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    Tringe, Susannah

    TitleCmpl Biologist Staff Sci/Engr
    SchoolLawrence Berkeley National Lab
    DepartmentJoint Genome Institute
    Address1 Cyclotron Road
    Berkeley CA 94720
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      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. Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe S, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017 Aug 08; 35(8):725-731. PMID: 28787424.
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      2. Fernández-González AJ, Martínez-Hidalgo P, Cobo-Díaz JF, Villadas PJ, Martínez-Molina E, Toro N, Tringe S, Fernández-López M. The rhizosphere microbiome of burned holm-oak: potential role of the genus Arthrobacter in the recovery of burned soils. Sci Rep. 2017 Jul 20; 7(1):6008. PMID: 28729641.
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      3. Tringe S. Single-cell genomics for the masses. Nat Biotechnol. 2017 Jul 12; 35(7):635-636. PMID: 28700562.
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      4. Lamit LJ, Romanowicz KJ, Potvin LR, Rivers AR, Singh K, Lennon JT, Tringe S, Kane ES, Lilleskov EA. Patterns and drivers of fungal community depth stratification in Sphagnum peat. FEMS Microbiol Ecol. 2017 Jul 01; 93(7). PMID: 28854677.
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      5. Staley C, Ferrieri AP, Tfaily MM, Cui Y, Chu RK, Wang P, Shaw JB, Ansong CK, Brewer H, Norbeck AD, Markillie M, do Amaral F, Tuleski T, Pellizzaro T, Agtuca B, Ferrieri R, Tringe S, Paša-Tolic L, Stacey G, Sadowsky MJ. Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism. Microbiome. 2017 Jun 24; 5(1):65. PMID: 28646918.
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      6. Gontang EA, Aylward FO, Carlos C, Glavina Del Rio T, Chovatia M, Fern A, Lo CC, Malfatti SA, Tringe S, Currie CR, Kolter R. Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach. PLoS One. 2017; 12(5):e0177189. PMID: 28545131.
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      7. Khdhiri M, Piché-Choquette S, Tremblay J, Tringe S, Constant P. The Tale of a Neglected Energy Source: Elevated Hydrogen Exposure Affects both Microbial Diversity and Function in Soil. Appl Environ Microbiol. 2017 Jun 01; 83(11). PMID: 28363961.
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      8. Jungbluth SP, Glavina Del Rio T, Tringe S, Stepanauskas R, Rappé MS. Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems. PeerJ. 2017; 5:e3134. PMID: 28396823.
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      9. Men Y, Yu K, Bælum J, Gao Y, Tremblay J, Prestat E, Stenuit B, Tringe S, Jansson J, Zhang T, Alvarez-Cohen L. Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions. Appl Environ Microbiol. 2017 Apr 15; 83(8). PMID: 28188205.
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      10. Kantor RS, Huddy RJ, Iyer R, Thomas BC, Brown CT, Anantharaman K, Tringe S, Hettich RL, Harrison ST, Banfield JF. Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation. Environ Sci Technol. 2017 Mar 07; 51(5):2944-2953. PMID: 28139919.
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      11. Meyer KM, Klein AM, Rodrigues JL, Nüsslein K, Tringe S, Mirza BS, Tiedje JM, Bohannan BJ. Conversion of Amazon rainforest to agriculture alters community traits of methane-cycling organisms. Mol Ecol. 2017 Mar; 26(6):1547-1556. PMID: 28100018.
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      12. Butterfield CN, Li Z, Andeer PF, Spaulding S, Thomas BC, Singh A, Hettich RL, Suttle KB, Probst AJ, Tringe S, Northen T, Pan C, Banfield JF. Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone. PeerJ. 2016; 4:e2687. PMID: 27843720.
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      13. Zargar K, Saville R, Phelan RM, Tringe S, Petzold CJ, Keasling JD, Beller HR. In vitro Characterization of Phenylacetate Decarboxylase, a Novel Enzyme Catalyzing Toluene Biosynthesis in an Anaerobic Microbial Community. Sci Rep. 2016 Aug 10; 6:31362. PMID: 27506494; PMCID: PMC4979209.
      14. Wagner MR, Lundberg DS, Del Rio TG, Tringe S, Dangl JL, Mitchell-Olds T. Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nat Commun. 2016 Jul 12; 7:12151. PMID: 27402057; PMCID: PMC4945892.
