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Items: 43


Correction: Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics.

Price MN, Zane GM, Kuehl JV, Melnyk RA, Wall JD, Deutschbauer AM, Arkin AP.

PLoS Genet. 2019 Apr 3;15(4):e1008106. doi: 10.1371/journal.pgen.1008106. eCollection 2019 Apr.


The selective pressures on the microbial community in a metal-contaminated aquifer.

Carlson HK, Price MN, Callaghan M, Aaring A, Chakraborty R, Liu H, Kuehl JV, Arkin AP, Deutschbauer AM.

ISME J. 2019 Apr;13(4):937-949. doi: 10.1038/s41396-018-0328-1. Epub 2018 Dec 6.


Dissimilatory Sulfate Reduction Under High Pressure by Desulfovibrio alaskensis G20.

Williamson AJ, Carlson HK, Kuehl JV, Huang LL, Iavarone AT, Deutschbauer A, Coates JD.

Front Microbiol. 2018 Jul 9;9:1465. doi: 10.3389/fmicb.2018.01465. eCollection 2018.


Mutant phenotypes for thousands of bacterial genes of unknown function.

Price MN, Wetmore KM, Waters RJ, Callaghan M, Ray J, Liu H, Kuehl JV, Melnyk RA, Lamson JS, Suh Y, Carlson HK, Esquivel Z, Sadeeshkumar H, Chakraborty R, Zane GM, Rubin BE, Wall JD, Visel A, Bristow J, Blow MJ, Arkin AP, Deutschbauer AM.

Nature. 2018 May;557(7706):503-509. doi: 10.1038/s41586-018-0124-0. Epub 2018 May 16.


Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics.

Price MN, Zane GM, Kuehl JV, Melnyk RA, Wall JD, Deutschbauer AM, Arkin AP.

PLoS Genet. 2018 Jan 11;14(1):e1007147. doi: 10.1371/journal.pgen.1007147. eCollection 2018 Jan. Erratum in: PLoS Genet. 2019 Apr 3;15(4):e1008106.


System-Wide Adaptations of Desulfovibrio alaskensis G20 to Phosphate-Limited Conditions.

Bosak T, Schubotz F, de Santiago-Torio A, Kuehl JV, Carlson HK, Watson N, Daye M, Summons RE, Arkin AP, Deutschbauer AM.

PLoS One. 2016 Dec 28;11(12):e0168719. doi: 10.1371/journal.pone.0168719. eCollection 2016.


Complete Genome Sequence of Cupriavidus basilensis 4G11, Isolated from the Oak Ridge Field Research Center Site.

Ray J, Waters RJ, Skerker JM, Kuehl JV, Price MN, Huang J, Chakraborty R, Arkin AP, Deutschbauer A.

Genome Announc. 2015 May 14;3(3). pii: e00322-15. doi: 10.1128/genomeA.00322-15.


Monofluorophosphate is a selective inhibitor of respiratory sulfate-reducing microorganisms.

Carlson HK, Stoeva MK, Justice NB, Sczesnak A, Mullan MR, Mosqueda LA, Kuehl JV, Deutschbauer AM, Arkin AP, Coates JD.

Environ Sci Technol. 2015 Mar 17;49(6):3727-36. doi: 10.1021/es505843z. Epub 2015 Mar 4.


Mechanisms of direct inhibition of the respiratory sulfate-reduction pathway by (per)chlorate and nitrate.

Carlson HK, Kuehl JV, Hazra AB, Justice NB, Stoeva MK, Sczesnak A, Mullan MR, Iavarone AT, Engelbrektson A, Price MN, Deutschbauer AM, Arkin AP, Coates JD.

ISME J. 2015 Jun;9(6):1295-305. doi: 10.1038/ismej.2014.216. Epub 2014 Nov 18.


The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20.

Price MN, Ray J, Wetmore KM, Kuehl JV, Bauer S, Deutschbauer AM, Arkin AP.

Front Microbiol. 2014 Oct 31;5:577. doi: 10.3389/fmicb.2014.00577. eCollection 2014.


Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20.

Kuehl JV, Price MN, Ray J, Wetmore KM, Esquivel Z, Kazakov AE, Nguyen M, Kuehn R, Davis RW, Hazen TC, Arkin AP, Deutschbauer A.

