Nathan C Verberkmoes

Nathan C Verberkmoes

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Nathan C Verberkmoes

Nathan C Verberkmoes

Publications by authors named "Nathan C Verberkmoes"

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

Front Microbiol 2017 6;8:1241. Epub 2017 Jul 6.

Department of Microbiology, The Ohio State University, ColumbusOH, United States.

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http://dx.doi.org/10.3389/fmicb.2017.01241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5498523PMC
July 2017

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

Proc Natl Acad Sci U S A 2016 Mar 16;113(9):2436-41. Epub 2016 Feb 16.

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721; Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721; Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ 85721;

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http://dx.doi.org/10.1073/pnas.1525139113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4780635PMC
March 2016

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

Environ Sci Technol 2015 Nov 4;49(22):13283-93. Epub 2015 Nov 4.

Department of Chemistry, The University of Texas at El Paso , 500 West University Ave., El Paso, Texas 79968, United States.

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http://dx.doi.org/10.1021/acs.est.5b03452DOI Listing
November 2015

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

BMC Genomics 2015 Nov 11;16:920. Epub 2015 Nov 11.

Genome Biology Division, New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA.

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http://dx.doi.org/10.1186/s12864-015-2083-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4642636PMC
November 2015

Discovery of a novel methanogen prevalent in thawing permafrost.

Nat Commun 2014 ;5:3212

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Queensland, Australia.

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http://dx.doi.org/10.1038/ncomms4212DOI Listing
October 2015

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

Nature 2015 May 4;521(7551):208-12. Epub 2015 Mar 4.

1] Earth Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California, 94720, USA [2] US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA [3] Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, Berkeley, California 94720, USA [4] Center for Permafrost Research (CENPERM), Department of Biology, Universitetsparken 15, University of Copenhagen, Copenhagen, DK-2100 Copenhagen, Denmark.

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http://dx.doi.org/10.1038/nature14238DOI Listing
May 2015

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

Mol Cell Proteomics 2014 Oct 18;13(10):2673-86. Epub 2014 Jul 18.

From the ‡Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, 06269;

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http://dx.doi.org/10.1074/mcp.M113.037259DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4188995PMC
October 2014

Twelve previously unknown phage genera are ubiquitous in global oceans.

Proc Natl Acad Sci U S A 2013 Jul 15;110(31):12798-803. Epub 2013 Jul 15.

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.

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http://dx.doi.org/10.1073/pnas.1305956110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3732932PMC
July 2013

Metaproteomics reveals abundant transposase expression in mutualistic endosymbionts.

mBio 2013 Jun 18;4(3):e00223-13. Epub 2013 Jun 18.

Symbiosis Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.

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http://dx.doi.org/10.1128/mBio.00223-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3684830PMC
June 2013

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

J Proteome Res 2012 Dec 19;11(12):6008-18. Epub 2012 Nov 19.

UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville-Tennessee 37996, United States.

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http://pubs.acs.org/doi/10.1021/pr300709k
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http://dx.doi.org/10.1021/pr300709kDOI Listing
December 2012

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

J Proteomics 2012 Sep 15;75(17):5206-14. Epub 2012 Jun 15.

Bioresource Engineering, McGill University, Ste.-Anne-de-Bellevue, Quebec, Canada H9X 3V9.

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http://linkinghub.elsevier.com/retrieve/pii/S187439191200430
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http://dx.doi.org/10.1016/j.jprot.2012.06.005DOI Listing
September 2012

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

J Ind Microbiol Biotechnol 2012 Jun 7;39(6):949-55. Epub 2012 Mar 7.

Department of Bioresource Engineering, Macdonald Campus, McGill University, Montreal, QC, Canada.

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http://dx.doi.org/10.1007/s10295-012-1094-0DOI Listing
June 2012

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

J Proteome Res 2012 Feb 25;11(2):861-70. Epub 2012 Jan 25.

Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory , Livermore, California, United States.

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http://dx.doi.org/10.1021/pr200693uDOI Listing
February 2012

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

Proteome Sci 2011 Oct 18;9:66. Epub 2011 Oct 18.

Department of Bioresource Engineering, Macdonald Campus, McGill University, Quebec, Canada.