      15. Ikeda-Ohtsubo W, Strassert JF, Köhler T, Mikaelyan A, Gregor I, McHardy AC, Tringe S, Hugenholtz P, Radek R, Brune A. 'Candidatus Adiutrix intracellularis', an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria and a putative homoacetogen. Environ Microbiol. 2016 Sep; 18(8):2548-64. PMID: 26914459.
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      16. Hausmann B, Knorr KH, Schreck K, Tringe S, Glavina Del Rio T, Loy A, Pester M. Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms. ISME J. 2016 Oct; 10(10):2365-75. PMID: 27015005; PMCID: PMC4930147 [Available on 04/01/17].
      17. Piché-Choquette S, Tremblay J, Tringe S, Constant P. H2-saturation of high affinity H2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups. PeerJ. 2016; 4:e1782. PMID: 26989620; PMCID: PMC4793312.
      18. Vavourakis CD, Ghai R, Rodriguez-Valera F, Sorokin DY, Tringe S, Hugenholtz P, Muyzer G. Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines. Front Microbiol. 2016; 7:211. PMID: 26941731; PMCID: PMC4766312.
      19. Beam JP, Bernstein HC, Jay ZJ, Kozubal MA, Jennings Rd, Tringe S, Inskeep WP. Assembly and Succession of Iron Oxide Microbial Mat Communities in Acidic Geothermal Springs. Front Microbiol. 2016; 7:25. PMID: 26913020; PMCID: PMC4753309.
      20. Fonseca-García C, Coleman-Derr D, Garrido E, Visel A, Tringe S, Partida-Martínez LP. The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity. Front Microbiol. 2016; 7:150. PMID: 26904020; PMCID: PMC4751269.
      21. Singer E, Bushnell B, Coleman-Derr D, Bowman B, Bowers RM, Levy A, Gies EA, Cheng JF, Copeland A, Klenk HP, Hallam SJ, Hugenholtz P, Tringe S, Woyke T. High-resolution phylogenetic microbial community profiling. ISME J. 2016 Aug; 10(8):2020-32. PMID: 26859772.
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      22. Oyserman BO, Noguera DR, del Rio TG, Tringe S, McMahon KD. Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis. ISME J. 2016 Apr; 10(4):810-22. PMID: 26555245; PMCID: PMC4796919.
      23. Hemme CL, Tu Q, Shi Z, Qin Y, Gao W, Deng Y, Nostrand JD, Wu L, He Z, Chain PS, Tringe S, Fields MW, Rubin EM, Tiedje JM, Hazen TC, Arkin AP, Zhou J. Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Front Microbiol. 2015; 6:1205. PMID: 26583008; PMCID: PMC4628106.
      24. Bowers RM, Clum A, Tice H, Lim J, Singh K, Ciobanu D, Ngan CY, Cheng JF, Tringe S, Woyke T. Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community. BMC Genomics. 2015 Oct 24; 16:856. PMID: 26496746; PMCID: PMC4619416.
      25. Coleman-Derr D, Desgarennes D, Fonseca-Garcia C, Gross S, Clingenpeel S, Woyke T, North G, Visel A, Partida-Martinez LP, Tringe S. Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. New Phytol. 2016 Jan; 209(2):798-811. PMID: 26467257.
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      26. Tremblay J, Singh K, Fern A, Kirton ES, He S, Woyke T, Lee J, Chen F, Dangl JL, Tringe S. Primer and platform effects on 16S rRNA tag sequencing. Front Microbiol. 2015; 6:771. PMID: 26300854; PMCID: PMC4523815.
      27. Lebeis SL, Paredes SH, Lundberg DS, Breakfield N, Gehring J, McDonald M, Malfatti S, Glavina del Rio T, Jones CD, Tringe S, Dangl JL. PLANT MICROBIOME. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science. 2015 Aug 21; 349(6250):860-4. PMID: 26184915.
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      28. Beam JP, Jay ZJ, Schmid MC, Rusch DB, Romine MF, Jennings Rde M, Kozubal MA, Tringe S, Wagner M, Inskeep WP. Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous 'streamer' community. ISME J. 2016 Jan; 10(1):210-24. PMID: 26140529; PMCID: PMC4681859.
      29. He S, Malfatti SA, McFarland JW, Anderson FE, Pati A, Huntemann M, Tremblay J, Glavina del Rio T, Waldrop MP, Windham-Myers L, Tringe S. Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions. MBio. 2015 May 19; 6(3):e00066-15. PMID: 25991679; PMCID: PMC4442139.
