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Magic Pools: Parallel Assessment of Transposon Delivery Vectors in Bacteria.

Liu H, Price MN, Waters RJ, Ray J, Carlson HK, Lamson JS, Chakraborty R, Arkin AP, Deutschbauer AM.

mSystems. 2018 Jan 16;3(1). pii: e00143-17. doi: 10.1128/mSystems.00143-17. eCollection 2018 Jan-Feb.


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.


A metabolic pathway for catabolizing levulinic acid in bacteria.

Rand JM, Pisithkul T, Clark RL, Thiede JM, Mehrer CR, Agnew DE, Campbell CE, Markley AL, Price MN, Ray J, Wetmore KM, Suh Y, Arkin AP, Deutschbauer AM, Amador-Noguez D, Pfleger BF.

Nat Microbiol. 2017 Dec;2(12):1624-1634. doi: 10.1038/s41564-017-0028-z. Epub 2017 Sep 25.


PaperBLAST: Text Mining Papers for Information about Homologs.

Price MN, Arkin AP.

mSystems. 2017 Aug 15;2(4). pii: e00039-17. doi: 10.1128/mSystems.00039-17. eCollection 2017 Jul-Aug.


Validating regulatory predictions from diverse bacteria with mutant fitness data.

Sagawa S, Price MN, Deutschbauer AM, Arkin AP.

PLoS One. 2017 May 24;12(5):e0178258. doi: 10.1371/journal.pone.0178258. eCollection 2017.


A Comparison of the Costs and Benefits of Bacterial Gene Expression.

Price MN, Wetmore KM, Deutschbauer AM, Arkin AP.

PLoS One. 2016 Oct 6;11(10):e0164314. doi: 10.1371/journal.pone.0164314. eCollection 2016.


A Theoretical Lower Bound for Selection on the Expression Levels of Proteins.

Price MN, Arkin AP.

Genome Biol Evol. 2016 Jul 2;8(6):1917-28. doi: 10.1093/gbe/evw126.


The essential gene set of a photosynthetic organism.

Rubin BE, Wetmore KM, Price MN, Diamond S, Shultzaberger RK, Lowe LC, Curtin G, Arkin AP, Deutschbauer A, Golden SS.

Proc Natl Acad Sci U S A. 2015 Dec 1;112(48):E6634-43. doi: 10.1073/pnas.1519220112. Epub 2015 Oct 27.


Determining Roles of Accessory Genes in Denitrification by Mutant Fitness Analyses.

Vaccaro BJ, Thorgersen MP, Lancaster WA, Price MN, Wetmore KM, Poole FL 2nd, Deutschbauer A, Arkin AP, Adams MW.

Appl Environ Microbiol. 2015 Oct 9;82(1):51-61. doi: 10.1128/AEM.02602-15. Print 2016 Jan 1.


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.


Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons.

Wetmore KM, Price MN, Waters RJ, Lamson JS, He J, Hoover CA, Blow MJ, Bristow J, Butland G, Arkin AP, Deutschbauer A.

MBio. 2015 May 12;6(3):e00306-15. doi: 10.1128/mBio.00306-15.


Novel mechanism for scavenging of hypochlorite involving a periplasmic methionine-rich Peptide and methionine sulfoxide reductase.

Melnyk RA, Youngblut MD, Clark IC, Carlson HK, Wetmore KM, Price MN, Iavarone AT, Deutschbauer AM, Arkin AP, Coates JD.

MBio. 2015 May 12;6(3):e00233-15. doi: 10.1128/mBio.00233-15.


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.


Towards an informative mutant phenotype for every bacterial gene.

Deutschbauer A, Price MN, Wetmore KM, Tarjan DR, Xu Z, Shao W, Leon D, Arkin AP, Skerker JM.

J Bacteriol. 2014 Oct;196(20):3643-55. doi: 10.1128/JB.01836-14. Epub 2014 Aug 11.


Conservation of transcription start sites within genes across a bacterial genus.

