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Items: 42

1.

Principles of Systems Biology, No. 30.

Garcia HG, Benzinger D, Rullan M, Milias-Argeitis A, Khammash M, Deutschbauer AM, Langdon EM, Gladfelter AS.

Cell Syst. 2018 Jul 25;7(1):1-2. doi: 10.1016/j.cels.2018.07.002.

PMID:
30048618
2.

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.

3.

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.

4.

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.

5.

Rapidly moving new bacteria to model-organism status.

Liu H, Deutschbauer AM.

Curr Opin Biotechnol. 2018 Jun;51:116-122. doi: 10.1016/j.copbio.2017.12.006. Epub 2018 Jan 6. Review.

PMID:
29316481
6.

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.

7.

Genome-wide identification of bacterial plant colonization genes.

Cole BJ, Feltcher ME, Waters RJ, Wetmore KM, Mucyn TS, Ryan EM, Wang G, Ul-Hasan S, McDonald M, Yoshikuni Y, Malmstrom RR, Deutschbauer AM, Dangl JL, Visel A.

PLoS Biol. 2017 Sep 22;15(9):e2002860. doi: 10.1371/journal.pbio.2002860. eCollection 2017 Sep.

8.

Mechanisms of Chromium and Uranium Toxicity in Pseudomonas stutzeri RCH2 Grown under Anaerobic Nitrate-Reducing Conditions.

Thorgersen MP, Lancaster WA, Ge X, Zane GM, Wetmore KM, Vaccaro BJ, Poole FL 2nd, Younkin AD, Deutschbauer AM, Arkin AP, Wall JD, Adams MWW.

Front Microbiol. 2017 Aug 10;8:1529. doi: 10.3389/fmicb.2017.01529. eCollection 2017.

9.

Draft Genome Sequences of Two Janthinobacteriumlividum Strains, Isolated from Pristine Groundwater Collected from the Oak Ridge Field Research Center.

Wu X, Deutschbauer AM, Kazakov AE, Wetmore KM, Cwick BA, Walker RM, Novichkov PS, Arkin AP, Chakraborty R.

Genome Announc. 2017 Jun 29;5(26). pii: e00582-17. doi: 10.1128/genomeA.00582-17.

10.

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.

11.

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.

12.

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.

13.

Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community.

Hemme CL, Green SJ, Rishishwar L, Prakash O, Pettenato A, Chakraborty R, Deutschbauer AM, Van Nostrand JD, Wu L, He Z, Jordan IK, Hazen TC, Arkin AP, Kostka JE, Zhou J.

MBio. 2016 Apr 5;7(2):e02234-15. doi: 10.1128/mBio.02234-15.

14.

Exometabolomics Assisted Design and Validation of Synthetic Obligate Mutualism.

Kosina SM, Danielewicz MA, Mohammed M, Ray J, Suh Y, Yilmaz S, Singh AK, Arkin AP, Deutschbauer AM, Northen TR.

ACS Synth Biol. 2016 Jul 15;5(7):569-76. doi: 10.1021/acssynbio.5b00236. Epub 2016 Feb 17.

15.

The Epigenomic Landscape of Prokaryotes.

Blow MJ, Clark TA, Daum CG, Deutschbauer AM, Fomenkov A, Fries R, Froula J, Kang DD, Malmstrom RR, Morgan RD, Posfai J, Singh K, Visel A, Wetmore K, Zhao Z, Rubin EM, Korlach J, Pennacchio LA, Roberts RJ.

PLoS Genet. 2016 Feb 12;12(2):e1005854. doi: 10.1371/journal.pgen.1005854. eCollection 2016 Feb. Erratum in: PLoS Genet. 2016 May;12(5):e1006064.

16.

Molybdenum Availability Is Key to Nitrate Removal in Contaminated Groundwater Environments.

Thorgersen MP, Lancaster WA, Vaccaro BJ, Poole FL, Rocha AM, Mehlhorn T, Pettenato A, Ray J, Waters RJ, Melnyk RA, Chakraborty R, Hazen TC, Deutschbauer AM, Arkin AP, Adams MW.