      30. Cantor M, Nordberg H, Smirnova T, Hess M, Tringe S, Dubchak I. Elviz - exploration of metagenome assemblies with an interactive visualization tool. BMC Bioinformatics. 2015 Apr 28; 16:130. PMID: 25928663; PMCID: PMC4432942.
      31. Luef B, Frischkorn KR, Wrighton KC, Holman HY, Birarda G, Thomas BC, Singh A, Williams KH, Siegerist CE, Tringe S, Downing KH, Comolli LR, Banfield JF. Diverse uncultivated ultra-small bacterial cells in groundwater. Nat Commun. 2015 Feb 27; 6:6372. PMID: 25721682.
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      32. Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, Frischkorn KR, Tringe S, Singh A, Markillie LM, Taylor RC, Williams KH, Banfield JF. Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr Biol. 2015 Mar 16; 25(6):690-701. PMID: 25702576.
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      33. Sharon I, Kertesz M, Hug LA, Pushkarev D, Blauwkamp TA, Castelle CJ, Amirebrahimi M, Thomas BC, Burstein D, Tringe S, Williams KH, Banfield JF. Accurate, multi-kb reads resolve complex populations and detect rare microorganisms. Genome Res. 2015 Apr; 25(4):534-43. PMID: 25665577; PMCID: PMC4381525.
      34. Hug LA, Thomas BC, Brown CT, Frischkorn KR, Williams KH, Tringe S, Banfield JF. Aquifer environment selects for microbial species cohorts in sediment and groundwater. ISME J. 2015 Aug; 9(8):1846-56. PMID: 25647349; PMCID: PMC4511941.
      35. Zhou J, He Z, Yang Y, Deng Y, Tringe S, Alvarez-Cohen L. High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. MBio. 2015 Jan 27; 6(1). PMID: 25626903; PMCID: PMC4324309.
      36. Nobu MK, Narihiro T, Rinke C, Kamagata Y, Tringe S, Woyke T, Liu WT. Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor. ISME J. 2015 Aug; 9(8):1710-22. PMID: 25615435; PMCID: PMC4511927.
      37. Aylward FO, Suen G, Biedermann PH, Adams AS, Scott JJ, Malfatti SA, Glavina del Rio T, Tringe S, Poulsen M, Raffa KF, Klepzig KD, Currie CR. Convergent bacterial microbiotas in the fungal agricultural systems of insects. MBio. 2014 Nov 18; 5(6):e02077. PMID: 25406380; PMCID: PMC4251994.
      38. O'Connor RM, Fung JM, Sharp KH, Benner JS, McClung C, Cushing S, Lamkin ER, Fomenkov AI, Henrissat B, Londer YY, Scholz MB, Posfai J, Malfatti S, Tringe S, Woyke T, Malmstrom RR, Coleman-Derr D, Altamia MA, Dedrick S, Kaluziak ST, Haygood MG, Distel DL. Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk. Proc Natl Acad Sci U S A. 2014 Nov 25; 111(47):E5096-104. PMID: 25385629; PMCID: PMC4250168.
      39. Prestat E, David MM, Hultman J, Tas N, Lamendella R, Dvornik J, Mackelprang R, Myrold DD, Jumpponen A, Tringe S, Holman E, Mavromatis K, Jansson JK. FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus. Nucleic Acids Res. 2014 Oct 29; 42(19):e145. PMID: 25260589; PMCID: PMC4231724.
      40. Wu YW, Tang YH, Tringe S, Simmons BA, Singer SW. MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome. 2014; 2:26. PMID: 25136443; PMCID: PMC4129434.
      41. Piao H, Lachman M, Malfatti S, Sczyrba A, Knierim B, Auer M, Tringe S, Mackie RI, Yeoman CJ, Hess M. Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling. Front Microbiol. 2014; 5:307. PMID: 25101058; PMCID: PMC4106096.
      42. Hawley ER, Malfatti SA, Pagani I, Huntemann M, Chen A, Foster B, Copeland A, del Rio TG, Pati A, Jansson JR, Gilbert JA, Tringe S, Lorenson TD, Hess M. Metagenomes from two microbial consortia associated with Santa Barbara seep oil. Mar Genomics. 2014 Dec; 18 Pt B:97-9. PMID: 24958360.
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      43. Coleman-Derr D, Tringe S. Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance. Front Microbiol. 2014; 5:283. PMID: 24936202; PMCID: PMC4047557.