Shao W, Price MN, Deutschbauer AM, Romine MF, Arkin AP.

MBio. 2014 Jul 1;5(4):e01398-14. doi: 10.1128/mBio.01398-14.


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.


Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates.

Skerker JM, Leon D, Price MN, Mar JS, Tarjan DR, Wetmore KM, Deutschbauer AM, Baumohl JK, Bauer S, Ibáñez AB, Mitchell VD, Wu CH, Hu P, Hazen T, Arkin AP.

Mol Syst Biol. 2013 Jun 18;9:674. doi: 10.1038/msb.2013.30.


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.


Variation among Desulfovibrio species in electron transfer systems used for syntrophic growth.

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

J Bacteriol. 2013 Mar;195(5):990-1004. doi: 10.1128/JB.01959-12. Epub 2012 Dec 21.


Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes.

Kazakov AE, Rodionov DA, Price MN, Arkin AP, Dubchak I, Novichkov PS.

J Bacteriol. 2013 Jan;195(1):29-38. doi: 10.1128/JB.01977-12. Epub 2012 Oct 19.


Metabolic footprinting of mutant libraries to map metabolite utilization to genotype.

Baran R, Bowen BP, Price MN, Arkin AP, Deutschbauer AM, Northen TR.

ACS Chem Biol. 2013 Jan 18;8(1):189-99. doi: 10.1021/cb300477w. Epub 2012 Oct 31.


An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.

McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P.

ISME J. 2012 Mar;6(3):610-8. doi: 10.1038/ismej.2011.139. Epub 2011 Dec 1.


Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions.

Deutschbauer A, Price MN, Wetmore KM, Shao W, Baumohl JK, Xu Z, Nguyen M, Tamse R, Davis RW, Arkin AP.

PLoS Genet. 2011 Nov;7(11):e1002385. doi: 10.1371/journal.pgen.1002385. Epub 2011 Nov 17.


Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium.

Rajeev L, Luning EG, Dehal PS, Price MN, Arkin AP, Mukhopadhyay A.

Genome Biol. 2011 Oct 12;12(10):R99. doi: 10.1186/gb-2011-12-10-r99.


Generalized schemes for high-throughput manipulation of the Desulfovibrio vulgaris genome.

Chhabra SR, Butland G, Elias DA, Chandonia JM, Fok OY, Juba TR, Gorur A, Allen S, Leung CM, Keller KL, Reveco S, Zane GM, Semkiw E, Prathapam R, Gold B, Singer M, Ouellet M, Szakal ED, Jorgens D, Price MN, Witkowska HE, Beller HR, Arkin AP, Hazen TC, Biggin MD, Auer M, Wall JD, Keasling JD.

Appl Environ Microbiol. 2011 Nov;77(21):7595-604. doi: 10.1128/AEM.05495-11. Epub 2011 Sep 9.


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.


Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough.

Chhabra SR, Joachimiak MP, Petzold CJ, Zane GM, Price MN, Reveco SA, Fok V, Johanson AR, Batth TS, Singer M, Chandonia JM, Joyner D, Hazen TC, Arkin AP, Wall JD, Singh AK, Keasling JD.

PLoS One. 2011;6(6):e21470. doi: 10.1371/journal.pone.0021470. Epub 2011 Jun 28.


Complete genome sequence and updated annotation of Desulfovibrio alaskensis G20.

Hauser LJ, Land ML, Brown SD, Larimer F, Keller KL, Rapp-Giles BJ, Price MN, Lin M, Bruce DC, Detter JC, Tapia R, Han CS, Goodwin LA, Cheng JF, Pitluck S, Copeland A, Lucas S, Nolan M, Lapidus AL, Palumbo AV, Wall JD.

J Bacteriol. 2011 Aug;193(16):4268-9. doi: 10.1128/JB.05400-11. Epub 2011 Jun 17.


Perceived and observed maternal relationship quality predict sexual debut by age 15.

