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Items: 29

1.

NifH-Harboring Bacterial Community Composition across an Alaskan Permafrost Thaw Gradient.

Penton CR, Yang C, Wu L, Wang Q, Zhang J, Liu F, Qin Y, Deng Y, Hemme CL, Zheng T, Schuur EA, Tiedje J, Zhou J.

Front Microbiol. 2016 Nov 24;7:1894. eCollection 2016.

2.

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.

3.

Comparative metagenomics reveals impact of contaminants on groundwater microbiomes.

Hemme CL, Tu Q, Shi Z, Qin Y, Gao W, Deng Y, Nostrand JD, Wu L, He Z, Chain PS, Tringe SG, Fields MW, Rubin EM, Tiedje JM, Hazen TC, Arkin AP, Zhou J.

Front Microbiol. 2015 Oct 31;6:1205. doi: 10.3389/fmicb.2015.01205. eCollection 2015.

4.

Efficient Genome Editing in Clostridium cellulolyticum via CRISPR-Cas9 Nickase.

Xu T, Li Y, Shi Z, Hemme CL, Li Y, Zhu Y, Van Nostrand JD, He Z, Zhou J.

Appl Environ Microbiol. 2015 Jul;81(13):4423-31. doi: 10.1128/AEM.00873-15. Epub 2015 Apr 24.

5.

Development of HuMiChip for functional profiling of human microbiomes.

Tu Q, He Z, Li Y, Chen Y, Deng Y, Lin L, Hemme CL, Yuan T, Van Nostrand JD, Wu L, Zhou X, Shi W, Li L, Xu J, Zhou J.

PLoS One. 2014 Mar 4;9(3):e90546. doi: 10.1371/journal.pone.0090546. eCollection 2014.

6.

Saliva microbiota carry caries-specific functional gene signatures.

Yang F, Ning K, Chang X, Yuan X, Tu Q, Yuan T, Deng Y, Hemme CL, Van Nostrand J, Cui X, He Z, Chen Z, Guo D, Yu J, Zhang Y, Zhou J, Xu J.

PLoS One. 2014 Feb 12;9(2):e76458. doi: 10.1371/journal.pone.0076458. eCollection 2014.

7.

GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis.

Tu Q, Yu H, He Z, Deng Y, Wu L, Van Nostrand JD, Zhou A, Voordeckers J, Lee YJ, Qin Y, Hemme CL, Shi Z, Xue K, Yuan T, Wang A, Zhou J.

Mol Ecol Resour. 2014 Sep;14(5):914-28. doi: 10.1111/1755-0998.12239. Epub 2014 Mar 14.

PMID:
24520909
8.

StressChip as a high-throughput tool for assessing microbial community responses to environmental stresses.

Zhou A, He Z, Qin Y, Lu Z, Deng Y, Tu Q, Hemme CL, Van Nostrand JD, Wu L, Hazen TC, Arkin AP, Zhou J.

Environ Sci Technol. 2013 Sep 3;47(17):9841-9. doi: 10.1021/es4018656. Epub 2013 Aug 13.

PMID:
23889170
9.

Multilocus sequence analysis of Thermoanaerobacter isolates reveals recombining, but differentiated, populations from geothermal springs of the Uzon Caldera, Kamchatka, Russia.

Wagner ID, Varghese LB, Hemme CL, Wiegel J.

Front Microbiol. 2013 Jun 21;4:169. doi: 10.3389/fmicb.2013.00169. eCollection 2013.

10.

Structure and regulation of the cellulose degradome in Clostridium cellulolyticum.

Xu C, Huang R, Teng L, Wang D, Hemme CL, Borovok I, He Q, Lamed R, Bayer EA, Zhou J, Xu J.

Biotechnol Biofuels. 2013 May 8;6(1):73. doi: 10.1186/1754-6834-6-73.

11.

Continuous cellulosic bioethanol fermentation by cyclic fed-batch cocultivation.

