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    Karaoz, Ulas

    TitleEarth Research Scientist
    SchoolLawrence Berkeley National Lab
    DepartmentClimate & Ecosystems
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/486-4118
    vCardDownload vCard

      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.
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      1. Jewell TN, Karaoz U, Bill M, Chakraborty R, Brodie EL, Williams KH, Beller HR. Metatranscriptomic Analysis Reveals Unexpectedly Diverse Microbial Metabolism in a Biogeochemical Hot Spot in an Alluvial Aquifer. Front Microbiol. 2017; 8:40. PMID: 28179898.
        View in: PubMed
      2. Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, Thomas BC, Singh A, Wilkins MJ, Karaoz U, Brodie EL, Williams KH, Hubbard SS, Banfield JF. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun. 2016 Oct 24; 7:13219. PMID: 27774985.
        View in: PubMed
      3. Couradeau E, Karaoz U, Lim HC, Nunes da Rocha U, Northen T, Brodie E, Garcia-Pichel F. Bacteria increase arid-land soil surface temperature through the production of sunscreens. Nat Commun. 2016 Jan 20; 7:10373. PMID: 26785770; PMCID: PMC4735820.
      4. Baran R, Brodie EL, Mayberry-Lewis J, Hummel E, Da Rocha UN, Chakraborty R, Bowen BP, Karaoz U, Cadillo-Quiroz H, Garcia-Pichel F, Northen TR. Exometabolite niche partitioning among sympatric soil bacteria. Nat Commun. 2015 Sep 22; 6:8289. PMID: 26392107; PMCID: PMC4595634.
      5. Ceja-Navarro JA, Vega FE, Karaoz U, Hao Z, Jenkins S, Lim HC, Kosina P, Infante F, Northen TR, Brodie EL. Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee. Nat Commun. 2015 Jul 14; 6:7618. PMID: 26173063; PMCID: PMC4510693.
      6. Nunes da Rocha U, Cadillo-Quiroz H, Karaoz U, Rajeev L, Klitgord N, Dunn S, Truong V, Buenrostro M, Bowen BP, Garcia-Pichel F, Mukhopadhyay A, Northen TR, Brodie EL. Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust. Front Microbiol. 2015; 6:277. PMID: 25926821; PMCID: PMC4396413.
      7. Srinivasan R, Karaoz U, Volegova M, MacKichan J, Kato-Maeda M, Miller S, Nadarajan R, Brodie EL, Lynch SV. Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens. PLoS One. 2015; 10(2):e0117617. PMID: 25658760; PMCID: PMC4319838.
      8. Beller HR, Yang L, Varadharajan C, Han R, Lim HC, Karaoz U, Molins S, Marcus MA, Brodie EL, Steefel CI, Nico PS. Divergent aquifer biogeochemical systems converge on similar and unexpected Cr(VI) reduction products. Environ Sci Technol. 2014 Sep 16; 48(18):10699-706. PMID: 25084058.
        View in: PubMed
      9. Ma Y, Madupu R, Karaoz U, Nossa CW, Yang L, Yooseph S, Yachimski PS, Brodie EL, Nelson KE, Pei Z. Human papillomavirus community in healthy persons, defined by metagenomics analysis of human microbiome project shotgun sequencing data sets. J Virol. 2014 May; 88(9):4786-97. PMID: 24522917; PMCID: PMC3993818.
      10. Nyyssönen M, Tran HM, Karaoz U, Weihe C, Hadi MZ, Martiny JB, Martiny AC, Brodie EL. Coupled high-throughput functional screening and next generation sequencing for identification of plant polymer decomposing enzymes in metagenomic libraries. Front Microbiol. 2013; 4:282. PMID: 24069019; PMCID: PMC3779933.
      11. Ceja-Navarro JA, Nguyen NH, Karaoz U, Gross SR, Herman DJ, Andersen GL, Bruns TD, Pett-Ridge J, Blackwell M, Brodie EL. Compartmentalized microbial composition, oxygen gradients and nitrogen fixation in the gut of Odontotaenius disjunctus. ISME J. 2014 Jan; 8(1):6-18. PMID: 23985746; PMCID: PMC3869013.
      12. Beller HR, Han R, Karaoz U, Lim H, Brodie EL. Genomic and physiological characterization of the chromate-reducing, aquifer-derived Firmicute Pelosinus sp. strain HCF1. Appl Environ Microbiol. 2013 Jan; 79(1):63-73. PMID: 23064329; PMCID: PMC3536105.
      13. Godoy-Vitorino F, Goldfarb KC, Karaoz U, Leal S, Garcia-Amado MA, Hugenholtz P, Tringe SG, 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.
      14. Goldfarb KC, Karaoz U, Hanson CA, Santee CA, Bradford MA, Treseder KK, Wallenstein MD, Brodie EL. Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance. Front Microbiol. 2011; 2:94. PMID: 21833332; PMCID: PMC3153052.
      15. DeSantis TZ, Keller K, Karaoz U, Alekseyenko AV, Singh NN, Brodie EL, Pei Z, Andersen GL, Larsen N. Simrank: Rapid and sensitive general-purpose k-mer search tool. BMC Ecol. 2011 Apr 27; 11:11. PMID: 21524302; PMCID: PMC3097142.
      16. Maldonado-Contreras A, Goldfarb KC, Godoy-Vitorino F, Karaoz U, Contreras M, Blaser MJ, Brodie EL, Dominguez-Bello MG. Structure of the human gastric bacterial community in relation to Helicobacter pylori status. ISME J. 2011 Apr; 5(4):574-9. PMID: 20927139; PMCID: PMC3105737.
      17. Cox MJ, Allgaier M, Taylor B, Baek MS, Huang YJ, Daly RA, Karaoz U, Andersen GL, Brown R, Fujimura KE, Wu B, Tran D, Koff J, Kleinhenz ME, Nielson D, Brodie EL, Lynch SV. Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients. PLoS One. 2010 Jun 23; 5(6):e11044. PMID: 20585638; PMCID: PMC2890402.
      18. Ivanov II, Atarashi K, Manel N, Brodie EL, Shima T, Karaoz U, Wei D, Goldfarb KC, Santee CA, Lynch SV, Tanoue T, Imaoka A, Itoh K, Takeda K, Umesaki Y, Honda K, Littman DR. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell. 2009 Oct 30; 139(3):485-98. PMID: 19836068; PMCID: PMC2796826.
      19. Yu L, Coelho JE, Zhang X, Fu Y, Tillman A, Karaoz U, Fredholm BB, Weng Z, Chen JF. Uncovering multiple molecular targets for caffeine using a drug target validation strategy combining A 2A receptor knockout mice with microarray profiling. Physiol Genomics. 2009 May 13; 37(3):199-210. PMID: 19258493; PMCID: PMC2685498.
      20. Karaoz U, Murali TM, Letovsky S, Zheng Y, Ding C, Cantor CR, Kasif S. Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci U S A. 2004 Mar 02; 101(9):2888-93. PMID: 14981259; PMCID: PMC365715.
      21. Logan BT, Karaoz U, Moreno PJ, Weng Z, Kasif S. Protein seer: a Web server for protein homology detection. Conf Proc IEEE Eng Med Biol Soc. 2004; 4:3064-7. PMID: 17270925.
        View in: PubMed

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