Eric Allen

Title(s)Professor, Scripps Institution of Oceanography Department
SchoolVc-marine Sciences
Address9500 Gilman Drive #
La Jolla CA 92093
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    Collapse Research 
    Collapse Research Activities and Funding
    Natural Sources and Microbial Transformation of Marine Halogenated Pollutants
    NIH R01ES030316Sep 15, 2018 - Jun 30, 2023
    Role: Co-Principal Investigator
    Phylogenetic Binning of Metagenomic Sequence Data
    NIH R21HG005107Aug 24, 2009 - Jul 31, 2012
    Role: Principal Investigator

    Collapse Bibliographic 
    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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Enrichable consortia of microbial symbionts degrade macroalgal polysaccharides in Kyphosus fish. mBio. 2024 May 08; 15(5):e0049624. Oliver A, Podell S, Wegley Kelly L, Sparagon WJ, Plominsky AM, Nelson RS, Laurens LML, Augyte S, Sims NA, Nelson CE, Allen EE. PMID: 38534158; PMCID: PMC11077953.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    2. Enrichable consortia of microbial symbionts degrade macroalgal polysaccharides in Kyphosus fish. bioRxiv. 2023 Nov 28. Oliver A, Podell S, Kelly LW, Sparagon WJ, Plominsky AM, Nelson RS, Laurens LML, Augyte S, Sims NA, Nelson CE, Allen EE. PMID: 38076955; PMCID: PMC10705383.
      View in: PubMed   Mentions:
    3. Herbivorous Fish Microbiome Adaptations to Sulfated Dietary Polysaccharides. Appl Environ Microbiol. 2023 05 31; 89(5):e0215422. Podell S, Oliver A, Kelly LW, Sparagon WJ, Plominsky AM, Nelson RS, Laurens LML, Augyte S, Sims NA, Nelson CE, Allen EE. PMID: 37133385; PMCID: PMC10231202.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    4. Terpene biosynthesis in marine sponge animals. Proc Natl Acad Sci U S A. 2023 02 28; 120(9):e2220934120. Wilson K, de Rond T, Burkhardt I, Steele TS, Schäfer RJB, Podell S, Allen EE, Moore BS. PMID: 36802428; PMCID: PMC9992776.
      View in: PubMed   Mentions: 7     Fields:    Translation:Animals
    5. Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species. Nat Commun. 2022 11 17; 13(1):6978. Minich JJ, Härer A, Vechinski J, Frable BW, Skelton ZR, Kunselman E, Shane MA, Perry DS, Gonzalez A, McDonald D, Knight R, Michael TP, Allen EE. PMID: 36396943; PMCID: PMC9671965.
      View in: PubMed   Mentions: 13     Fields:    Translation:Animals
    6. The Natural Product Domain Seeker version 2 (NaPDoS2) webtool relates ketosynthase phylogeny to biosynthetic function. J Biol Chem. 2022 10; 298(10):102480. Klau LJ, Podell S, Creamer KE, Demko AM, Singh HW, Allen EE, Moore BS, Ziemert N, Letzel AC, Jensen PR. PMID: 36108739; PMCID: PMC9582728.
      View in: PubMed   Mentions: 21     Fields:    
    7. Phenotypic and transcriptional response of Daphnia pulicaria to the combined effects of temperature and predation. PLoS One. 2022; 17(7):e0265103. Oliver A, Cavalheri HB, Lima TG, Jones NT, Podell S, Zarate D, Allen E, Burton RS, Shurin JB. PMID: 35834446; PMCID: PMC9282536.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    8. Fine scale transitions of the microbiota and metabolome along the gastrointestinal tract of herbivorous fishes. Anim Microbiome. 2022 May 23; 4(1):33. Sparagon WJ, Gentry EC, Minich JJ, Vollbrecht L, Laurens LML, Allen EE, Sims NA, Dorrestein PC, Kelly LW, Nelson CE. PMID: 35606844; PMCID: PMC9128220.