Jiang HL, He Q, He Z, Hemme CL, Wu L, Zhou J.

Appl Environ Microbiol. 2013 Mar;79(5):1580-9. doi: 10.1128/AEM.02617-12. Epub 2012 Dec 28.

12.

Genome-wide analysis of acetivibrio cellulolyticus provides a blueprint of an elaborate cellulosome system.

Dassa B, Borovok I, Lamed R, Henrissat B, Coutinho P, Hemme CL, Huang Y, Zhou J, Bayer EA.

BMC Genomics. 2012 May 30;13:210. doi: 10.1186/1471-2164-13-210.

13.

Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough.

Zhou A, Chen YI, Zane GM, He Z, Hemme CL, Joachimiak MP, Baumohl JK, He Q, Fields MW, Arkin AP, Wall JD, Hazen TC, Zhou J.

Appl Environ Microbiol. 2012 Feb;78(4):1168-77. doi: 10.1128/AEM.05666-11. Epub 2011 Dec 9.

14.

Correlation of genomic and physiological traits of thermoanaerobacter species with biofuel yields.

Hemme CL, Fields MW, He Q, Deng Y, Lin L, Tu Q, Mouttaki H, Zhou A, Feng X, Zuo Z, Ramsay BD, He Z, Wu L, Van Nostrand J, Xu J, Tang YJ, Wiegel J, Phelps TJ, Zhou J.

Appl Environ Microbiol. 2011 Nov;77(22):7998-8008. doi: 10.1128/AEM.05677-11. Epub 2011 Sep 23.

15.

Mechanisms of enhanced cellulosic bioethanol fermentation by co-cultivation of Clostridium and Thermoanaerobacter spp.

He Q, Hemme CL, Jiang H, He Z, Zhou J.

Bioresour Technol. 2011 Oct;102(20):9586-92. doi: 10.1016/j.biortech.2011.07.098. Epub 2011 Aug 4.

PMID:
21868218
16.

How sulphate-reducing microorganisms cope with stress: lessons from systems biology.

Zhou J, He Q, Hemme CL, Mukhopadhyay A, Hillesland K, Zhou A, He Z, Van Nostrand JD, Hazen TC, Stahl DA, Wall JD, Arkin AP.

Nat Rev Microbiol. 2011 Jun;9(6):452-66. doi: 10.1038/nrmicro2575. Epub 2011 May 16. Review.

PMID:
21572460
17.

Isolation and characterization of Shigella flexneri G3, capable of effective cellulosic saccharification under mesophilic conditions.

Wang A, Gao L, Ren N, Xu J, Liu C, Cao G, Yu H, Liu W, Hemme CL, He Z, Zhou J.

Appl Environ Microbiol. 2011 Jan;77(2):517-23. doi: 10.1128/AEM.01230-10. Epub 2010 Nov 19.

18.

Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production.

Hemme CL, Mouttaki H, Lee YJ, Zhang G, Goodwin L, Lucas S, Copeland A, Lapidus A, Glavina del Rio T, Tice H, Saunders E, Brettin T, Detter JC, Han CS, Pitluck S, Land ML, Hauser LJ, Kyrpides N, Mikhailova N, He Z, Wu L, Van Nostrand JD, Henrissat B, He Q, Lawson PA, Tanner RS, Lynd LR, Wiegel J, Fields MW, Arkin AP, Schadt CW, Stevenson BS, McInerney MJ, Yang Y, Dong H, Xing D, Ren N, Wang A, Huhnke RL, Mielenz JR, Ding SY, Himmel ME, Taghavi S, van der Lelie D, Rubin EM, Zhou J.

J Bacteriol. 2010 Dec;192(24):6494-6. doi: 10.1128/JB.01064-10. Epub 2010 Oct 1.

19.

Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough.