      44. Singh G, Srinivasan R, Cheng J, Peng Z, Fujimura K, Baek MS, Panzer AR, Tringe S, Chen F, Sorek R, Weng L, Bristow J, Wiener-Kronish JP, Lynch SV. Rearrangement of a large novel Pseudomonas aeruginosa gene island in strains isolated from a patient developing ventilator-associated pneumonia. J Clin Microbiol. 2014 Jul; 52(7):2430-8. PMID: 24789195; PMCID: PMC4097748.
      45. Wagner MR, Lundberg DS, Coleman-Derr D, Tringe S, Dangl JL, Mitchell-Olds T. Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecol Lett. 2014 Jun; 17(6):717-26. PMID: 24698177; PMCID: PMC4048358.
      46. Howe AC, Jansson JK, Malfatti SA, Tringe S, Tiedje JM, Brown CT. Tackling soil diversity with the assembly of large, complex metagenomes. Proc Natl Acad Sci U S A. 2014 Apr 01; 111(13):4904-9. PMID: 24632729; PMCID: PMC3977251.
      47. Williams TJ, Allen MA, DeMaere MZ, Kyrpides NC, Tringe S, Woyke T, Cavicchioli R. Microbial ecology of an Antarctic hypersaline lake: genomic assessment of ecophysiology among dominant haloarchaea. ISME J. 2014 Aug; 8(8):1645-58. PMID: 24553470; PMCID: PMC4817606.
      48. Hawley ER, Piao H, Scott NM, Malfatti S, Pagani I, Huntemann M, Chen A, Glavina Del Rio T, Foster B, Copeland A, Jansson J, Pati A, Tringe S, Gilbert JA, Lorenson TD, Hess M. Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California. Stand Genomic Sci. 2014 Jun 15; 9(3):1259-74. PMID: 25197496; PMCID: PMC4149020.
      49. Lindemann SR, Moran JJ, Stegen JC, Renslow RS, Hutchison JR, Cole JK, Dohnalkova AC, Tremblay J, Singh K, Malfatti SA, Chen F, Tringe S, Beyenal H, Fredrickson JK. The epsomitic phototrophic microbial mat of Hot Lake, Washington: community structural responses to seasonal cycling. Front Microbiol. 2013; 4:323. PMID: 24312082; PMCID: PMC3826063.
      50. Jay ZJ, Rusch DB, Tringe S, Bailey C, Jennings RM, Inskeep WP. Predominant Acidilobus-like populations from geothermal environments in yellowstone national park exhibit similar metabolic potential in different hypoxic microbial communities. Appl Environ Microbiol. 2014 Jan; 80(1):294-305. PMID: 24162572; PMCID: PMC3911027.
      51. Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Pillay M, Ratner A, Huang J, Pagani I, Tringe S, Huntemann M, Billis K, Varghese N, Tennessen K, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC. IMG/M 4 version of the integrated metagenome comparative analysis system. Nucleic Acids Res. 2014 Jan; 42(Database issue):D568-73. PMID: 24136997; PMCID: PMC3964948.
      52. DeMaere MZ, Williams TJ, Allen MA, Brown MV, Gibson JA, Rich J, Lauro FM, Dyall-Smith M, Davenport KW, Woyke T, Kyrpides NC, Tringe S, Cavicchioli R. High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake. Proc Natl Acad Sci U S A. 2013 Oct 15; 110(42):16939-44. PMID: 24082106; PMCID: PMC3801024.
      53. Scully ED, Geib SM, Hoover K, Tien M, Tringe S, Barry KW, Glavina del Rio T, Chovatia M, Herr JR, Carlson JE. Metagenomic profiling reveals lignocellulose degrading system in a microbial community associated with a wood-feeding beetle. PLoS One. 2013; 8(9):e73827. PMID: 24023907; PMCID: PMC3762729.
      54. Hug LA, Castelle CJ, Wrighton KC, Thomas BC, Sharon I, Frischkorn KR, Williams KH, Tringe S, Banfield JF. Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling. Microbiome. 2013 Aug 05; 1(1):22. PMID: 24450983; PMCID: PMC3971608.
      55. Rivers AR, Sharma S, Tringe S, Martin J, Joye SB, Moran MA. Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill. ISME J. 2013 Dec; 7(12):2315-29. PMID: 23902988; PMCID: PMC3834857.
      56. Flowers JJ, He S, Malfatti S, del Rio TG, Tringe S, Hugenholtz P, McMahon KD. Comparative genomics of two 'Candidatus Accumulibacter' clades performing biological phosphorus removal. ISME J. 2013 Dec; 7(12):2301-14. PMID: 23887171; PMCID: PMC3834850.