      View in: PubMed   Mentions: 6  
    9. Variation in Survival and Gut Microbiome Composition of Hatchery-Grown Native Oysters at Various Locations within the Puget Sound. Microbiol Spectr. 2022 06 29; 10(3):e0198221. Kunselman E, Minich JJ, Horwith M, Gilbert JA, Allen EE. PMID: 35536036; PMCID: PMC9241838.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    10. Microbiomes of Hadal Fishes across Trench Habitats Contain Similar Taxa and Known Piezophiles. mSphere. 2022 04 27; 7(2):e0003222. Blanton JM, Peoples LM, Gerringer ME, Iacuaniello CM, Gallo ND, Linley TD, Jamieson AJ, Drazen JC, Bartlett DH, Allen EE. PMID: 35306867; PMCID: PMC9044967.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
    11. Defining and quantifying the core microbiome: Challenges and prospects. Proc Natl Acad Sci U S A. 2021 12 21; 118(51). Neu AT, Allen EE, Roy K. PMID: 34862327; PMCID: PMC8713806.
      View in: PubMed   Mentions: 132     Fields:    Translation:HumansAnimalsPHPublic Health
    12. Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom. Sci Rep. 2021 08 02; 11(1):15592. Oliver A, Podell S, Pinowska A, Traller JC, Smith SR, McClure R, Beliaev A, Bohutskyi P, Hill EA, Rabines A, Zheng H, Allen LZ, Kuo A, Grigoriev IV, Allen AE, Hazlebeck D, Allen EE. PMID: 34341414; PMCID: PMC8329260.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    13. Genetic Suppression of Lethal Mutations in Fatty Acid Biosynthesis Mediated by a Secondary Lipid Synthase. Appl Environ Microbiol. 2021 05 26; 87(12):e0003521. Allemann MN, Allen EE. PMID: 33837011; PMCID: PMC8174602.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    14. Impacts of the Marine Hatchery Built Environment, Water and Feed on Mucosal Microbiome Colonization Across Ontogeny in Yellowtail Kingfish, Seriola lalandi. Front Mar Sci. 2021 May; 8. Minich JJ, Nowak B, Elizur A, Knight R, Fielder S, Allen EE. PMID: 36248701; PMCID: PMC9563383.
      View in: PubMed   Mentions: 7  
    15. Decade-scale stability and change in a marine bivalve microbiome. Mol Ecol. 2021 03; 30(5):1237-1250. Neu AT, Hughes IV, Allen EE, Roy K. PMID: 33432685.
      View in: PubMed   Mentions: 5     Fields:    Translation:Animals
    16. Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. Microbiome. 2021 01 22; 9(1):25. Minich JJ, Ali F, Marotz C, Belda-Ferre P, Chiang L, Shaffer JP, Carpenter CS, McDonald D, Gilbert J, Allard SM, Allen EE, Knight R, Sweeney DA, Swafford AD. PMID: 33482920; PMCID: PMC7821463.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    17. Non-targeted tandem mass spectrometry enables the visualization of organic matter chemotype shifts in coastal seawater. Chemosphere. 2021 May; 271:129450. Petras D, Minich JJ, Cancelada LB, Torres RR, Kunselman E, Wang M, White ME, Allen EE, Prather KA, Aluwihare LI, Dorrestein PC. PMID: 33460888; PMCID: PMC7969459.
      View in: PubMed   Mentions: 13     Fields:    
    18. Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. Res Sq. 2020 Dec 15. Minich J, Ali F, Marotz C, Belda-Ferre P, Chiang L, Shaffer JP, Carpenter CS, McDonald D, Gilbert J, Allard SM, Allen EE, Knight R, Sweeney DA, Swafford AD. PMID: 32839765; PMCID: PMC7444291.
      View in: PubMed   Mentions:
    19. The Southern Bluefin Tuna Mucosal Microbiome Is Influenced by Husbandry Method, Net Pen Location, and Anti-parasite Treatment. Front Microbiol. 2020; 11:2015. Minich JJ, Power C, Melanson M, Knight R, Webber C, Rough K, Bott NJ, Nowak B, Allen EE. PMID: 32983024; PMCID: PMC7476325.
      View in: PubMed   Mentions: 5  
    20. Sierra Nevada mountain lake microbial communities are structured by temperature, resources and geographic location. Mol Ecol. 2020 06; 29(11):2080-2093. Schulhof MA, Allen AE, Allen EE, Mladenov N, McCrow JP, Jones NT, Blanton J, Cavalheri HB, Kaul D, Symons CC, Shurin JB. PMID: 32578266.