Zhou A, He Z, Redding-Johanson AM, Mukhopadhyay A, Hemme CL, Joachimiak MP, Luo F, Deng Y, Bender KS, He Q, Keasling JD, Stahl DA, Fields MW, Hazen TC, Arkin AP, Wall JD, Zhou J.

Environ Microbiol. 2010 Oct;12(10):2645-57. doi: 10.1111/j.1462-2920.2010.02234.x.

PMID:
20482586
20.

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.

PMID:
20445634
21.

GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity.

He Z, Deng Y, Van Nostrand JD, Tu Q, Xu M, Hemme CL, Li X, Wu L, Gentry TJ, Yin Y, Liebich J, Hazen TC, Zhou J.

ISME J. 2010 Sep;4(9):1167-79. doi: 10.1038/ismej.2010.46. Epub 2010 Apr 29.

PMID:
20428223
22.

Succession of the bacterial community and dynamics of hydrogen producers in a hydrogen-producing bioreactor.

Huang Y, Zong W, Yan X, Wang R, Hemme CL, Zhou J, Zhou Z.

Appl Environ Microbiol. 2010 May;76(10):3387-90. doi: 10.1128/AEM.02444-09. Epub 2010 Mar 19.

23.

Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community.

Hemme CL, Deng Y, Gentry TJ, Fields MW, Wu L, Barua S, Barry K, Tringe SG, Watson DB, He Z, Hazen TC, Tiedje JM, Rubin EM, Zhou J.

ISME J. 2010 May;4(5):660-72. doi: 10.1038/ismej.2009.154. Epub 2010 Feb 25.

PMID:
20182523
24.

Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation.

He Z, Zhou A, Baidoo E, He Q, Joachimiak MP, Benke P, Phan R, Mukhopadhyay A, Hemme CL, Huang K, Alm EJ, Fields MW, Wall J, Stahl D, Hazen TC, Keasling JD, Arkin AP, Zhou J.

Appl Environ Microbiol. 2010 Mar;76(5):1574-86. doi: 10.1128/AEM.02141-09. Epub 2009 Dec 28.

25.

Characterization of the central metabolic pathways in Thermoanaerobacter sp. strain X514 via isotopomer-assisted metabolite analysis.

Feng X, Mouttaki H, Lin L, Huang R, Wu B, Hemme CL, He Z, Zhang B, Hicks LM, Xu J, Zhou J, Tang YJ.

Appl Environ Microbiol. 2009 Aug;75(15):5001-8. doi: 10.1128/AEM.00715-09. Epub 2009 Jun 12.

26.

Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough.

Bender KS, Yen HC, Hemme CL, Yang Z, He Z, He Q, Zhou J, Huang KH, Alm EJ, Hazen TC, Arkin AP, Wall JD.

Appl Environ Microbiol. 2007 Sep;73(17):5389-400. Epub 2007 Jul 13.

27.

Genomic insights into gene regulation of Desulfovibrio vulgaris Hildenborough.

Hemme CL, Wall JD.

OMICS. 2004 Spring;8(1):43-55.

PMID:
15107236
28.

The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.

Heidelberg JF, Seshadri R, Haveman SA, Hemme CL, Paulsen IT, Kolonay JF, Eisen JA, Ward N, Methe B, Brinkac LM, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Fouts D, Haft DH, Selengut J, Peterson JD, Davidsen TM, Zafar N, Zhou L, Radune D, Dimitrov G, Hance M, Tran K, Khouri H, Gill J, Utterback TR, Feldblyum TV, Wall JD, Voordouw G, Fraser CM.

Nat Biotechnol. 2004 May;22(5):554-9. Epub 2004 Apr 11.

PMID:
15077118
29.

TIMP-1 contact sites and perturbations of stromelysin 1 mapped by NMR and a paramagnetic surface probe.

Arumugam S, Hemme CL, Yoshida N, Suzuki K, Nagase H, Berjanskii M, Wu B, Van Doren SR.

Biochemistry. 1998 Jul 7;37(27):9650-7.

PMID:
9657677

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