      57. D'haeseleer P, Gladden JM, Allgaier M, Chain PS, Tringe S, Malfatti SA, Aldrich JT, Nicora CD, Robinson EW, Paša-Tolic L, Hugenholtz P, Simmons BA, Singer SW. Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. PLoS One. 2013; 8(7):e68465. PMID: 23894306; PMCID: PMC3716776.
      58. Klatt CG, Inskeep WP, Herrgard MJ, Jay ZJ, Rusch DB, Tringe S, Niki Parenteau M, Ward DM, Boomer SM, Bryant DA, Miller SR. Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments. Front Microbiol. 2013; 4:106. PMID: 23761787; PMCID: PMC3669762.
      59. Takacs-Vesbach C, Inskeep WP, Jay ZJ, Herrgard MJ, Rusch DB, Tringe S, Kozubal MA, Hamamura N, Macur RE, Fouke BW, Reysenbach AL, McDermott TR, Jennings Rd, Hengartner NW, Xie G. Metagenome sequence analysis of filamentous microbial communities obtained from geochemically distinct geothermal channels reveals specialization of three aquificales lineages. Front Microbiol. 2013; 4:84. PMID: 23755042; PMCID: PMC3665934.
      60. Inskeep WP, Jay ZJ, Herrgard MJ, Kozubal MA, Rusch DB, Tringe S, Macur RE, Jennings Rd, Boyd ES, Spear JR, Roberto FF. Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry. Front Microbiol. 2013; 4:95. PMID: 23720654; PMCID: PMC3654217.
      61. Inskeep WP, Jay ZJ, Tringe S, Herrgård MJ, Rusch DB. The YNP Metagenome Project: Environmental Parameters Responsible for Microbial Distribution in the Yellowstone Geothermal Ecosystem. Front Microbiol. 2013; 4:67. PMID: 23653623; PMCID: PMC3644721.
      62. He S, Ivanova N, Kirton E, Allgaier M, Bergin C, Scheffrahn RH, Kyrpides NC, Warnecke F, Tringe S, Hugenholtz P. Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites. PLoS One. 2013; 8(4):e61126. PMID: 23593407; PMCID: PMC3625147.
      63. Aylward FO, Burnum-Johnson KE, Tringe S, Teiling C, Tremmel DM, Moeller JA, Scott JJ, Barry KW, Piehowski PD, Nicora CD, Malfatti SA, Monroe ME, Purvine SO, Goodwin LA, Smith RD, Weinstock GM, Gerardo NM, Suen G, Lipton MS, Currie CR. Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens. Appl Environ Microbiol. 2013 Jun; 79(12):3770-8. PMID: 23584789; PMCID: PMC3675943.
      64. Peiffer JA, Spor A, Koren O, Jin Z, Tringe S, Dangl JL, Buckler ES, Ley RE. Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc Natl Acad Sci U S A. 2013 Apr 16; 110(16):6548-53. PMID: 23576752; PMCID: PMC3631645.
      65. Deangelis KM, D'Haeseleer P, Chivian D, Simmons B, Arkin AP, Mavromatis K, Malfatti S, Tringe S, Hazen TC. Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron. Stand Genomic Sci. 2013; 7(3):382-98. PMID: 24019987; PMCID: PMC3764933.
      66. Beck DA, Kalyuzhnaya MG, Malfatti S, Tringe S, Glavina Del Rio T, Ivanova N, Lidstrom ME, Chistoserdova L. A metagenomic insight into freshwater methane-utilizing communities and evidence for cooperation between the Methylococcaceae and the Methylophilaceae. PeerJ. 2013; 1:e23. PMID: 23638358; PMCID: PMC3628875.
      67. Gori F, Tringe S, Folino G, van Hijum SA, Op den Camp HJ, Jetten MS, Marchiori E. Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes. BMC Genomics. 2013 Jan 16; 14:7. PMID: 23324532; PMCID: PMC3618311.
      68. Dodsworth JA, Blainey PC, Murugapiran SK, Swingley WD, Ross CA, Tringe S, Chain PS, Scholz MB, Lo CC, Raymond J, Quake SR, Hedlund BP. Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nat Commun. 2013; 4:1854. PMID: 23673639; PMCID: PMC3878185.
      69. Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH, Wu D, Tringe S, Singer SW, Eisen JA, Banfield JF. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat Commun. 2013; 4:2120. PMID: 23979677; PMCID: PMC3903129.
      70. Burow LC, Woebken D, Marshall IP, Lindquist EA, Bebout BM, Prufert-Bebout L, Hoehler TM, Tringe S, Pett-Ridge J, Weber PK, Spormann AM, Singer SW. Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics. ISME J. 2013 Apr; 7(4):817-29. PMID: 23190731; PMCID: PMC3603402.
