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Items: 1 to 50 of 79

1.

Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome.

Maier TV, Lucio M, Lee LH, VerBerkmoes NC, Brislawn CJ, Bernhardt J, Lamendella R, McDermott JE, Bergeron N, Heinzmann SS, Morton JT, González A, Ackermann G, Knight R, Riedel K, Krauss RM, Schmitt-Kopplin P, Jansson JK.

MBio. 2017 Oct 17;8(5). pii: e01343-17. doi: 10.1128/mBio.01343-17.

2.

Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept.

Duhaime MB, Solonenko N, Roux S, Verberkmoes NC, Wichels A, Sullivan MB.

Front Microbiol. 2017 Jul 6;8:1241. doi: 10.3389/fmicb.2017.01241. eCollection 2017.

3.

Illuminating structural proteins in viral "dark matter" with metaproteomics.

Brum JR, Ignacio-Espinoza JC, Kim EH, Trubl G, Jones RM, Roux S, VerBerkmoes NC, Rich VI, Sullivan MB.

Proc Natl Acad Sci U S A. 2016 Mar 1;113(9):2436-41. doi: 10.1073/pnas.1525139113. Epub 2016 Feb 16.

4.

Tissue-specific transcriptomics and proteomics of a filarial nematode and its Wolbachia endosymbiont.

Luck AN, Anderson KG, McClung CM, VerBerkmoes NC, Foster JM, Michalski ML, Slatko BE.

BMC Genomics. 2015 Nov 11;16:920. doi: 10.1186/s12864-015-2083-2.

5.

Environmental Effects of Nanoceria on Seed Production of Common Bean (Phaseolus vulgaris): A Proteomic Analysis.

Majumdar S, Almeida IC, Arigi EA, Choi H, VerBerkmoes NC, Trujillo-Reyes J, Flores-Margez JP, White JC, Peralta-Videa JR, Gardea-Torresdey JL.

Environ Sci Technol. 2015 Nov 17;49(22):13283-93. doi: 10.1021/acs.est.5b03452. Epub 2015 Nov 4.

PMID:
26488752
6.

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes.

Hultman J, Waldrop MP, Mackelprang R, David MM, McFarland J, Blazewicz SJ, Harden J, Turetsky MR, McGuire AD, Shah MB, VerBerkmoes NC, Lee LH, Mavrommatis K, Jansson JK.

Nature. 2015 May 14;521(7551):208-12. doi: 10.1038/nature14238. Epub 2015 Mar 4.

PMID:
25739499
7.

Life-style and genome structure of marine Pseudoalteromonas siphovirus B8b isolated from the northwestern Mediterranean Sea.

Lara E, Holmfeldt K, Solonenko N, Sà EL, Ignacio-Espinoza JC, Cornejo-Castillo FM, Verberkmoes NC, Vaqué D, Sullivan MB, Acinas SG.

PLoS One. 2015 Jan 14;10(1):e0114829. doi: 10.1371/journal.pone.0114829. eCollection 2015.

8.

Proteomic identification of mammalian cell surface derived glycosylphosphatidylinositol-anchored proteins through selective glycan enrichment.

Cortes LK, Vainauskas S, Dai N, McClung CM, Shah M, Benner JS, Corrêa IR Jr, VerBerkmoes NC, Taron CH.

Proteomics. 2014 Nov;14(21-22):2471-84. doi: 10.1002/pmic.201400148.

9.

Colonization state influences the hemocyte proteome in a beneficial squid-Vibrio symbiosis.

Schleicher TR, VerBerkmoes NC, Shah M, Nyholm SV.

Mol Cell Proteomics. 2014 Oct;13(10):2673-86. doi: 10.1074/mcp.M113.037259. Epub 2014 Jul 18.

10.

Discovery of a novel methanogen prevalent in thawing permafrost.

Mondav R, Woodcroft BJ, Kim EH, McCalley CK, Hodgkins SB, Crill PM, Chanton J, Hurst GB, VerBerkmoes NC, Saleska SR, Hugenholtz P, Rich VI, Tyson GW.

Nat Commun. 2014;5:3212. doi: 10.1038/ncomms4212.

