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    Kuehl, Jennifer

    TitleResearch Assoc Principal
    SchoolLawrence Berkeley National Lab
    DepartmentEnviron Genomics & Systems Bio
    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. Bosak T, Schubotz F, de Santiago-Torio A, Kuehl J, Carlson HK, Watson N, Daye M, Summons RE, Arkin AP, Deutschbauer AM. System-Wide Adaptations of Desulfovibrio alaskensis G20 to Phosphate-Limited Conditions. PLoS One. 2016; 11(12):e0168719. PMID: 28030630.
        View in: PubMed
      2. Ray J, Waters RJ, Skerker JM, Kuehl J, Price MN, Huang J, Chakraborty R, Arkin AP, Deutschbauer A. Complete Genome Sequence of Cupriavidus basilensis 4G11, Isolated from the Oak Ridge Field Research Center Site. Genome Announc. 2015 May 14; 3(3). PMID: 25977418; PMCID: PMC4432324.
      3. Carlson HK, Stoeva MK, Justice NB, Sczesnak A, Mullan MR, Mosqueda LA, Kuehl J, Deutschbauer AM, Arkin AP, Coates JD. Monofluorophosphate is a selective inhibitor of respiratory sulfate-reducing microorganisms. Environ Sci Technol. 2015 Mar 17; 49(6):3727-36. PMID: 25698072.
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      4. Carlson HK, Kuehl J, Hazra AB, Justice NB, Stoeva MK, Sczesnak A, Mullan MR, Iavarone AT, Engelbrektson A, Price MN, Deutschbauer AM, Arkin AP, Coates JD. Mechanisms of direct inhibition of the respiratory sulfate-reduction pathway by (per)chlorate and nitrate. ISME J. 2015 Jun; 9(6):1295-305. PMID: 25405978; PMCID: PMC4438318.
      5. Price MN, Ray J, Wetmore KM, Kuehl J, Bauer S, Deutschbauer AM, Arkin AP. The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20. Front Microbiol. 2014; 5:577. PMID: 25400629; PMCID: PMC4215793.
      6. Gowda H, Ivanisevic J, Johnson CH, Kurczy ME, Benton HP, Rinehart D, Nguyen T, Ray J, Kuehl J, Arevalo B, Westenskow PD, Wang J, Arkin AP, Deutschbauer AM, Patti GJ, Siuzdak G. Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses. Anal Chem. 2014 Jul 15; 86(14):6931-9. PMID: 24934772; PMCID: PMC4215863.
      7. Kuehl J, Price MN, Ray J, Wetmore KM, Esquivel Z, Kazakov AE, Nguyen M, Kuehn R, Davis RW, Hazen TC, Arkin AP, Deutschbauer A. Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20. MBio. 2014 May 27; 5(3):e01041-14. PMID: 24865553; PMCID: PMC4045070.
      8. Korte HL, Fels SR, Christensen GA, Price MN, Kuehl J, Zane GM, Deutschbauer AM, Arkin AP, Wall JD. Genetic basis for nitrate resistance in Desulfovibrio strains. Front Microbiol. 2014; 5:153. PMID: 24795702; PMCID: PMC4001038.
      9. Meyer B, Kuehl J, Price MN, Ray J, Deutschbauer AM, Arkin AP, Stahl DA. The energy-conserving electron transfer system used by Desulfovibrio alaskensis strain G20 during pyruvate fermentation involves reduction of endogenously formed fumarate and cytoplasmic and membrane-bound complexes, Hdr-Flox and Rnf. Environ Microbiol. 2014 Nov; 16(11):3463-86. PMID: 24447568.
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      10. Novichkov PS, Li X, Kuehl J, Deutschbauer AM, Arkin AP, Price MN, Rodionov DA. Control of methionine metabolism by the SahR transcriptional regulator in Proteobacteria. Environ Microbiol. 2014 Jan; 16(1):1-8. PMID: 24118949.
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      11. Meyer B, Kuehl J, Deutschbauer AM, Arkin AP, Stahl DA. Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes. J Bacteriol. 2013 Nov; 195(21):4900-14. PMID: 23974031; PMCID: PMC3807489.
      12. Price MN, Deutschbauer AM, Skerker JM, Wetmore KM, Ruths T, Mar JS, Kuehl J, Shao W, Arkin AP. Indirect and suboptimal control of gene expression is widespread in bacteria. Mol Syst Biol. 2013 Apr 16; 9:660. PMID: 23591776; PMCID: PMC3658271.