      View in: PubMed   Mentions: 3     Fields:    
    21. A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes. Microbiome. 2020 06 23; 8(1):97. Podell S, Blanton JM, Oliver A, Schorn MA, Agarwal V, Biggs JS, Moore BS, Allen EE. PMID: 32576248; PMCID: PMC7313196.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    22. Genetic regulation of the bacterial omega-3 polyunsaturated fatty acid biosynthesis pathway. J Bacteriol. 2020 Jun 08. Allemann MN, Allen EE. PMID: 32513681; PMCID: PMC8404712.
      View in: PubMed   Mentions: 4     Fields:    
    23. Microbial Ecology of Atlantic Salmon (Salmo salar) Hatcheries: Impacts of the Built Environment on Fish Mucosal Microbiota. Appl Environ Microbiol. 2020 06 02; 86(12). Minich JJ, Poore GD, Jantawongsri K, Johnston C, Bowie K, Bowman J, Knight R, Nowak B, Allen EE. PMID: 32303543; PMCID: PMC7267192.
      View in: PubMed   Mentions: 34     Fields:    Translation:AnimalsPHPublic Health
    24. Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicus. mSphere. 2020 05 20; 5(3). Minich JJ, Petrus S, Michael JD, Michael TP, Knight R, Allen EE. PMID: 32434844; PMCID: PMC7380571.
      View in: PubMed   Mentions: 21     Fields:    Translation:Animals
    25. Visualizing 'omic feature rankings and log-ratios using Qurro. NAR Genom Bioinform. 2020 Jun; 2(2):lqaa023. Fedarko MW, Martino C, Morton JT, González A, Rahman G, Marotz CA, Minich JJ, Allen EE, Knight R. PMID: 32391521; PMCID: PMC7194218.
      View in: PubMed   Mentions: 71  
    26. Multi-Omic Profiling of Melophlus Sponges Reveals Diverse Metabolomic and Microbiome Architectures that Are Non-overlapping with Ecological Neighbors. Mar Drugs. 2020 Feb 19; 18(2). Mohanty I, Podell S, Biggs JS, Garg N, Allen EE, Agarwal V. PMID: 32092934; PMCID: PMC7074536.
      View in: PubMed   Mentions: 12     Fields:    Translation:Animals
    27. Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection. ISME J. 2019 11; 13(11):2817-2833. 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. PMID: 31320727; PMCID: PMC6794264.
      View in: PubMed   Mentions: 28     Fields:    Translation:AnimalsCells
    28. Comparative Genomics of Cyanobacterial Symbionts Reveals Distinct, Specialized Metabolism in Tropical Dysideidae Sponges. mBio. 2019 05 14; 10(3). Schorn MA, Jordan PA, Podell S, Blanton JM, Agarwal V, Biggs JS, Allen EE, Moore BS. PMID: 31088928; PMCID: PMC6520454.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCells
    29. Linkage of Marine Bacterial Polyunsaturated Fatty Acid and Long-Chain Hydrocarbon Biosynthesis. Front Microbiol. 2019; 10:702. Allemann MN, Shulse CN, Allen EE. PMID: 31024488; PMCID: PMC6463001.
      View in: PubMed   Mentions: 5  
    30. Diversity and composition of intertidal gastropod microbiomes across a major marine biogeographic boundary. Environ Microbiol Rep. 2019 06; 11(3):434-447. Neu AT, Allen EE, Roy K. PMID: 30834681.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    31. Microbial Community Diversity Within Sediments from Two Geographically Separated Hadal Trenches. Front Microbiol. 2019; 10:347. Peoples LM, Grammatopoulou E, Pombrol M, Xu X, Osuntokun O, Blanton J, Allen EE, Nunnally CC, Drazen JC, Mayor DJ, Bartlett DH. PMID: 30930856; PMCID: PMC6428765.
      View in: PubMed   Mentions: 37  
    32. High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity. mSystems. 2018 Nov-Dec; 3(6). Minich JJ, Humphrey G, Benitez RAS, Sanders J, Swafford A, Allen EE, Knight R. PMID: 30417111; PMCID: PMC6222042.
