Research Topics
| Nathan C VerberkmoesSummaryAffiliation: Oak Ridge National Laboratory Country: USA Publications
| Collaborators
|
Detail Information
Publications
Systems biology: Functional analysis of natural microbial consortia using community proteomicsNathan C Verberkmoes
Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
Nat Rev Microbiol 7:196-205. 2009..We discuss the first applications of proteogenomics and its potential for studying the physiology, ecology and evolution of microbial populations and communities...
Determination and comparison of the baseline proteomes of the versatile microbe Rhodopseudomonas palustris under its major metabolic statesNathan C Verberkmoes
Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
J Proteome Res 5:287-98. 2006..Proteins known to be associated with specialized growth states such as nitrogen fixation, photoautotrophic, or growth on benzoate, were observed to be up-regulated under those states...- Comparative temporal proteomics of a response regulator (SO2426)-deficient strain and wild-type Shewanella oneidensis MR-1 during chromate transformationKaruna Chourey
Environmental Sciences Division, Oak Ridge National Laboratory, Tennessee 37831, USA
J Proteome Res 8:59-71. 2009..In addition, the proteome data sets were mined for amino acids with potential post-translational modifications (PTMs) indicative of a level of gene expression regulation extending beyond the transcriptional control imposed by SO2426... - Characterization of the 70S Ribosome from Rhodopseudomonas palustris using an integrated "top-down" and "bottom-up" mass spectrometric approachMichael Brad Strader
Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6131, USA
J Proteome Res 3:965-78. 2004..To our knowledge, this is the most comprehensive protein complex analysis to date that integrates two MS techniques... 
Global molecular and morphological effects of 24-hour chromium(VI) exposure on Shewanella oneidensis MR-1Karuna Chourey
Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
Appl Environ Microbiol 72:6331-44. 2006....- ProRata: A quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluationChongle Pan
Chemical Sciences Division, Computational Biology Institute, Genome Science and Technology Graduate School, Oak Ridge National Laboratory-University of Tennessee, Oak Ridge, Tennessee 37830, USA
Anal Chem 78:7121-31. 2006..The profile likelihood algorithm was integrated into a quantitative proteomics program, called ProRata, freely available at www.MSProRata.org... - A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometryChongle Pan
Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
BMC Bioinformatics 11:118. 2010..The improved spectral quality enables more accurate de novo sequencing for identification of post-translational modifications and amino acid polymorphisms... - Molecular dynamics of the Shewanella oneidensis response to chromate stressSteven D Brown
Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
Mol Cell Proteomics 5:1054-71. 2006.... - Expressed peptide tags: an additional layer of data for genome annotationAlon Savidor
Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
J Proteome Res 5:3048-58. 2006..7% and 12.9% for P. ramorum and P. sojae, respectively) suggested modification to current gene calls or identified novel genes that were missed by the current genome annotation of these organisms... - MS2Grouper: group assessment and synthetic replacement of duplicate proteomic tandem mass spectraDavid L Tabb
Life Sciences Division, Oak Ridge Laboratory, Oak Ridge, Tennessee 37831, USA
J Am Soc Mass Spectrom 16:1250-61. 2005..This strategy is shown to be effective in reducing spectral counts by up to 20% in LC-MS/MS datasets from protein standard mixtures and proteomes, reducing database search times without a concomitant reduction in identified peptides... - Detecting differential and correlated protein expression in label-free shotgun proteomicsBing Zhang
Computer Science and Mathematics Division, Computational Biology Institute, Chemical Science Division, and Life Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
J Proteome Res 5:2909-18. 2006.... - Transcriptomic and proteomic characterization of the Fur modulon in the metal-reducing bacterium Shewanella oneidensisXiu Feng Wan
Environmental Sciences Division, Oak Ridge National Laboratory, P O Box 2008, Oak Ridge, TN 37831 6038, USA
J Bacteriol 186:8385-400. 2004.... - Integrating 'top-down" and "bottom-up" mass spectrometric approaches for proteomic analysis of Shewanella oneidensisNathan C Verberkmoes
Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6365, USA
J Proteome Res 1:239-52. 2002..A total of 868 proteins from virtually every functional class, including hypotheticals, were identified from this organism... - Shotgun metaproteomics of the human distal gut microbiotaNathan C Verberkmoes
Oak Ridge National Laboratory, Chemical and Life Sciences Divisions, Oak Ridge, TN, USA
ISME J 3:179-89. 2009..Several unknown proteins represented previously undescribed microbial pathways or host immune responses, revealing a novel complex interplay between the human host and its associated microbes... - Evaluation of "shotgun" proteomics for identification of biological threat agents in complex environmental matrixes: experimental simulationsNathan C Verberkmoes