      13. Meyer B, Kuehl J, Deutschbauer AM, Price MN, Arkin AP, Stahl DA. Variation among Desulfovibrio species in electron transfer systems used for syntrophic growth. J Bacteriol. 2013 Mar; 195(5):990-1004. PMID: 23264581; PMCID: PMC3571329.
      14. Baker RH, Kuehl J, Wilkinson GS. The Enhancer of split complex arose prior to the diversification of schizophoran flies and is strongly conserved between Drosophila and stalk-eyed flies (Diopsidae). BMC Evol Biol. 2011 Dec 08; 11:354. PMID: 22151427; PMCID: PMC3261227.
      15. Price MN, Deutschbauer AM, Kuehl J, Liu H, Witkowska HE, Arkin AP. Evidence-based annotation of transcripts and proteins in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. J Bacteriol. 2011 Oct; 193(20):5716-27. PMID: 21840973; PMCID: PMC3187205.
      16. de Vries LE, Vallès Y, Agersø Y, Vaishampayan PA, García-Montaner A, Kuehl J, Christensen H, Barlow M, Francino MP. The gut as reservoir of antibiotic resistance: microbial diversity of tetracycline resistance in mother and infant. PLoS One. 2011; 6(6):e21644. PMID: 21738748; PMCID: PMC3125294.
      17. Karol KG, Arumuganathan K, Boore JL, Duffy AM, Everett KD, Hall JD, Hansen SK, Kuehl J, Mandoli DF, Mishler BD, Olmstead RG, Renzaglia KS, Wolf PG. Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages. BMC Evol Biol. 2010 Oct 23; 10:321. PMID: 20969798; PMCID: PMC3087542.
      18. Guisinger MM, Kuehl J, Boore JL, Jansen RK. Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usage. Mol Biol Evol. 2011 Jan; 28(1):583-600. PMID: 20805190.
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      19. Oliver MJ, Murdock AG, Mishler BD, Kuehl J, Boore JL, Mandoli DF, Everett KD, Wolf PG, Duffy AM, Karol KG. Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes. BMC Genomics. 2010 Feb 27; 11:143. PMID: 20187961; PMCID: PMC2841679.
      20. Guisinger MM, Chumley TW, Kuehl J, Boore JL, Jansen RK. Implications of the plastid genome sequence of typha (typhaceae, poales) for understanding genome evolution in poaceae. J Mol Evol. 2010 Feb; 70(2):149-66. PMID: 20091301.
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      21. Vaishampayan PA, Kuehl J, Froula JL, Morgan JL, Ochman H, Francino MP. Comparative metagenomics and population dynamics of the gut microbiota in mother and infant. Genome Biol Evol. 2010 Jan 06; 2:53-66. PMID: 20333224; PMCID: PMC2839348.
      22. McNeal JR, Kuehl J, Boore JL, Leebens-Mack J, dePamphilis CW. Parallel loss of plastid introns and their maturase in the genus Cuscuta. PLoS One. 2009 Jun 19; 4(6):e5982. PMID: 19543388; PMCID: PMC2694360.
      23. Cai Z, Guisinger M, Kim HG, Ruck E, Blazier JC, McMurtry V, Kuehl J, Boore J, Jansen RK. Extensive reorganization of the plastid genome of Trifolium subterraneum (Fabaceae) is associated with numerous repeated sequences and novel DNA insertions. J Mol Evol. 2008 Dec; 67(6):696-704. PMID: 19018585.
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      24. Guisinger MM, Kuehl J, Boore JL, Jansen RK. Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions. Proc Natl Acad Sci U S A. 2008 Nov 25; 105(47):18424-9. PMID: 19011103; PMCID: PMC2587588.
      25. Macey JR, Kuehl J, Larson A, Robinson MD, Ugurtas IH, Ananjeva NB, Rahman H, Javed HI, Osman RM, Doumma A, Papenfuss TJ. Socotra Island the forgotten fragment of Gondwana: unmasking chameleon lizard history with complete mitochondrial genomic data. Mol Phylogenet Evol. 2008 Dec; 49(3):1015-8. PMID: 18832039.
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      26. McCoy SR, Kuehl J, Boore JL, Raubeson LA. The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates. BMC Evol Biol. 2008 May 01; 8:130. PMID: 18452621; PMCID: PMC2386820.