PMID:
24526077
11.

Twelve previously unknown phage genera are ubiquitous in global oceans.

Holmfeldt K, Solonenko N, Shah M, Corrier K, Riemann L, Verberkmoes NC, Sullivan MB.

Proc Natl Acad Sci U S A. 2013 Jul 30;110(31):12798-803. doi: 10.1073/pnas.1305956110. Epub 2013 Jul 15.

12.

Metaproteomics reveals abundant transposase expression in mutualistic endosymbionts.

Kleiner M, Young JC, Shah M, VerBerkmoes NC, Dubilier N.

MBio. 2013 Jun 18;4(3):e00223-13. doi: 10.1128/mBio.00223-13.

13.

New group in the Leptospirillum clade: cultivation-independent community genomics, proteomics, and transcriptomics of the new species "Leptospirillum group IV UBA BS".

Goltsman DS, Dasari M, Thomas BC, Shah MB, VerBerkmoes NC, Hettich RL, Banfield JF.

Appl Environ Microbiol. 2013 Sep;79(17):5384-93. doi: 10.1128/AEM.00202-13. Epub 2013 May 3.

14.

The two-faced T cell epitope: examining the host-microbe interface with JanusMatrix.

Moise L, Gutierrez AH, Bailey-Kellogg C, Terry F, Leng Q, Abdel Hady KM, VerBerkmoes NC, Sztein MB, Losikoff PT, Martin WD, Rothman AL, De Groot AS.

Hum Vaccin Immunother. 2013 Jul;9(7):1577-86. doi: 10.4161/hv.24615. Epub 2013 Apr 12.

15.

Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease.

Erickson AR, Cantarel BL, Lamendella R, Darzi Y, Mongodin EF, Pan C, Shah M, Halfvarson J, Tysk C, Henrissat B, Raes J, Verberkmoes NC, Fraser CM, Hettich RL, Jansson JK.

PLoS One. 2012;7(11):e49138. doi: 10.1371/journal.pone.0049138. Epub 2012 Nov 28.

16.

Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community.

Handley KM, VerBerkmoes NC, Steefel CI, Williams KH, Sharon I, Miller CS, Frischkorn KR, Chourey K, Thomas BC, Shah MB, Long PE, Hettich RL, Banfield JF.

ISME J. 2013 Apr;7(4):800-16. doi: 10.1038/ismej.2012.148. Epub 2012 Nov 29.

17.

Coupling a detergent lysis/cleanup methodology with intact protein fractionation for enhanced proteome characterization.

Sharma R, Dill BD, Chourey K, Shah M, VerBerkmoes NC, Hettich RL.

J Proteome Res. 2012 Dec 7;11(12):6008-18. doi: 10.1021/pr300709k. Epub 2012 Nov 19.

PMID:
23126408
18.

Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla.

Wrighton KC, Thomas BC, Sharon I, Miller CS, Castelle CJ, VerBerkmoes NC, Wilkins MJ, Hettich RL, Lipton MS, Williams KH, Long PE, Banfield JF.

Science. 2012 Sep 28;337(6102):1661-5. Erratum in: Science. 2012 Nov 9;338(6108):742.

PMID:
23019650
19.

The temporal analysis of yeast exponential phase using shotgun proteomics as a fermentation monitoring technique.

Huang EL, Orsat V, Shah MB, Hettich RL, VerBerkmoes NC, Lefsrud MG.

J Proteomics. 2012 Sep 18;75(17):5206-14. doi: 10.1016/j.jprot.2012.06.005. Epub 2012 Jun 15.

PMID:
22705714
20.

Phage-induced expression of CRISPR-associated proteins is revealed by shotgun proteomics in Streptococcus thermophilus.

Young JC, Dill BD, Pan C, Hettich RL, Banfield JF, Shah M, Fremaux C, Horvath P, Barrangou R, Verberkmoes NC.

PLoS One. 2012;7(5):e38077. doi: 10.1371/journal.pone.0038077. Epub 2012 May 30.

21.

Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use.