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http://dx.doi.org/10.1186/1477-5956-9-66DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3212805PMC
October 2011

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

ISME J 2011 May 11;5(5):856-65. Epub 2010 Nov 11.

Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA.

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http://dx.doi.org/10.1038/ismej.2010.168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105774PMC
May 2011

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

ISME J 2010 Nov 20;4(11):1398-409. Epub 2010 May 20.

Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.

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http://dx.doi.org/10.1038/ismej.2010.64DOI Listing
November 2010

Metabolome-proteome differentiation coupled to microbial divergence.

mBio 2010 Oct 26;1(5). Epub 2010 Oct 26.

Department of Earth and Planetary Science, University of California, Berkeley, California, USA.

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http://dx.doi.org/10.1128/mBio.00246-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2962434PMC
October 2010

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

J Proteome Res 2010 May;9(5):2148-59

Graduate School of Genome Science & Technology, University of Tennessee, Knoxville, Tennessee 37830, USA.

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http://dx.doi.org/10.1021/pr900877aDOI Listing
May 2010

Enigmatic, ultrasmall, uncultivated Archaea.

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

Department of Earth and Planetary Science and Environmental Science, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1073/pnas.0914470107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889320PMC
May 2010

Cultivation and quantitative proteomic analyses of acidophilic microbial communities.

ISME J 2010 Apr 24;4(4):520-30. Epub 2009 Dec 24.

Microbiology Graduate Group, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1038/ismej.2009.139DOI Listing
April 2010

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

J Proteome Res 2009 Apr;8(4):1953-64

Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, 750 07 Uppsala, Sweden.

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http://dx.doi.org/10.1021/pr800897cDOI Listing
April 2009

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

Nat Rev Microbiol 2009 Mar;7(3):196-205

Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.

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http://dx.doi.org/10.1038/nrmicro2080DOI Listing
March 2009

Shotgun metaproteomics of the human distal gut microbiota.

ISME J 2009 Feb 30;3(2):179-89. Epub 2008 Oct 30.

Oak Ridge National Laboratory, Chemical and Life Sciences Divisions, Oak Ridge, TN, USA.

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http://dx.doi.org/10.1038/ismej.2008.108DOI Listing
February 2009

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

Anal Chem 2008 Dec;80(24):9517-25

Graduate School of Genome Science and Technology, Oak Ridge National Laboratory-University of Tennessee, Knoxville, Tennessee 37830, USA.

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http://dx.doi.org/10.1021/ac801707sDOI Listing
December 2008

Implications of strain- and species-level sequence divergence for community and isolate shotgun proteomic analysis.

J Proteome Res 2007 Aug 28;6(8):3152-61. Epub 2007 Jun 28.

Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA.

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http://pubs.acs.org/doi/abs/10.1021/pr0701005
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http://dx.doi.org/10.1021/pr0701005DOI Listing
August 2007

Dosage-dependent proteome response of Shewanella oneidensis MR-1 to acute chromate challenge.

J Proteome Res 2007 May 27;6(5):1745-57. Epub 2007 Mar 27.

Graduate School of Genome Science and Technology, Oak Ridge National Laboratory-University of Tennessee-Knoxville, Tennessee 37830, USA.

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http://dx.doi.org/10.1021/pr060502xDOI Listing
May 2007

Detecting differential and correlated protein expression in label-free shotgun proteomics.

J Proteome Res 2006 Nov;5(11):2909-18

Computer Science and Mathematics Division, Computational Biology Institute, Chemical Science Division, and Life Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA.

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http://dx.doi.org/10.1021/pr0600273DOI Listing
November 2006

Expressed peptide tags: an additional layer of data for genome annotation.

J Proteome Res 2006 Nov;5(11):3048-58

Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA.

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http://dx.doi.org/10.1021/pr060134xDOI Listing
November 2006

ProRata: A quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluation.

Anal Chem 2006 Oct;78(20):7121-31

Chemical Sciences Division, Computational Biology Institute, Genome Science and Technology Graduate School, Oak Ridge National Laboratory-University of Tennessee, Oak Ridge, Tennessee 37830, USA.

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http://dx.doi.org/10.1021/ac060654bDOI Listing
October 2006

Molecular dynamics of the Shewanella oneidensis response to chromate stress.