MBio. 2014 May 27;5(3):e01041-14. doi: 10.1128/mBio.01041-14.


Genetic basis for nitrate resistance in Desulfovibrio strains.

Korte HL, Fels SR, Christensen GA, Price MN, Kuehl JV, Zane GM, Deutschbauer AM, Arkin AP, Wall JD.

Front Microbiol. 2014 Apr 21;5:153. doi: 10.3389/fmicb.2014.00153. eCollection 2014.


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.

Meyer B, Kuehl JV, Price MN, Ray J, Deutschbauer AM, Arkin AP, Stahl DA.

Environ Microbiol. 2014 Nov;16(11):3463-86. doi: 10.1111/1462-2920.12405. Epub 2014 Mar 5.


Control of methionine metabolism by the SahR transcriptional regulator in Proteobacteria.

Novichkov PS, Li X, Kuehl JV, Deutschbauer AM, Arkin AP, Price MN, Rodionov DA.

Environ Microbiol. 2014 Jan;16(1):1-8. doi: 10.1111/1462-2920.12273. Epub 2013 Oct 9.


Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes.

Meyer B, Kuehl JV, Deutschbauer AM, Arkin AP, Stahl DA.

J Bacteriol. 2013 Nov;195(21):4900-14. doi: 10.1128/JB.00504-13. Epub 2013 Aug 23.


Indirect and suboptimal control of gene expression is widespread in bacteria.

Price MN, Deutschbauer AM, Skerker JM, Wetmore KM, Ruths T, Mar JS, Kuehl JV, Shao W, Arkin AP.

Mol Syst Biol. 2013 Apr 16;9:660. doi: 10.1038/msb.2013.16.


Evidence-based annotation of transcripts and proteins in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.

Price MN, Deutschbauer AM, Kuehl JV, Liu H, Witkowska HE, Arkin AP.

J Bacteriol. 2011 Oct;193(20):5716-27. doi: 10.1128/JB.05563-11. Epub 2011 Aug 12.


The gut as reservoir of antibiotic resistance: microbial diversity of tetracycline resistance in mother and infant.

de Vries LE, Vallès Y, Agersø Y, Vaishampayan PA, García-Montaner A, Kuehl JV, Christensen H, Barlow M, Francino MP.

PLoS One. 2011;6(6):e21644. doi: 10.1371/journal.pone.0021644. Epub 2011 Jun 28.


Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages.

Karol KG, Arumuganathan K, Boore JL, Duffy AM, Everett KD, Hall JD, Hansen SK, Kuehl JV, Mandoli DF, Mishler BD, Olmstead RG, Renzaglia KS, Wolf PG.

BMC Evol Biol. 2010 Oct 23;10:321. doi: 10.1186/1471-2148-10-321.


Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usage.

Guisinger MM, Kuehl JV, Boore JL, Jansen RK.

Mol Biol Evol. 2011 Jan;28(1):583-600. doi: 10.1093/molbev/msq229. Epub 2010 Aug 30. Erratum in: Mol Biol Evol. 2011 Apr;28(4):1543.


Comparative metagenomics and population dynamics of the gut microbiota in mother and infant.

Vaishampayan PA, Kuehl JV, Froula JL, Morgan JL, Ochman H, Francino MP.

Genome Biol Evol. 2010 Jan 6;2:53-66. doi: 10.1093/gbe/evp057.


Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes.

Oliver MJ, Murdock AG, Mishler BD, Kuehl JV, Boore JL, Mandoli DF, Everett KD, Wolf PG, Duffy AM, Karol KG.

BMC Genomics. 2010 Feb 27;11:143. doi: 10.1186/1471-2164-11-143.


Implications of the plastid genome sequence of typha (typhaceae, poales) for understanding genome evolution in poaceae.

Guisinger MM, Chumley TW, Kuehl JV, Boore JL, Jansen RK.

J Mol Evol. 2010 Feb;70(2):149-66. doi: 10.1007/s00239-009-9317-3. Epub 2010 Jan 21.


Parallel loss of plastid introns and their maturase in the genus Cuscuta.