      71. Kozubal MA, Romine M, Jennings Rd, Jay ZJ, Tringe S, Rusch DB, Beam JP, McCue LA, Inskeep WP. Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park. ISME J. 2013 Mar; 7(3):622-34. PMID: 23151644; PMCID: PMC3578567.
      72. Hunt DE, Lin Y, Church MJ, Karl DM, Tringe S, Izzo LK, Johnson ZI. Relationship between abundance and specific activity of bacterioplankton in open ocean surface waters. Appl Environ Microbiol. 2013 Jan; 79(1):177-84. PMID: 23087033; PMCID: PMC3536108.
      73. Worden AZ, Janouskovec J, McRose D, Engman A, Welsh RM, Malfatti S, Tringe S, Keeling PJ. Global distribution of a wild alga revealed by targeted metagenomics. Curr Biol. 2012 Sep 11; 22(17):R675-7. PMID: 22974991.
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      74. Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, Del Rio TG, Edgar RC, Eickhorst T, Ley RE, Hugenholtz P, Tringe S, Dangl JL. Defining the core Arabidopsis thaliana root microbiome. Nature. 2012 Aug 02; 488(7409):86-90. PMID: 22859206; PMCID: PMC4074413.
      75. Hollister EB, Forrest AK, Wilkinson HH, Ebbole DJ, Tringe S, Malfatti SA, Holtzapple MT, Gentry TJ. Mesophilic and thermophilic conditions select for unique but highly parallel microbial communities to perform carboxylate platform biomass conversion. PLoS One. 2012; 7(6):e39689. PMID: 22761870; PMCID: PMC3382152.
      76. Mason OU, Hazen TC, Borglin S, Chain PS, Dubinsky EA, Fortney JL, Han J, Holman HY, Hultman J, Lamendella R, Mackelprang R, Malfatti S, Tom LM, Tringe S, Woyke T, Zhou J, Rubin EM, Jansson JK. Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. ISME J. 2012 Sep; 6(9):1715-27. PMID: 22717885; PMCID: PMC3498917.
      77. Baelum J, Borglin S, Chakraborty R, Fortney JL, Lamendella R, Mason OU, Auer M, Zemla M, Bill M, Conrad ME, Malfatti SA, Tringe S, Holman HY, Hazen TC, Jansson JK. Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill. Environ Microbiol. 2012 Sep; 14(9):2405-16. PMID: 22616650.
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      78. van der Lelie D, Taghavi S, McCorkle SM, Li LL, Malfatti SA, Monteleone D, Donohoe BS, Ding SY, Adney WS, Himmel ME, Tringe S. The metagenome of an anaerobic microbial community decomposing poplar wood chips. PLoS One. 2012; 7(5):e36740. PMID: 22629327; PMCID: PMC3357426.
      79. van de Vossenberg J, Woebken D, Maalcke WJ, Wessels HJ, Dutilh BE, Kartal B, Janssen-Megens EM, Roeselers G, Yan J, Speth D, Gloerich J, Geerts W, van der Biezen E, Pluk W, Francoijs KJ, Russ L, Lam P, Malfatti SA, Tringe S, Haaijer SC, Op den Camp HJ, Stunnenberg HG, Amann R, Kuypers MM, Jetten MS. The metagenome of the marine anammox bacterium 'Candidatus Scalindua profunda' illustrates the versatility of this globally important nitrogen cycle bacterium. Environ Microbiol. 2013 May; 15(5):1275-89. PMID: 22568606; PMCID: PMC3655542.
      80. Kozubal MA, Macur RE, Jay ZJ, Beam JP, Malfatti SA, Tringe S, Kocar BD, Borch T, Inskeep WP. Microbial iron cycling in acidic geothermal springs of yellowstone national park: integrating molecular surveys, geochemical processes, and isolation of novel fe-active microorganisms. Front Microbiol. 2012; 3:109. PMID: 22470372; PMCID: PMC3312321.
      81. Aylward FO, Burnum KE, Scott JJ, Suen G, Tringe S, Adams SM, Barry KW, Nicora CD, Piehowski PD, Purvine SO, Starrett GJ, Goodwin LA, Smith RD, Lipton MS, Currie CR. Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens. ISME J. 2012 Sep; 6(9):1688-701. PMID: 22378535; PMCID: PMC3498920.
