doi: 10.1128/genomeA.00823-16.

22.

Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem.

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.

ISME J. 2015 Dec;9(12):2697-711. doi: 10.1038/ismej.2015.66. Epub 2015 Apr 28.

23.

De novo sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, reveal a variable genomic landscape.

Tully BJ, Emerson JB, Andrade K, Brocks JJ, Allen EE, Banfield JF, Heidelberg KB.

Archaea. 2015 Feb 1;2015:875784. doi: 10.1155/2015/875784. eCollection 2015.

24.

Adaptive laboratory evolution of Escherichia coli K-12 MG1655 for growth at high hydrostatic pressure.

Marietou A, Nguyen AT, Allen EE, Bartlett DH.

Front Microbiol. 2015 Jan 7;5:749. doi: 10.3389/fmicb.2014.00749. eCollection 2014.

25.

Metagenome sequencing of the microbial community of a solar saltern crystallizer pond at cáhuil lagoon, chile.

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.

Genome Announc. 2014 Nov 13;2(6). pii: e01172-14. doi: 10.1128/genomeA.01172-14.

26.

Biosynthesis of polybrominated aromatic organic compounds by marine bacteria.

Agarwal V, El Gamal AA, Yamanaka K, Poth D, Kersten RD, Schorn M, Allen EE, Moore BS.

Nat Chem Biol. 2014 Aug;10(8):640-7. doi: 10.1038/nchembio.1564. Epub 2014 Jun 29.

27.

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing.

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.

PLoS Biol. 2014 Jun 24;12(6):e1001889. doi: 10.1371/journal.pbio.1001889. eCollection 2014 Jun. No abstract available.

28.

Characterization of cyanobacterial hydrocarbon composition and distribution of biosynthetic pathways.

Coates RC, Podell S, Korobeynikov A, Lapidus A, Pevzner P, Sherman DH, Allen EE, Gerwick L, Gerwick WH.

PLoS One. 2014 Jan 27;9(1):e85140. doi: 10.1371/journal.pone.0085140. eCollection 2014.

29.

Draft Genome Sequence of "Candidatus Halobonum tyrrellensis" Strain G22, Isolated from the Hypersaline Waters of Lake Tyrrell, Australia.

Ugalde JA, Narasingarao P, Kuo S, Podell S, Allen EE.

Genome Announc. 2013 Dec 12;1(6). pii: e01001-13. doi: 10.1128/genomeA.01001-13.

30.

Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community.

Podell S, Emerson JB, Jones CM, Ugalde JA, Welch S, Heidelberg KB, Banfield JF, Allen EE.

ISME J. 2014 May;8(5):979-90. doi: 10.1038/ismej.2013.221. Epub 2013 Dec 12.

31.

Composite bacterial hopanoids and their microbial producers across oxygen gradients in the water column of the California Current.

Kharbush JJ, Ugalde JA, Hogle SL, Allen EE, Aluwihare LI.

Appl Environ Microbiol. 2013 Dec;79(23):7491-501. doi: 10.1128/AEM.02367-13. Epub 2013 Sep 27. Erratum in: Appl Environ Microbiol. 2014 May;80(10):3283.

32.

Microbial life in a fjord: metagenomic analysis of a microbial mat in Chilean patagonia.

Ugalde JA, Gallardo MJ, Belmar C, Muñoz P, Ruiz-Tagle N, Ferrada-Fuentes S, Espinoza C, Allen EE, Gallardo VA.

PLoS One. 2013 Aug 28;8(8):e71952. doi: 10.1371/journal.pone.0071952. eCollection 2013.

33.

Association of rhizobia with a marine polychaete.

Summers MM, Katz S, Allen EE, Rouse GW.

Environ Microbiol Rep. 2013 Aug;5(4):492-8. doi: 10.1111/1758-2229.12043. Epub 2013 Mar 18.

34.

Virus-host and CRISPR dynamics in Archaea-dominated hypersaline Lake Tyrrell, Victoria, Australia.

Emerson JB, Andrade K, Thomas BC, Norman A, Allen EE, Heidelberg KB, Banfield JF.

Archaea. 2013;2013:370871. doi: 10.1155/2013/370871. Epub 2013 Jun 18.

35.

Synthesis of spirocarbamate oxindoles via intramolecular trapping of a β-silyl carbocation by an N-Boc group.

Shupe BH, Allen EE, MacDonald JP, Wilson SO, Franz AK.

Org Lett. 2013 Jul 5;15(13):3218-21. doi: 10.1021/ol4010867. Epub 2013 Jun 12.

PMID:
23758331
36.

Assembly-driven community genomics of a hypersaline microbial ecosystem.

Podell S, Ugalde JA, Narasingarao P, Banfield JF, Heidelberg KB, Allen EE.