      View in: PubMed   Mentions: 30     Fields:    
    33. Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles. ISME J. 2019 02; 13(2):468-481. Podell S, Blanton JM, Neu A, Agarwal V, Biggs JS, Moore BS, Allen EE. PMID: 30291328; PMCID: PMC6331548.
      View in: PubMed   Mentions: 21     Fields:    Translation:AnimalsCells
    34. Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus). Microbiologyopen. 2018 12; 7(6):e00716. Minich JJ, Zhu Q, Xu ZZ, Amir A, Ngochera M, Simwaka M, Allen EE, Zidana H, Knight R. PMID: 30168288; PMCID: PMC6291788.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    35. Distinctive Archaeal Composition of an Artisanal Crystallizer Pond and Functional Insights Into Salt-Saturated Hypersaline Environment Adaptation. Front Microbiol. 2018; 9:1800. 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. PMID: 30154761; PMCID: PMC6102401.
      View in: PubMed   Mentions: 8  
    36. Bacterioplankton drawdown of coral mass-spawned organic matter. ISME J. 2018 09; 12(9):2238-2251. Guillemette R, Kaneko R, Blanton J, Tan J, Witt M, Hamilton S, Allen EE, Medina M, Hamasaki K, Koch BP, Azam F. PMID: 29884827; PMCID: PMC6092384.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    37. 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 08; 20(8):2727-2742. Plominsky AM, Trefault N, Podell S, Blanton JM, De la Iglesia R, Allen EE, von Dassow P, Ulloa O. PMID: 29575531.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    38. Characterization and Application of Marine Microbial Omega-3 Polyunsaturated Fatty Acid Synthesis. Methods Enzymol. 2018; 605:3-32. Allemann MN, Allen EE. PMID: 29909829.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    39. Vertically distinct microbial communities in the Mariana and Kermadec trenches. PLoS One. 2018; 13(4):e0195102. Peoples LM, Donaldson S, Osuntokun O, Xia Q, Nelson A, Blanton J, Allen EE, Church MJ, Bartlett DH. PMID: 29621268; PMCID: PMC5886532.
      View in: PubMed   Mentions: 31     Fields:    Translation:PHPublic Health
    40. KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples. mSystems. 2018 May-Jun; 3(3). 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. PMID: 29577086; PMCID: PMC5864415.
      View in: PubMed   Mentions: 75     Fields:    
    41. Metagenomic discovery of polybrominated diphenyl ether biosynthesis by marine sponges. Nat Chem Biol. 2017 05; 13(5):537-543. 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. PMID: 28319100; PMCID: PMC5391271.
      View in: PubMed   Mentions: 58     Fields:    Translation:AnimalsCells
    42. 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. Leao T, Castelão G, Korobeynikov A, Monroe EA, Podell S, Glukhov E, Allen EE, Gerwick WH, Gerwick L. PMID: 28265051; PMCID: PMC5373345.
      View in: PubMed   Mentions: 36     Fields:    Translation:Cells
    43. Fatty Acid Biosynthesis Pathways in Methylomicrobium buryatense 5G(B1). Front Microbiol. 2016; 7:2167. Demidenko A, Akberdin IR, Allemann M, Allen EE, Kalyuzhnaya MG. PMID: 28119683; PMCID: PMC5222806.
      View in: PubMed   Mentions: 16  
    44. Use of plankton-derived vitamin B1 precursors, especially thiazole-related precursor, by key marine picoeukaryotic phytoplankton. ISME J. 2017 03; 11(3):753-765. Paerl RW, Bouget FY, Lozano JC, Vergé V, Schatt P, Allen EE, Palenik B, Azam F. PMID: 27935586; PMCID: PMC5322297.
      View in: PubMed   Mentions: 26     Fields:    Translation:Animals
    45. Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype. Biotechnol Biofuels. 2016; 9:258. 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. PMID: 27933100; PMCID: PMC5124317.
      View in: PubMed   Mentions: 30  
    46. 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). Fuentes-Valdés JJ, Plominsky AM, Allen EE, Tamames J, Vásquez M. PMID: 27563040; PMCID: PMC5000824.
