Eppley, John

TitleSoftware Developer 4
InstitutionLawrence Berkeley National Lab
DepartmentJoint Genome Institute
Address1 Cyclotron Road
Berkeley CA 94720
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    1. Aylward FO, Boeuf D, Mende DR, Wood-Charlson EM, Vislova A, Eppley J, Romano AE, DeLong EF. Diel cycling and long-term persistence of viruses in the ocean's euphotic zone. Proc Natl Acad Sci U S A. 2017 Oct 24; 114(43):11446-11451. PMID: 29073070.
      View in: PubMed
    2. Mende DR, Bryant JA, Aylward FO, Eppley J, Nielsen T, Karl DM, DeLong EF. Environmental drivers of a microbial genomic transition zone in the ocean's interior. Nat Microbiol. 2017 Oct; 2(10):1367-1373. PMID: 28808230.
      View in: PubMed
    3. Wilson ST, Aylward FO, Ribalet F, Barone B, Casey JR, Connell PE, Eppley J, Ferrón S, Fitzsimmons JN, Hayes CT, Romano AE, Turk-Kubo KA, Vislova A, Armbrust EV, Caron DA, Church MJ, Zehr JP, Karl DM, DeLong EF. Coordinated regulation of growth, activity and transcription in natural populations of the unicellular nitrogen-fixing cyanobacterium Crocosphaera. Nat Microbiol. 2017 Jul 31; 2:17118. PMID: 28758990.
      View in: PubMed
    4. Mende DR, Aylward FO, Eppley J, Nielsen TN, DeLong EF. Improved Environmental Genomes via Integration of Metagenomic and Single-Cell Assemblies. Front Microbiol. 2016; 7:143. PMID: 26904016; PMCID: PMC4749706.
    5. Bryant JA, Aylward FO, Eppley J, Karl DM, Church MJ, DeLong EF. Wind and sunlight shape microbial diversity in surface waters of the North Pacific Subtropical Gyre. ISME J. 2016 06; 10(6):1308-22. PMID: 26645474.
      View in: PubMed
    6. Fontanez KM, Eppley J, Samo TJ, Karl DM, DeLong EF. Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre. Front Microbiol. 2015; 6:469. PMID: 26042105; PMCID: PMC4436931.
    7. Aylward FO, Eppley J, Smith JM, Chavez FP, Scholin CA, DeLong EF. Microbial community transcriptional networks are conserved in three domains at ocean basin scales. Proc Natl Acad Sci U S A. 2015 Apr 28; 112(17):5443-8. PMID: 25775583; PMCID: PMC4418921.
    8. Lincoln SA, Wai B, Eppley J, Church MJ, Summons RE, DeLong EF. Reply to Schouten et al.: Marine Group II planktonic Euryarchaeota are significant contributors to tetraether lipids in the ocean. Proc Natl Acad Sci U S A. 2014 Oct 14; 111(41):E4286. PMID: 25239231; PMCID: PMC4205656.
    9. Ottesen EA, Young CR, Gifford SM, Eppley J, Marin R, Schuster SC, Scholin CA, DeLong EF. Ocean microbes. Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages. Science. 2014 Jul 11; 345(6193):207-12. PMID: 25013074.
      View in: PubMed
    10. Lincoln SA, Wai B, Eppley J, Church MJ, Summons RE, DeLong EF. Planktonic Euryarchaeota are a significant source of archaeal tetraether lipids in the ocean. Proc Natl Acad Sci U S A. 2014 Jul 08; 111(27):9858-63. PMID: 24946804; PMCID: PMC4103328.
    11. Durham BP, Grote J, Whittaker KA, Bender SJ, Luo H, Grim SL, Brown JM, Casey JR, Dron A, Florez-Leiva L, Krupke A, Luria CM, Mine AH, Nigro OD, Pather S, Talarmin A, Wear EK, Weber TS, Wilson JM, Church MJ, DeLong EF, Karl DM, Steward GF, Eppley J, Kyrpides NC, Schuster S, Rappé MS. Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome. Stand Genomic Sci. 2014 Jun 15; 9(3):632-45. PMID: 25197450; PMCID: PMC4148974.
    12. Ottesen EA, Young CR, Eppley J, Ryan JP, Chavez FP, Scholin CA, DeLong EF. Pattern and synchrony of gene expression among sympatric marine microbial populations. Proc Natl Acad Sci U S A. 2013 Feb 05; 110(6):E488-97. PMID: 23345438; PMCID: PMC3568374.
    13. Bryant JA, Stewart FJ, Eppley J, DeLong EF. Microbial community phylogenetic and trait diversity declines with depth in a marine oxygen minimum zone. Ecology. 2012 Jul; 93(7):1659-73. PMID: 22919912.
      View in: PubMed
    14. Grote J, Bayindirli C, Bergauer K, Carpintero de Moraes P, Chen H, D'Ambrosio L, Edwards B, Fernández-Gómez B, Hamisi M, Logares R, Nguyen D, Rii YM, Saeck E, Schutte C, Widner B, Church MJ, Steward GF, Karl DM, Delong EF, Eppley J, Schuster SC, Kyrpides NC, Rappé MS. Draft genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria. Stand Genomic Sci. 2011 Dec 31; 5(3):269-78. PMID: 22675578; PMCID: PMC3368413.
    15. Stewart FJ, Sharma AK, Bryant JA, Eppley J, DeLong EF. Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities. Genome Biol. 2011; 12(3):R26. PMID: 21426537; PMCID: PMC3129676.
    16. Rich VI, Pham VD, Eppley J, Shi Y, DeLong EF. Time-series analyses of Monterey Bay coastal microbial picoplankton using a 'genome proxy' microarray. Environ Microbiol. 2011 Jan; 13(1):116-134. PMID: 20695878.
      View in: PubMed
    17. Shi Y, Tyson GW, Eppley J, DeLong EF. Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. ISME J. 2011 Jun; 5(6):999-1013. PMID: 21151004; PMCID: PMC3131857.
    18. Eppley J, Tyson GW, Getz WM, Banfield JF. Strainer: software for analysis of population variation in community genomic datasets. BMC Bioinformatics. 2007 Oct 17; 8:398. PMID: 17941997; PMCID: PMC2110895.
    19. Eppley J, Tyson GW, Getz WM, Banfield JF. Genetic exchange across a species boundary in the archaeal genus ferroplasma. Genetics. 2007 Sep; 177(1):407-16. PMID: 17603112; PMCID: PMC2013692.
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