Kleiner M, Wentrup C, Lott C, Teeling H, Wetzel S, Young J, Chang YJ, Shah M, VerBerkmoes NC, Zarzycki J, Fuchs G, Markert S, Hempel K, Voigt B, Becher D, Liebeke M, Lalk M, Albrecht D, Hecker M, Schweder T, Dubilier N.

Proc Natl Acad Sci U S A. 2012 May 8;109(19):E1173-82. doi: 10.1073/pnas.1121198109. Epub 2012 Apr 18.

22.

Shotgun proteomic monitoring of Clostridium acetobutylicum during stationary phase of butanol fermentation using xylose and comparison with the exponential phase.

Sivagnanam K, Raghavan VG, Shah M, Hettich RL, Verberkmoes NC, Lefsrud MG.

J Ind Microbiol Biotechnol. 2012 Jun;39(6):949-55. doi: 10.1007/s10295-012-1094-0. Epub 2012 Mar 7.

PMID:
22395897
23.

Metal affinity enrichment increases the range and depth of proteome identification for extracellular microbial proteins.

Wheeler KE, Erickson BK, Mueller R, Singer SW, Verberkmoes NC, Hwang M, Thelen MP, Hettich RL.

J Proteome Res. 2012 Feb 3;11(2):861-70. doi: 10.1021/pr200693u. Epub 2012 Jan 25.

PMID:
22191549
24.

Global transcriptomic and proteomic responses of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation.

Lee PK, Dill BD, Louie TS, Shah M, Verberkmoes NC, Andersen GL, Zinder SH, Alvarez-Cohen L.

Appl Environ Microbiol. 2012 Mar;78(5):1424-36. doi: 10.1128/AEM.06792-11. Epub 2011 Dec 16.

25.

Strategies for metagenomic-guided whole-community proteomics of complex microbial environments.

Cantarel BL, Erickson AR, VerBerkmoes NC, Erickson BK, Carey PA, Pan C, Shah M, Mongodin EF, Jansson JK, Fraser-Liggett CM, Hettich RL.

PLoS One. 2011;6(11):e27173. doi: 10.1371/journal.pone.0027173. Epub 2011 Nov 23.

26.

Microbes in thawing permafrost: the unknown variable in the climate change equation.

Graham DE, Wallenstein MD, Vishnivetskaya TA, Waldrop MP, Phelps TJ, Pfiffner SM, Onstott TC, Whyte LG, Rivkina EM, Gilichinsky DA, Elias DA, Mackelprang R, VerBerkmoes NC, Hettich RL, Wagner D, Wullschleger SD, Jansson JK.

ISME J. 2012 Apr;6(4):709-12. doi: 10.1038/ismej.2011.163. Epub 2011 Nov 17. No abstract available.

27.

Comparative shotgun proteomic analysis of Clostridium acetobutylicum from butanol fermentation using glucose and xylose.

Sivagnanam K, Raghavan VG, Shah M, Hettich RL, Verberkmoes NC, Lefsrud MG.

Proteome Sci. 2011 Oct 18;9:66. doi: 10.1186/1477-5956-9-66.

28.

Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analyses.

Men Y, Feil H, Verberkmoes NC, Shah MB, Johnson DR, Lee PK, West KA, Zinder SH, Andersen GL, Alvarez-Cohen L.

ISME J. 2012 Feb;6(2):410-21. doi: 10.1038/ismej.2011.111. Epub 2011 Sep 1.

29.

Identification of biofilm matrix-associated proteins from an acid mine drainage microbial community.

Jiao Y, D'haeseleer P, Dill BD, Shah M, Verberkmoes NC, Hettich RL, Banfield JF, Thelen MP.

Appl Environ Microbiol. 2011 Aug;77(15):5230-7. doi: 10.1128/AEM.03005-10. Epub 2011 Jun 17.

30.

Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm community.

Mueller RS, Dill BD, Pan C, Belnap CP, Thomas BC, VerBerkmoes NC, Hettich RL, Banfield JF.

Environ Microbiol. 2011 Aug;13(8):2279-92. doi: 10.1111/j.1462-2920.2011.02486.x. Epub 2011 Apr 25.

PMID:
21518216
31.

Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics.

Gobler CJ, Berry DL, Dyhrman ST, Wilhelm SW, Salamov A, Lobanov AV, Zhang Y, Collier JL, Wurch LL, Kustka AB, Dill BD, Shah M, VerBerkmoes NC, Kuo A, Terry A, Pangilinan J, Lindquist EA, Lucas S, Paulsen IT, Hattenrath-Lehmann TK, Talmage SC, Walker EA, Koch F, Burson AM, Marcoval MA, Tang YZ, Lecleir GR, Coyne KJ, Berg GM, Bertrand EM, Saito MA, Gladyshev VN, Grigoriev IV.

Proc Natl Acad Sci U S A. 2011 Mar 15;108(11):4352-7. doi: 10.1073/pnas.1016106108. Epub 2011 Feb 23.

32.

Environmental proteomics of microbial plankton in a highly productive coastal upwelling system.

Sowell SM, Abraham PE, Shah M, Verberkmoes NC, Smith DP, Barofsky DF, Giovannoni SJ.

ISME J. 2011 May;5(5):856-65. doi: 10.1038/ismej.2010.168. Epub 2010 Nov 11.

33.

Analysis of biostimulated microbial communities from two field experiments reveals temporal and spatial differences in proteome profiles.

Callister SJ, Wilkins MJ, Nicora CD, Williams KH, Banfield JF, VerBerkmoes NC, Hettich RL, N'Guessan L, Mouser PJ, Elifantz H, Smith RD, Lovley DR, Lipton MS, Long PE.

Environ Sci Technol. 2010 Dec 1;44(23):8897-903. doi: 10.1021/es101029f. Epub 2010 Nov 8.

PMID:
21058662
34.

Metabolome-proteome differentiation coupled to microbial divergence.

Wilmes P, Bowen BP, Thomas BC, Mueller RS, Denef VJ, VerBerkmoes NC, Hettich RL, Northen TR, Banfield JF.

MBio. 2010 Oct 26;1(5). pii: e00246-10. doi: 10.1128/mBio.00246-10.

35.

Ecological distribution and population physiology defined by proteomics in a natural microbial community.

Mueller RS, Denef VJ, Kalnejais LH, Suttle KB, Thomas BC, Wilmes P, Smith RL, Nordstrom DK, McCleskey RB, Shah MB, Verberkmoes NC, Hettich RL, Banfield JF.

Mol Syst Biol. 2010 Jun 8;6:374. doi: 10.1038/msb.2010.30.

36.

Posttranslational modification and sequence variation of redox-active proteins correlate with biofilm life cycle in natural microbial communities.

Singer SW, Erickson BK, VerBerkmoes NC, Hwang M, Shah MB, Hettich RL, Banfield JF, Thelen MP.

ISME J. 2010 Nov;4(11):1398-409. doi: 10.1038/ismej.2010.64. Epub 2010 May 20.

PMID:
20485387
37.

Proteomics reveals a core molecular response of Pseudomonas putida F1 to acute chromate challenge.

Thompson DK, Chourey K, Wickham GS, Thieman SB, VerBerkmoes NC, Zhang B, McCarthy AT, Rudisill MA, Shah M, Hettich RL.

BMC Genomics. 2010 May 19;11:311. doi: 10.1186/1471-2164-11-311.

38.

Enigmatic, ultrasmall, uncultivated Archaea.

Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, Land ML, Verberkmoes NC, Hettich RL, Banfield JF.

Proc Natl Acad Sci U S A. 2010 May 11;107(19):8806-11. doi: 10.1073/pnas.0914470107. Epub 2010 Apr 26.

39.

Computational prediction and experimental validation of signal peptide cleavages in the extracellular proteome of a natural microbial community.

Erickson BK, Mueller RS, VerBerkmoes NC, Shah M, Singer SW, Thelen MP, Banfield JF, Hettich RL.

J Proteome Res. 2010 May 7;9(5):2148-59. doi: 10.1021/pr900877a.

PMID:
20218729
40.

A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry.

Pan C, Park BH, McDonald WH, Carey PA, Banfield JF, VerBerkmoes NC, Hettich RL, Samatova NF.