Mol Cell Proteomics 2006 Jun 8;5(6):1054-71. Epub 2006 Mar 8.

Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA.

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http://www.mcponline.org/lookup/doi/10.1074/mcp.M500394-MCP2
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http://dx.doi.org/10.1074/mcp.M500394-MCP200DOI Listing
June 2006

Proteogenomic approaches for the molecular characterization of natural microbial communities.

OMICS 2005 ;9(4):301-33

Department of Earth and Planetary Science, and Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA.

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http://www.liebertpub.com/doi/10.1089/omi.2005.9.301
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http://dx.doi.org/10.1089/omi.2005.9.301DOI Listing
March 2006

MASPIC: intensity-based tandem mass spectrometry scoring scheme that improves peptide identification at high confidence.

Anal Chem 2005 Dec;77(23):7581-93

Graduate School of Genome Science and Technology, University of Tennessee--Oak Ridge National Laboratory, 37830-8026, USA.

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http://dx.doi.org/10.1021/ac0501745DOI Listing
December 2005

MS2Grouper: group assessment and synthetic replacement of duplicate proteomic tandem mass spectra.

J Am Soc Mass Spectrom 2005 Aug;16(8):1250-61

Life Sciences Division, Oak Ridge Laboratory, Oak Ridge, Tennessee 37831, USA.

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http://dx.doi.org/10.1016/j.jasms.2005.04.010DOI Listing
August 2005

Community proteomics of a natural microbial biofilm.

Science 2005 Jun 5;308(5730):1915-20. Epub 2005 May 5.

Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1126/science. 1109070DOI Listing
June 2005

Characterization of the 70S Ribosome from Rhodopseudomonas palustris using an integrated "top-down" and "bottom-up" mass spectrometric approach.

J Proteome Res 2004 Sep-Oct;3(5):965-78

Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6131, USA.

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http://dx.doi.org/10.1021/pr049940zDOI Listing
March 2005

Evaluation of "shotgun" proteomics for identification of biological threat agents in complex environmental matrixes: experimental simulations.

Anal Chem 2005 Feb;77(3):923-32

Graduate School of Genome Science and Technology, University of Tennessee--Oak Ridge National Laboratory, 1060 Commerce Park, Oak Ridge, TN 37830-8026, USA.

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http://dx.doi.org/10.1021/ac049127nDOI Listing
February 2005

Mass spectrometric approaches for characterizing bacterial proteomes.

Expert Rev Proteomics 2004 Dec;1(4):433-47

Genome Science & Technology Graduate School, University of Tennessee, Knoxville, TN 37996, USA.

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http://dx.doi.org/10.1586/14789450.1.4.433DOI Listing
December 2004

Synthesis and biophysical characterization of a multidomain peptide from a Saccharomyces cerevisiae G protein-coupled receptor.

J Biol Chem 2003 Dec 21;278(52):52537-45. Epub 2003 Oct 21.

Department of Chemistry, College of Staten Island and Institute for Macromolecular Assemblies, City University of New York, Staten Island, New York 10314, USA.

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http://dx.doi.org/10.1074/jbc.M309467200DOI Listing
December 2003

Integrating 'top-down" and "bottom-up" mass spectrometric approaches for proteomic analysis of Shewanella oneidensis.

J Proteome Res 2002 May-Jun;1(3):239-52

Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6365, USA.

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http://dx.doi.org/10.1021/pr025508aDOI Listing
April 2003

Intact protein analysis for site-directed mutagenesis overexpression products: plasmid-encoded R67 dihydrofolate reductase.

Anal Biochem 2002 Jun;305(1):68-81

Organic and Biological Mass Spectrometry Group, Oak Ridge National Laboratory, Building 5510, Oak Ridge, TN 37831-6365, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S000326970295636
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http://dx.doi.org/10.1006/abio.2002.5636DOI Listing
June 2002

The chain length dependence of helix formation of the second transmembrane domain of a G protein-coupled receptor of Saccharomyces cerevisiae.

J Biol Chem 2002 Apr 19;277(17):14483-92. Epub 2002 Feb 19.

Department of Chemistry, The College of Staten Island of the City University of New York, Staten Island, New York 10314, USA.

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http://dx.doi.org/10.1074/jbc.M111382200DOI Listing
April 2002