      27. McNeal JR, Arumugunathan K, Kuehl J, Boore JL, Depamphilis CW. Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae). BMC Biol. 2007 Dec 13; 5:55. PMID: 18078516; PMCID: PMC2242782.
      28. Wickett NJ, Zhang Y, Hansen SK, Roper JM, Kuehl J, Plock SA, Wolf PG, DePamphilis CW, Boore JL, Goffinet B. Functional gene losses occur with minimal size reduction in the plastid genome of the parasitic liverwort Aneura mirabilis. Mol Biol Evol. 2008 Feb; 25(2):393-401. PMID: 18056074.
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      29. Jansen RK, Cai Z, Raubeson LA, Daniell H, Depamphilis CW, Leebens-Mack J, Müller KF, Guisinger-Bellian M, Haberle RC, Hansen AK, Chumley TW, Lee SB, Peery R, McNeal JR, Kuehl J, Boore JL. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci U S A. 2007 Dec 04; 104(49):19369-74. PMID: 18048330; PMCID: PMC2148296.
      30. McNeal JR, Kuehl J, Boore JL, de Pamphilis CW. Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta. BMC Plant Biol. 2007 Oct 24; 7:57. PMID: 17956636; PMCID: PMC2216012.
      31. Hoegg S, Boore JL, Kuehl J, Meyer A. Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni. BMC Genomics. 2007 Sep 10; 8:317. PMID: 17845724; PMCID: PMC2080641.
      32. Hansen DR, Dastidar SG, Cai Z, Penaflor C, Kuehl J, Boore JL, Jansen RK. Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae). Mol Phylogenet Evol. 2007 Nov; 45(2):547-63. PMID: 17644003.
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      33. Timme RE, Kuehl J, Boore JL, Jansen RK. A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats. Am J Bot. 2007 Mar; 94(3):302-12. PMID: 21636403.
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      34. Cai Z, Penaflor C, Kuehl J, Leebens-Mack J, Carlson JE, dePamphilis CW, Boore JL, Jansen RK. Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids. BMC Evol Biol. 2006 Oct 04; 6:77. PMID: 17020608; PMCID: PMC1626487.
      35. McNeal JR, Leebens-Mack JH, Arumuganathan K, Kuehl J, Boore JL, DePamphilis CW. Using partial genomic fosmid libraries for sequencing complete organellar genomes. Biotechniques. 2006 Jul; 41(1):69-73. PMID: 16869516.
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      36. Medina M, Collins AG, Takaoka TL, Kuehl J, Boore JL. Naked corals: skeleton loss in Scleractinia. Proc Natl Acad Sci U S A. 2006 Jun 13; 103(24):9096-100. PMID: 16754865; PMCID: PMC1482572.
      37. Macey JR, Fong JJ, Kuehl J, Shafiei S, Ananjeva NB, Papenfuss TJ, Boore JL. The complete mitochondrial genome of a gecko and the phylogenetic position of the Middle Eastern Teratoscincus keyserlingii. Mol Phylogenet Evol. 2005 Jul; 36(1):188-93. PMID: 15904865.
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      38. Leebens-Mack J, Raubeson LA, Cui L, Kuehl J, Fourcade MH, Chumley TW, Boore JL, Jansen RK, depamphilis CW. Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone. Mol Biol Evol. 2005 Oct; 22(10):1948-63. PMID: 15944438.
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      39. Wolf PG, Karol KG, Mandoli DF, Kuehl J, Arumuganathan K, Ellis MW, Mishler BD, Kelch DG, Olmstead RG, Boore JL. The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae). Gene. 2005 May 09; 350(2):117-28. PMID: 15788152.
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      40. Jansen RK, Raubeson LA, Boore JL, dePamphilis CW, Chumley TW, Haberle RC, Wyman SK, Alverson AJ, Peery R, Herman SJ, Fourcade HM, Kuehl J, McNeal JR, Leebens-Mack J, Cui L. Methods for obtaining and analyzing whole chloroplast genome sequences. Methods Enzymol. 2005; 395:348-84. PMID: 15865976.
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      41. Macey JR, Papenfuss TJ, Kuehl J, Fourcade HM, Boore JL. Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequences. Mol Phylogenet Evol. 2004 Oct; 33(1):22-31. PMID: 15324836.
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