McNeal JR, Kuehl JV, Boore JL, Leebens-Mack J, dePamphilis CW.

PLoS One. 2009 Jun 19;4(6):e5982. doi: 10.1371/journal.pone.0005982.


Extensive reorganization of the plastid genome of Trifolium subterraneum (Fabaceae) is associated with numerous repeated sequences and novel DNA insertions.

Cai Z, Guisinger M, Kim HG, Ruck E, Blazier JC, McMurtry V, Kuehl JV, Boore J, Jansen RK.

J Mol Evol. 2008 Dec;67(6):696-704. doi: 10.1007/s00239-008-9180-7.


Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions.

Guisinger MM, Kuehl JV, Boore JL, Jansen RK.

Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18424-9. doi: 10.1073/pnas.0806759105. Epub 2008 Nov 14.


Socotra Island the forgotten fragment of Gondwana: unmasking chameleon lizard history with complete mitochondrial genomic data.

Macey JR, Kuehl JV, Larson A, Robinson MD, Ugurtas IH, Ananjeva NB, Rahman H, Javed HI, Osman RM, Doumma A, Papenfuss TJ.

Mol Phylogenet Evol. 2008 Dec;49(3):1015-8. doi: 10.1016/j.ympev.2008.08.024. Epub 2008 Sep 7. No abstract available.


The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates.

McCoy SR, Kuehl JV, Boore JL, Raubeson LA.

BMC Evol Biol. 2008 May 1;8:130. doi: 10.1186/1471-2148-8-130.


Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae).

McNeal JR, Arumugunathan K, Kuehl JV, Boore JL, Depamphilis CW.

BMC Biol. 2007 Dec 13;5:55.


Functional gene losses occur with minimal size reduction in the plastid genome of the parasitic liverwort Aneura mirabilis.

Wickett NJ, Zhang Y, Hansen SK, Roper JM, Kuehl JV, Plock SA, Wolf PG, DePamphilis CW, Boore JL, Goffinet B.

Mol Biol Evol. 2008 Feb;25(2):393-401. Epub 2007 Dec 1.


Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns.

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 JV, Boore JL.

Proc Natl Acad Sci U S A. 2007 Dec 4;104(49):19369-74. Epub 2007 Nov 28.


Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids.

Cai Z, Penaflor C, Kuehl JV, Leebens-Mack J, Carlson JE, dePamphilis CW, Boore JL, Jansen RK.

BMC Evol Biol. 2006 Oct 4;6:77.


Using partial genomic fosmid libraries for sequencing complete organellar genomes.

McNeal JR, Leebens-Mack JH, Arumuganathan K, Kuehl JV, Boore JL, DePamphilis CW.

Biotechniques. 2006 Jul;41(1):69-73.


Naked corals: skeleton loss in Scleractinia.

Medina M, Collins AG, Takaoka TL, Kuehl JV, Boore JL.

Proc Natl Acad Sci U S A. 2006 Jun 13;103(24):9096-100. Epub 2006 Jun 5.


Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone.

Leebens-Mack J, Raubeson LA, Cui L, Kuehl JV, Fourcade MH, Chumley TW, Boore JL, Jansen RK, depamphilis CW.

Mol Biol Evol. 2005 Oct;22(10):1948-63. Epub 2005 Jun 8.


The complete mitochondrial genome of a gecko and the phylogenetic position of the Middle Eastern Teratoscincus keyserlingii.

Macey JR, Fong JJ, Kuehl JV, Shafiei S, Ananjeva NB, Papenfuss TJ, Boore JL.

Mol Phylogenet Evol. 2005 Jul;36(1):188-93. No abstract available.


Methods for obtaining and analyzing whole chloroplast genome sequences.

Jansen RK, Raubeson LA, Boore JL, dePamphilis CW, Chumley TW, Haberle RC, Wyman SK, Alverson AJ, Peery R, Herman SJ, Fourcade HM, Kuehl JV, McNeal JR, Leebens-Mack J, Cui L.

Methods Enzymol. 2005;395:348-84.


Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequences.

Macey JR, Papenfuss TJ, Kuehl JV, Fourcade HM, Boore JL.

Mol Phylogenet Evol. 2004 Oct;33(1):22-31.


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