      82. Brisson VL, West KA, Lee PK, Tringe S, Brodie EL, Alvarez-Cohen L. Metagenomic analysis of a stable trichloroethene-degrading microbial community. ISME J. 2012 Sep; 6(9):1702-14. PMID: 22378537; PMCID: PMC3498913.
      83. Gilbert J, Li LL, Taghavi S, McCorkle SM, Tringe S, van der Lelie D. Bioprospecting metagenomics for new glycoside hydrolases. Methods Mol Biol. 2012; 908:141-51. PMID: 22843397.
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      84. Harhangi HR, Le Roy M, van Alen T, Hu BL, Groen J, Kartal B, Tringe S, Quan ZX, Jetten MS, Op den Camp HJ. Hydrazine synthase, a unique phylomarker with which to study the presence and biodiversity of anammox bacteria. Appl Environ Microbiol. 2012 Feb; 78(3):752-8. PMID: 22138989; PMCID: PMC3264106.
      85. Gori F, Tringe S, Kartal B, Marchiori E, Machiori E, Jetten MS. The metagenomic basis of anammox metabolism in Candidatus 'Brocadia fulgida'. Biochem Soc Trans. 2011 Dec; 39(6):1799-804. PMID: 22103529.
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      86. Berg Miller ME, Yeoman CJ, Chia N, Tringe S, Angly FE, Edwards RA, Flint HJ, Lamed R, Bayer EA, White BA. Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome. Environ Microbiol. 2012 Jan; 14(1):207-27. PMID: 22004549.
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      87. Godoy-Vitorino F, Goldfarb KC, Karaoz U, Leal S, Garcia-Amado MA, Hugenholtz P, Tringe S, Brodie EL, Dominguez-Bello MG. Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows. ISME J. 2012 Mar; 6(3):531-41. PMID: 21938024; PMCID: PMC3280141.
      88. Li LL, Taghavi S, McCorkle SM, Zhang YB, Blewitt MG, Brunecky R, Adney WS, Himmel ME, Brumm P, Drinkwater C, Mead DA, Tringe S, Lelie Dv. Bioprospecting metagenomics of decaying wood: mining for new glycoside hydrolases. Biotechnol Biofuels. 2011 Aug 04; 4(1):23. PMID: 21816041; PMCID: PMC3171299.
      89. Pope PB, Smith W, Denman SE, Tringe S, Barry K, Hugenholtz P, McSweeney CS, McHardy AC, Morrison M. Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies. Science. 2011 Jul 29; 333(6042):646-8. PMID: 21719642.
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      90. Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T, Mackie RI, Pennacchio LA, Tringe S, Visel A, Woyke T, Wang Z, Rubin EM. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science. 2011 Jan 28; 331(6016):463-7. PMID: 21273488.
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      91. Suen G, Scott JJ, Aylward FO, Adams SM, Tringe S, Pinto-Tomás AA, Foster CE, Pauly M, Weimer PJ, Barry KW, Goodwin LA, Bouffard P, Li L, Osterberger J, Harkins TT, Slater SC, Donohue TJ, Currie CR. An insect herbivore microbiome with high plant biomass-degrading capacity. PLoS Genet. 2010 Sep 23; 6(9):e1001129. PMID: 20885794; PMCID: PMC2944797.
      92. He S, Wurtzel O, Singh K, Froula JL, Yilmaz S, Tringe S, Wang Z, Chen F, Lindquist EA, Sorek R, Hugenholtz P. Validation of two ribosomal RNA removal methods for microbial metatranscriptomics. Nat Methods. 2010 Oct; 7(10):807-12. PMID: 20852648.
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      93. Lykidis A, Chen CL, Tringe S, McHardy AC, Copeland A, Kyrpides NC, Hugenholtz P, Macarie H, Olmos A, Monroy O, Liu WT. Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium. ISME J. 2011 Jan; 5(1):122-30. PMID: 20686509; PMCID: PMC3105669.
      94. Hollister EB, Forrest AK, Wilkinson HH, Ebbole DJ, Malfatti SA, Tringe S, Holtzapple MT, Gentry TJ. Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production. Appl Microbiol Biotechnol. 2010 Sep; 88(1):389-99. PMID: 20676626.
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      95. Pope PB, Denman SE, Jones M, Tringe S, Barry K, Malfatti SA, McHardy AC, Cheng JF, Hugenholtz P, McSweeney CS, Morrison M. Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. Proc Natl Acad Sci U S A. 2010 Aug 17; 107(33):14793-8. PMID: 20668243; PMCID: PMC2930436.