Graduate School of Genome Science and Technology, University of Tennessee--Oak Ridge National Laboratory, 1060 Commerce Park, Oak Ridge, TN 37830-8026, USA
Anal Chem 77:923-32. 2005..This study points to the potential application of this technology for biological threat agent detection but highlights many areas of needed research before the technology will be useful in real world samples... - MASPIC: intensity-based tandem mass spectrometry scoring scheme that improves peptide identification at high confidenceChandrasegaran Narasimhan
Graduate School of Genome Science and Technology, University of Tennessee Oak Ridge National Laboratory, 37830 8026, USA
Anal Chem 77:7581-93. 2005..All these investigations show MASPIC to be a versatile and reliable system for peptide tandem mass spectral identification... - Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's diseaseAlison R Erickson
Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
PLoS ONE 7:e49138. 2012.... - Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm communityRyan S Mueller
University of California, Berkeley, California 94720, USA
Environ Microbiol 13:2279-92. 2011..These findings provide unprecedented insight into the physiological changes that may result from competitive interactions within communities in natural environments... - A computational method for assessing peptide- identification reliability in tandem mass spectrometry analysis with SEQUESTJane Razumovskaya
Life Sciences Division, Oak Ridge National Laboratory, TN, USA
Proteomics 4:961-9. 2004..This method improves the sensitivity and specificity of peptide identification compared to the standard filtering procedure used in the SEQUEST package, and provides a basis for estimating the reliability of protein identifications... - Intact protein analysis for site-directed mutagenesis overexpression products: plasmid-encoded R67 dihydrofolate reductaseNathan C Verberkmoes
Organic and Biological Mass Spectrometry Group, Oak Ridge National Laboratory, Building 5510, Oak Ridge, TN 37831-6365, USA
Anal Biochem 305:68-81. 2002..The ion/ion reaction approach achieved the same results as the proteolytic-digestion-based methodology in a much shorter analysis time... - Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removalPaul Wilmes
Department of Earth and Planetary Sciences, University of California at Berkeley, Berkeley, CA 94720, USA
ISME J 2:853-64. 2008.... - Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteriaIan Lo
University of California, Berkeley, California 94720, USA
Nature 446:537-41. 2007.... - Mass spectrometric approaches for characterizing bacterial proteomesNathan C Verberkmoes
Genome Science and Technology Graduate School, University of Tennessee, Knoxville, TN 37996, USA
Expert Rev Proteomics 1:433-47. 2004..This level of global protein information about an organism such as a bacterium can be combined with genomic and metabolomic data to enable a systems biology approach for understanding how these organisms live and function... - Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial communityChris Jeans
Chemistry Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
ISME J 2:542-50. 2008..Due to its abundance, cellular location and Fe(2+) oxidation activity at very low pH, we propose that Cyt(572) provides a critical function for fitness within the ecological niche of these acidophilic microbial communities... - Implications of strain- and species-level sequence divergence for community and isolate shotgun proteomic analysisVincent J Denef
Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
J Proteome Res 6:3152-61. 2007..4% reduction of the initial protein coverage per 1% amino acid divergence and total identification loss at 86% AAI. Consequently, shotgun proteomics is capable of cross-strain identifications but avoids most cross-species false positives... - Community proteomics of a natural microbial biofilmRachna J Ram
Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, CA 94720, USA
Science 308:1915-20. 2005..We validated and estimated the relative abundance and cellular localization of 357 unique and 215 conserved novel proteins and determined that one abundant novel protein is a cytochrome central to iron oxidation and AMD formation... - Dosage-dependent proteome response of Shewanella oneidensis MR-1 to acute chromate challengeMelissa R Thompson
Graduate School of Genome Science and Technology, Oak Ridge National Laboratory University of Tennessee Knoxville, Tennessee 37830, USA
J Proteome Res 6:1745-57. 2007..The results presented in this work demonstrate the dynamic dosage response of S. oneidensis to sub-toxic levels of chromate... - Synthesis and biophysical characterization of a multidomain peptide from a Saccharomyces cerevisiae G protein-coupled receptorFred Naider
Department of Chemistry, College of Staten Island and Institute for Macromolecular Assemblies, City University of New York, Staten Island, New York 10314, USA
J Biol Chem 278:52537-45. 2003..This study demonstrated that the tail of Ste2p can be used as a hydrophilic template to study transmembrane domain structure using techniques such as CD and NMR spectroscopy...