      View in: PubMed   Mentions:
    47. Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem. ISME J. 2015 Dec; 9(12):2697-711. 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. PMID: 25918833; PMCID: PMC4817636.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    48. De novo sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, reveal a variable genomic landscape. Archaea. 2015; 2015:875784. Tully BJ, Emerson JB, Andrade K, Brocks JJ, Allen EE, Banfield JF, Heidelberg KB. PMID: 25709557; PMCID: PMC4330952.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    49. Adaptive laboratory evolution of Escherichia coli K-12 MG1655 for growth at high hydrostatic pressure. Front Microbiol. 2014; 5:749. Marietou A, Nguyen AT, Allen EE, Bartlett DH. PMID: 25610434; PMCID: PMC4285802.
      View in: PubMed   Mentions: 8  
    50. Metagenome sequencing of the microbial community of a solar saltern crystallizer pond at cáhuil lagoon, chile. Genome Announc. 2014 Nov 13; 2(6). 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. PMID: 25395641; PMCID: PMC4241667.
      View in: PubMed   Mentions: 12  
    51. Biosynthesis of polybrominated aromatic organic compounds by marine bacteria. Nat Chem Biol. 2014 Aug; 10(8):640-7. Agarwal V, El Gamal AA, Yamanaka K, Poth D, Kersten RD, Schorn M, Allen EE, Moore BS. PMID: 24974229; PMCID: PMC4104138.
      View in: PubMed   Mentions: 112     Fields:    Translation:Cells
    52. 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. 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. PMID: 24959919; PMCID: PMC4068987.
      View in: PubMed   Mentions: 426     Fields:    Translation:AnimalsCellsPHPublic Health
    53. Characterization of cyanobacterial hydrocarbon composition and distribution of biosynthetic pathways. PLoS One. 2014; 9(1):e85140. Coates RC, Podell S, Korobeynikov A, Lapidus A, Pevzner P, Sherman DH, Allen EE, Gerwick L, Gerwick WH. PMID: 24475038; PMCID: PMC3903477.
      View in: PubMed   Mentions: 63     Fields:    Translation:Cells
    54. Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community. ISME J. 2014 May; 8(5):979-90. Podell S, Emerson JB, Jones CM, Ugalde JA, Welch S, Heidelberg KB, Banfield JF, Allen EE. PMID: 24335829; PMCID: PMC3996697.
      View in: PubMed   Mentions: 49     Fields:    Translation:Cells
    55. 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). Ugalde JA, Narasingarao P, Kuo S, Podell S, Allen EE. PMID: 24336364; PMCID: PMC3861417.
      View in: PubMed   Mentions: 4  
    56. 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. Kharbush JJ, Ugalde JA, Hogle SL, Allen EE, Aluwihare LI. PMID: 24077702; PMCID: PMC3837760.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    57. Microbial life in a fjord: metagenomic analysis of a microbial mat in Chilean patagonia. PLoS One. 2013; 8(8):e71952. Ugalde JA, Gallardo MJ, Belmar C, Muñoz P, Ruiz-Tagle N, Ferrada-Fuentes S, Espinoza C, Allen EE, Gallardo VA. PMID: 24015199; PMCID: PMC3756073.
      View in: PubMed   Mentions: 4     Fields:    Translation:CellsPHPublic Health
    58. Virus-host and CRISPR dynamics in Archaea-dominated hypersaline Lake Tyrrell, Victoria, Australia. Archaea. 2013; 2013:370871. Emerson JB, Andrade K, Thomas BC, Norman A, Allen EE, Heidelberg KB, Banfield JF. PMID: 23853523; PMCID: PMC3703381.
      View in: PubMed   Mentions: 41     Fields:    Translation:Cells
    59. Assembly-driven community genomics of a hypersaline microbial ecosystem. PLoS One. 2013; 8(4):e61692. Podell S, Ugalde JA, Narasingarao P, Banfield JF, Heidelberg KB, Allen EE. PMID: 23637883; PMCID: PMC3630111.