Price MN, Hyde JS.

J Youth Adolesc. 2011 Dec;40(12):1595-606. doi: 10.1007/s10964-011-9641-y. Epub 2011 Mar 8.


A universal TagModule collection for parallel genetic analysis of microorganisms.

Oh J, Fung E, Price MN, Dehal PS, Davis RW, Giaever G, Nislow C, Arkin AP, Deutschbauer A.

Nucleic Acids Res. 2010 Aug;38(14):e146. doi: 10.1093/nar/gkq419. Epub 2010 May 21.


Impact of elevated nitrate on sulfate-reducing bacteria: a comparative study of Desulfovibrio vulgaris.

He Q, He Z, Joyner DC, Joachimiak M, Price MN, Yang ZK, Yen HC, Hemme CL, Chen W, Fields MM, Stahl DA, Keasling JD, Keller M, Arkin AP, Hazen TC, Wall JD, Zhou J.

ISME J. 2010 Nov;4(11):1386-97. doi: 10.1038/ismej.2010.59. Epub 2010 May 6.


FastTree 2--approximately maximum-likelihood trees for large alignments.

Price MN, Dehal PS, Arkin AP.

PLoS One. 2010 Mar 10;5(3):e9490. doi: 10.1371/journal.pone.0009490.


MicrobesOnline: an integrated portal for comparative and functional genomics.

Dehal PS, Joachimiak MP, Price MN, Bates JT, Baumohl JK, Chivian D, Friedland GD, Huang KH, Keller K, Novichkov PS, Dubchak IL, Alm EJ, Arkin AP.

Nucleic Acids Res. 2010 Jan;38(Database issue):D396-400. doi: 10.1093/nar/gkp919. Epub 2009 Nov 11.


When two isn't better than one: predictors of early sexual activity in adolescence using a cumulative risk model.

Price MN, Hyde JS.

J Youth Adolesc. 2009 Sep;38(8):1059-71. doi: 10.1007/s10964-008-9351-2. Epub 2008 Oct 16.


FastTree: computing large minimum evolution trees with profiles instead of a distance matrix.

Price MN, Dehal PS, Arkin AP.

Mol Biol Evol. 2009 Jul;26(7):1641-50. doi: 10.1093/molbev/msp077. Epub 2009 Apr 17.


FastBLAST: homology relationships for millions of proteins.

Price MN, Dehal PS, Arkin AP.

PLoS One. 2008;3(10):e3589. doi: 10.1371/journal.pone.0003589. Epub 2008 Oct 31.


Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli.

Price MN, Dehal PS, Arkin AP.

Genome Biol. 2008 Jan 7;9(1):R4. doi: 10.1186/gb-2008-9-1-r4.


The life-cycle of operons.

Price MN, Arkin AP, Alm EJ.

PLoS Genet. 2006 Jun;2(6):e96. Epub 2006 Jun 23. Erratum in: PLoS Genet. 2006 Jul;2(7):e126.


The histidine operon is ancient.

Price MN, Alm EJ, Arkin AP.

J Mol Evol. 2006 Jun;62(6):807-8. Epub 2006 Apr 11. No abstract available.


The MicrobesOnline Web site for comparative genomics.

Alm EJ, Huang KH, Price MN, Koche RP, Keller K, Dubchak IL, Arkin AP.

Genome Res. 2005 Jul;15(7):1015-22.


Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication.

Price MN, Alm EJ, Arkin AP.

Nucleic Acids Res. 2005 Jun 7;33(10):3224-34. Print 2005.


Operon formation is driven by co-regulation and not by horizontal gene transfer.

Price MN, Huang KH, Arkin AP, Alm EJ.

Genome Res. 2005 Jun;15(6):809-19.


A novel method for accurate operon predictions in all sequenced prokaryotes.

Price MN, Huang KH, Alm EJ, Arkin AP.

Nucleic Acids Res. 2005 Feb 8;33(3):880-92. Print 2005.

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