BMC Bioinformatics. 2010 Mar 5;11:118. doi: 10.1186/1471-2105-11-118.

41.

Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities.

Denef VJ, Kalnejais LH, Mueller RS, Wilmes P, Baker BJ, Thomas BC, VerBerkmoes NC, Hettich RL, Banfield JF.

Proc Natl Acad Sci U S A. 2010 Feb 9;107(6):2383-90. doi: 10.1073/pnas.0907041107. Epub 2010 Feb 2.

42.

Cultivation and quantitative proteomic analyses of acidophilic microbial communities.

Belnap CP, Pan C, VerBerkmoes NC, Power ME, Samatova NF, Carver RL, Hettich RL, Banfield JF.

ISME J. 2010 Apr;4(4):520-30. doi: 10.1038/ismej.2009.139. Epub 2009 Dec 24.

PMID:
20033068
43.

Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation.

Wilkins MJ, Verberkmoes NC, Williams KH, Callister SJ, Mouser PJ, Elifantz H, N'guessan AL, Thomas BC, Nicora CD, Shah MB, Abraham P, Lipton MS, Lovley DR, Hettich RL, Long PE, Banfield JF.

Appl Environ Microbiol. 2009 Oct;75(20):6591-9. doi: 10.1128/AEM.01064-09. Epub 2009 Aug 28.

44.

Impact of phenolic substrate and growth temperature on the Arthrobacter chlorophenolicus proteome.

Unell M, Abraham PE, Shah M, Zhang B, Rückert C, VerBerkmoes NC, Jansson JK.

J Proteome Res. 2009 Apr;8(4):1953-64. doi: 10.1021/pr800897c.

PMID:
19714879
45.

Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) bacteria in acid mine drainage biofilms.

Goltsman DS, Denef VJ, Singer SW, VerBerkmoes NC, Lefsrud M, Mueller RS, Dick GJ, Sun CL, Wheeler KE, Zemla A, Baker BJ, Hauser L, Land M, Shah MB, Thelen MP, Hettich RL, Banfield JF.

Appl Environ Microbiol. 2009 Jul;75(13):4599-615. doi: 10.1128/AEM.02943-08. Epub 2009 May 8.

46.

Differential accumulation of form I RubisCO in Rhodopseudomonas palustris CGA010 under Photoheterotrophic growth conditions with reduced carbon sources.

Joshi GS, Romagnoli S, Verberkmoes NC, Hettich RL, Pelletier D, Tabita FR.

J Bacteriol. 2009 Jul;191(13):4243-50. doi: 10.1128/JB.01795-08. Epub 2009 Apr 17.

47.

Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla.

Mahowald MA, Rey FE, Seedorf H, Turnbaugh PJ, Fulton RS, Wollam A, Shah N, Wang C, Magrini V, Wilson RK, Cantarel BL, Coutinho PM, Henrissat B, Crock LW, Russell A, Verberkmoes NC, Hettich RL, Gordon JI.

Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5859-64. doi: 10.1073/pnas.0901529106. Epub 2009 Mar 24.

48.

Systems biology: Functional analysis of natural microbial consortia using community proteomics.

VerBerkmoes NC, Denef VJ, Hettich RL, Banfield JF.

Nat Rev Microbiol. 2009 Mar;7(3):196-205. doi: 10.1038/nrmicro2080. Review.

PMID:
19219053
49.

Comparative temporal proteomics of a response regulator (SO2426)-deficient strain and wild-type Shewanella oneidensis MR-1 during chromate transformation.

Chourey K, Thompson MR, Shah M, Zhang B, Verberkmoes NC, Thompson DK, Hettich RL.

J Proteome Res. 2009 Jan;8(1):59-71. doi: 10.1021/pr800776d.

PMID:
19118451
50.

Experimental approach for deep proteome measurements from small-scale microbial biomass samples.

Thompson MR, Chourey K, Froelich JM, Erickson BK, VerBerkmoes NC, Hettich RL.

Anal Chem. 2008 Dec 15;80(24):9517-25. doi: 10.1021/ac801707s.

PMID:
19072265

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