Appl Environ Microbiol. 2015 Aug;81(15):4976-83. doi: 10.1128/AEM.00917-15. Epub 2015 May 15.

17.

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.

18.

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.

PMID:
25698072
19.

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.

20.

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.

21.

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.

22.

Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses.

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.

Anal Chem. 2014 Jul 15;86(14):6931-9. doi: 10.1021/ac500734c. Epub 2014 Jun 25.

23.

Metabolomic data streaming for biology-dependent data acquisition.

Rinehart D, Johnson CH, Nguyen T, Ivanisevic J, Benton HP, Lloyd J, Arkin AP, Deutschbauer AM, Patti GJ, Siuzdak G.

Nat Biotechnol. 2014 Jun;32(6):524-7. doi: 10.1038/nbt.2927. No abstract available.

24.

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.

25.

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.

PMID:
24447568
26.

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.

PMID:
24118949
27.

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.

28.

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.

29.

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.

30.

Draft Genome Sequence for Desulfovibrio africanus Strain PCS.

Brown SD, Utturkar SM, Arkin AP, Deutschbauer AM, Elias DA, Hazen TC, Chakraborty R.

Genome Announc. 2013 Apr 11;1(2):e0014413. doi: 10.1128/genomeA.00144-13.

31.

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.

32.

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.

PMID:
23082955
33.

Draft genome sequence of Pelosinus fermentans JBW45, isolated during in situ stimulation for Cr(VI) reduction.

Bowen De León K, Young ML, Camilleri LB, Brown SD, Skerker JM, Deutschbauer AM, Arkin AP, Fields MW.

J Bacteriol. 2012 Oct;194(19):5456-7. doi: 10.1128/JB.01224-12.

34.

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.

35.

Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches.

McClellan AJ, Xia Y, Deutschbauer AM, Davis RW, Gerstein M, Frydman J.

Cell. 2007 Oct 5;131(1):121-35.

36.

Genomics for environmental microbiology.

Deutschbauer AM, Chivian D, Arkin AP.

Curr Opin Biotechnol. 2006 Jun;17(3):229-35. Epub 2006 May 2. Review.

PMID:
16650754
37.

Quantitative trait loci mapped to single-nucleotide resolution in yeast.

Deutschbauer AM, Davis RW.

Nat Genet. 2005 Dec;37(12):1333-40. Epub 2005 Nov 6.

PMID:
16273108
38.

Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast.

Deutschbauer AM, Jaramillo DF, Proctor M, Kumm J, Hillenmeyer ME, Davis RW, Nislow C, Giaever G.

Genetics. 2005 Apr;169(4):1915-25. Epub 2005 Feb 16.

39.

Sister-chromatid cohesion mediated by the alternative RF-CCtf18/Dcc1/Ctf8, the helicase Chl1 and the polymerase-alpha-associated protein Ctf4 is essential for chromatid disjunction during meiosis II.

Petronczki M, Chwalla B, Siomos MF, Yokobayashi S, Helmhart W, Deutschbauer AM, Davis RW, Watanabe Y, Nasmyth K.

J Cell Sci. 2004 Jul 15;117(Pt 16):3547-59. Epub 2004 Jun 29.

40.

Gene function on a genomic scale.

Steinmetz LM, Deutschbauer AM.

J Chromatogr B Analyt Technol Biomed Life Sci. 2002 Dec 25;782(1-2):151-63.

PMID:
12458004
41.

Parallel phenotypic analysis of sporulation and postgermination growth in Saccharomyces cerevisiae.

Deutschbauer AM, Williams RM, Chu AM, Davis RW.

Proc Natl Acad Sci U S A. 2002 Nov 26;99(24):15530-5. Epub 2002 Nov 13.

42.

Systematic screen for human disease genes in yeast.

Steinmetz LM, Scharfe C, Deutschbauer AM, Mokranjac D, Herman ZS, Jones T, Chu AM, Giaever G, Prokisch H, Oefner PJ, Davis RW.

Nat Genet. 2002 Aug;31(4):400-4. Epub 2002 Jul 22.

PMID:
12134146

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