      96. Cuvelier ML, Allen AE, Monier A, McCrow JP, Messié M, Tringe S, Woyke T, Welsh RM, Ishoey T, Lee JH, Binder BJ, DuPont CL, Latasa M, Guigand C, Buck KR, Hilton J, Thiagarajan M, Caler E, Read B, Lasken RS, Chavez FP, Worden AZ. Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton. Proc Natl Acad Sci U S A. 2010 Aug 17; 107(33):14679-84. PMID: 20668244; PMCID: PMC2930470.
      97. Ivanova N, Tringe S, Liolios K, Liu WT, Morrison N, Hugenholtz P, Kyrpides NC. A call for standardized classification of metagenome projects. Environ Microbiol. 2010 Jul; 12(7):1803-5. PMID: 20653767.
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      98. Hemme CL, Deng Y, Gentry TJ, Fields MW, Wu L, Barua S, Barry K, Tringe S, Watson DB, He Z, Hazen TC, Tiedje JM, Rubin EM, Zhou J. Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community. ISME J. 2010 May; 4(5):660-72. PMID: 20182523.
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      99. Walsh DA, Zaikova E, Howes CG, Song YC, Wright JJ, Tringe S, Tortell PD, Hallam SJ. Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones. Science. 2009 Oct 23; 326(5952):578-82. PMID: 19900896.
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      100. Duncan KE, Gieg LM, Parisi VA, Tanner RS, Tringe S, Bristow J, Suflita JM. Biocorrosive thermophilic microbial communities in Alaskan North Slope oil facilities. Environ Sci Technol. 2009 Oct 15; 43(20):7977-84. PMID: 19921923.
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      101. Tringe S, Hugenholtz P. A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol. 2008 Oct; 11(5):442-6. PMID: 18817891.
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      102. Kalyuzhnaya MG, Lapidus A, Ivanova N, Copeland AC, McHardy AC, Szeto E, Salamov A, Grigoriev IV, Suciu D, Levine SR, Markowitz VM, Rigoutsos I, Tringe S, Bruce DC, Richardson PM, Lidstrom ME, Chistoserdova L. High-resolution metagenomics targets specific functional types in complex microbial communities. Nat Biotechnol. 2008 Sep; 26(9):1029-34. PMID: 18711340.
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      103. Tringe S, Zhang T, Liu X, Yu Y, Lee WH, Yap J, Yao F, Suan ST, Ing SK, Haynes M, Rohwer F, Wei CL, Tan P, Bristow J, Rubin EM, Ruan Y. The airborne metagenome in an indoor urban environment. PLoS One. 2008 Apr 02; 3(4):e1862. PMID: 18382653; PMCID: PMC2270337.
      104. Warnecke F, Luginbühl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, Cayouette M, McHardy AC, Djordjevic G, Aboushadi N, Sorek R, Tringe S, Podar M, Martin HG, Kunin V, Dalevi D, Madejska J, Kirton E, Platt D, Szeto E, Salamov A, Barry K, Mikhailova N, Kyrpides NC, Matson EG, Ottesen EA, Zhang X, Hernández M, Murillo C, Acosta LG, Rigoutsos I, Tamayo G, Green BD, Chang C, Rubin EM, Mathur EJ, Robertson DE, Hugenholtz P, Leadbetter JR. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature. 2007 Nov 22; 450(7169):560-5. PMID: 18033299.
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      105. von Mering C, Hugenholtz P, Raes J, Tringe S, Doerks T, Jensen LJ, Ward N, Bork P. Quantitative phylogenetic assessment of microbial communities in diverse environments. Science. 2007 Feb 23; 315(5815):1126-30. PMID: 17272687.
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      106. Tringe S, Willis J, Liberatore KL, Ruby SW. The WTM genes in budding yeast amplify expression of the stress-inducible gene RNR3. Genetics. 2006 Nov; 174(3):1215-28. PMID: 16980392; PMCID: PMC1667055.
      107. Tringe S, Rubin EM. Metagenomics: DNA sequencing of environmental samples. Nat Rev Genet. 2005 Nov; 6(11):805-14. PMID: 16304596.
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      108. Tringe S, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM. Comparative metagenomics of microbial communities. Science. 2005 Apr 22; 308(5721):554-7. PMID: 15845853.
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      109. Tringe S, Wagner A, Ruby SW. Enriching for direct regulatory targets in perturbed gene-expression profiles. Genome Biol. 2004; 5(4):R29. PMID: 15059262; PMCID: PMC395788.

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