      View in: PubMed   Mentions: 51     Fields:    Translation:CellsPHPublic Health
    60. Association of rhizobia with a marine polychaete. Environ Microbiol Rep. 2013 Aug; 5(4):492-8. Summers MM, Katz S, Allen EE, Rouse GW. PMID: 23864561.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    61. Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly. Appl Environ Microbiol. 2012 Sep; 78(17):6309-20. Emerson JB, Thomas BC, Andrade K, Allen EE, Heidelberg KB, Banfield JF. PMID: 22773627; PMCID: PMC3416638.
      View in: PubMed   Mentions: 50     Fields:    Translation:CellsPHPublic Health
    62. 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. Mosier AC, Allen EE, Kim M, Ferriera S, Francis CA. PMID: 22461555; PMCID: PMC3318490.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    63. 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. Mosier AC, Allen EE, Kim M, Ferriera S, Francis CA. PMID: 22461554; PMCID: PMC3318456.
      View in: PubMed   Mentions: 24     Fields:    Translation:Cells
    64. The natural product domain seeker NaPDoS: a phylogeny based bioinformatic tool to classify secondary metabolite gene diversity. PLoS One. 2012; 7(3):e34064. Ziemert N, Podell S, Penn K, Badger JH, Allen E, Jensen PR. PMID: 22479523; PMCID: PMC3315503.
      View in: PubMed   Mentions: 204     Fields:    Translation:CellsPHPublic Health
    65. Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic. ISME J. 2012 Jul; 6(7):1403-14. 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. PMID: 22278668; PMCID: PMC3379637.
      View in: PubMed   Mentions: 55     Fields:    Translation:Cells
    66. Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria. Biol Direct. 2011 Oct 10; 6:52. Ugalde JA, Podell S, Narasingarao P, Allen EE. PMID: 21985229; PMCID: PMC3198991.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    67. De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J. 2012 Jan; 6(1):81-93. Narasingarao P, Podell S, Ugalde JA, Brochier-Armanet C, Emerson JB, Brocks JJ, Heidelberg KB, Banfield JF, Allen EE. PMID: 21716304; PMCID: PMC3246234.
      View in: PubMed   Mentions: 160     Fields:    Translation:Cells
    68. Going deeper: metagenome of a hadopelagic microbial community. PLoS One. 2011; 6(5):e20388. 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. PMID: 21629664; PMCID: PMC3101246.
      View in: PubMed   Mentions: 45     Fields:    Translation:Cells
    69. Widespread occurrence of secondary lipid biosynthesis potential in microbial lineages. PLoS One. 2011; 6(5):e20146. Shulse CN, Allen EE. PMID: 21629834; PMCID: PMC3098273.
      View in: PubMed   Mentions: 35     Fields:    Translation:Cells
    70. 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. 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. PMID: 21555588; PMCID: PMC3102346.
      View in: PubMed   Mentions: 42     Fields:    Translation:Cells
    71. Diversity and distribution of microbial long-chain fatty acid biosynthetic genes in the marine environment. Environ Microbiol. 2011 Mar; 13(3):684-95. Shulse CN, Allen EE. PMID: 21105981.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    72. 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. Eloe EA, Shulse CN, Fadrosh DW, Williamson SJ, Allen EE, Bartlett DH. PMID: 23761307.
      View in: PubMed   Mentions: 71     Fields:    
    73. Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Res. 2011 Jan; 39(Database issue):D546-51. Sun S, Chen J, Li W, Altintas I, Lin A, Peltier S, Stocks K, Allen EE, Ellisman M, Grethe J, Wooley J. PMID: 21045053; PMCID: PMC3013694.
      View in: PubMed   Mentions: 149     Fields:    
    74. Mercury speciation in marine sediments under sulfate-limited conditions. Environ Sci Technol. 2010 May 15; 44(10):3752-7. Han S, Narasingarao P, Obraztsova A, Gieskes J, Hartmann AC, Tebo BM, Allen EE, Deheyn DD. PMID: 20429556.
      View in: PubMed   Mentions: 6     Fields:    Translation:PHPublic Health
    75. Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species. Genome Res. 2010 Jul; 20(7):908-16. 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. PMID: 20413674; PMCID: PMC2892092.