PLoS One. 2013 Apr 18;8(4):e61692. doi: 10.1371/journal.pone.0061692. Print 2013.

37.

Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly.

Emerson JB, Thomas BC, Andrade K, Allen EE, Heidelberg KB, Banfield JF.

Appl Environ Microbiol. 2012 Sep;78(17):6309-20. doi: 10.1128/AEM.01212-12. Epub 2012 Jul 6.

38.

Genome sequence of "Candidatus Nitrosopumilus salaria" BD31, an ammonia-oxidizing archaeon from the San Francisco Bay estuary.

Mosier AC, Allen EE, Kim M, Ferriera S, Francis CA.

J Bacteriol. 2012 Apr;194(8):2121-2. doi: 10.1128/JB.00013-12.

39.

Genome sequence of "Candidatus Nitrosoarchaeum limnia" BG20, a low-salinity ammonia-oxidizing archaeon from the San Francisco Bay estuary.

Mosier AC, Allen EE, Kim M, Ferriera S, Francis CA.

J Bacteriol. 2012 Apr;194(8):2119-20. doi: 10.1128/JB.00007-12.

40.

Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic.

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.

ISME J. 2012 Jul;6(7):1403-14. doi: 10.1038/ismej.2011.201. Epub 2012 Jan 26.

41.

Development and evaluation of a prototype search engine to meet public health information needs.

Keeling JW, Turner AM, Allen EE, Rowe SA, Merrill JA, Liddy ED, Turtle HR.

AMIA Annu Symp Proc. 2011;2011:693-700. Epub 2011 Oct 22.

42.

Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria.

Ugalde JA, Podell S, Narasingarao P, Allen EE.

Biol Direct. 2011 Oct 10;6:52. doi: 10.1186/1745-6150-6-52.

43.

Compositional differences in particle-associated and free-living microbial assemblages from an extreme deep-ocean environment.

Eloe EA, Shulse CN, Fadrosh DW, Williamson SJ, Allen EE, Bartlett DH.

Environ Microbiol Rep. 2011 Aug;3(4):449-58. doi: 10.1111/j.1758-2229.2010.00223.x. Epub 2010 Nov 24.

PMID:
23761307
44.

De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities.

Narasingarao P, Podell S, Ugalde JA, Brochier-Armanet C, Emerson JB, Brocks JJ, Heidelberg KB, Banfield JF, Allen EE.

ISME J. 2012 Jan;6(1):81-93. doi: 10.1038/ismej.2011.78. Epub 2011 Jun 30.

45.

Widespread occurrence of secondary lipid biosynthesis potential in microbial lineages.

Shulse CN, Allen EE.

PLoS One. 2011;6(5):e20146. doi: 10.1371/journal.pone.0020146. Epub 2011 May 19.

46.

Going deeper: metagenome of a hadopelagic microbial community.

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.

PLoS One. 2011;6(5):e20388. doi: 10.1371/journal.pone.0020388. Epub 2011 May 24.

47.

Genomic insights into the physiology and ecology of the marine filamentous cyanobacterium Lyngbya majuscula.

Jones AC, Monroe EA, Podell S, Hess WR, Klages S, Esquenazi E, Niessen S, Hoover H, Rothmann M, Lasken RS, Yates JR 3rd, Reinhardt R, Kube M, Burkart MD, Allen EE, Dorrestein PC, Gerwick WH, Gerwick L.

Proc Natl Acad Sci U S A. 2011 May 24;108(21):8815-20. doi: 10.1073/pnas.1101137108. Epub 2011 May 9.

48.

Diversity and distribution of microbial long-chain fatty acid biosynthetic genes in the marine environment.

Shulse CN, Allen EE.

Environ Microbiol. 2011 Mar;13(3):684-95. doi: 10.1111/j.1462-2920.2010.02373.x. Epub 2010 Nov 24.

PMID:
21105981
49.

Pilot multimethod trial of a school-ethos intervention to reduce substance use: building hypotheses about upstream pathways to prevention.

Bonell CP, Sorhaindo AM, Allen EE, Strange VJ, Wiggins M, Fletcher A, Oakley AR, Bond LM, Flay BR, Patton GC, Rhodes T.

J Adolesc Health. 2010 Dec;47(6):555-63. doi: 10.1016/j.jadohealth.2010.04.011. Epub 2010 Jun 20.

PMID:
21094432
50.

Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource.

Sun S, Chen J, Li W, Altintas I, Lin A, Peltier S, Stocks K, Allen EE, Ellisman M, Grethe J, Wooley J.

Nucleic Acids Res. 2011 Jan;39(Database issue):D546-51. doi: 10.1093/nar/gkq1102. Epub 2010 Nov 2.

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