      View in: PubMed   Mentions: 107     Fields:    Translation:AnimalsCells
    76. Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria. ISME J. 2009 Oct; 3(10):1193-203. Penn K, Jenkins C, Nett M, Udwary DW, Gontang EA, McGlinchey RP, Foster B, Lapidus A, Podell S, Allen EE, Moore BS, Jensen PR. PMID: 19474814; PMCID: PMC2749086.
      View in: PubMed   Mentions: 107     Fields:    Translation:Cells
    77. A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm. BMC Bioinformatics. 2008 Oct 07; 9:419. Podell S, Gaasterland T, Allen EE. PMID: 18840280; PMCID: PMC2573894.
      View in: PubMed   Mentions: 22     Fields:    Translation:Cells
    78. Metabolic versatility of the Riftia pachyptila endosymbiont revealed through metagenomics. Environ Microbiol. 2008 Mar; 10(3):727-37. Robidart JC, Bench SR, Feldman RA, Novoradovsky A, Podell SB, Gaasterland T, Allen EE, Felbeck H. PMID: 18237306.
      View in: PubMed   Mentions: 64     Fields:    Translation:AnimalsCells
    79. Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature. 2007 Mar 29; 446(7135):537-41. 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. PMID: 17344860.
      View in: PubMed   Mentions: 82     Fields:    Translation:Cells
    80. Genome dynamics in a natural archaeal population. Proc Natl Acad Sci U S A. 2007 Feb 06; 104(6):1883-8. Allen EE, Tyson GW, Whitaker RJ, Detter JC, Richardson PM, Banfield JF. PMID: 17267615; PMCID: PMC1794283.
      View in: PubMed   Mentions: 57     Fields:    Translation:Cells
    81. Lineages of acidophilic archaea revealed by community genomic analysis. Science. 2006 Dec 22; 314(5807):1933-5. Baker BJ, Tyson GW, Webb RI, Flanagan J, Hugenholtz P, Allen EE, Banfield JF. PMID: 17185602.
      View in: PubMed   Mentions: 85     Fields:    Translation:Cells
    82. 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. Tyson GW, Lo I, Baker BJ, Allen EE, Hugenholtz P, Banfield JF. PMID: 16204553; PMCID: PMC1266007.
      View in: PubMed   Mentions: 75     Fields:    Translation:Cells
    83. Community genomics in microbial ecology and evolution. Nat Rev Microbiol. 2005 Jun; 3(6):489-98. Allen EE, Banfield JF. PMID: 15931167.
      View in: PubMed   Mentions: 66     Fields:    
    84. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature. 2004 Mar 04; 428(6978):37-43. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. PMID: 14961025.
      View in: PubMed   Mentions: 749     Fields:    Translation:CellsPHPublic Health
    85. The genome of a motile marine Synechococcus. Nature. 2003 Aug 28; 424(6952):1037-42. 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. PMID: 12917641.
      View in: PubMed   Mentions: 185     Fields:    Translation:Cells
    86. Structure and regulation of the omega-3 polyunsaturated fatty acid synthase genes from the deep-sea bacterium Photobacterium profundum strain SS9. Microbiology (Reading). 2002 Jun; 148(Pt 6):1903-1913. Allen EE, Bartlett DH. PMID: 12055309.
      View in: PubMed   Mentions: 49     Fields:    Translation:CellsPHPublic Health
    87. FabF is required for piezoregulation of cis-vaccenic acid levels and piezophilic growth of the deep-Sea bacterium Photobacterium profundum strain SS9. J Bacteriol. 2000 Mar; 182(5):1264-71. Allen EE, Bartlett DH. PMID: 10671446; PMCID: PMC94411.
      View in: PubMed   Mentions: 24     Fields:    Translation:CellsPHPublic Health
    88. 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. 1999 Apr; 65(4):1710-20. Allen EE, Facciotti D, Bartlett DH. PMID: 10103272; PMCID: PMC91242.
      View in: PubMed   Mentions: 62     Fields:    Translation:CellsPHPublic Health
    89. A conjecture of Procesi and the straightening algorithm of Rota. Proc Natl Acad Sci U S A. 1992 May 01; 89(9):3980-4. Allen EE. PMID: 11607289; PMCID: PMC525615.
      View in: PubMed   Mentions:    Fields:    
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