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List of works by Nathan C. Verberkmoes

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

scientific article

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

scientific article published in September 2004

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

scholarly article

Community proteomics of a natural microbial biofilm

scientific article published on 5 May 2005

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

scientific article

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

scientific article (publication date: 18 October 2011)

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

scientific article published in January 2009

Cultivation and quantitative proteomic analyses of acidophilic microbial communities

scientific article

Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community

scientific article published on 28 February 2008

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

scientific article published on 17 April 2009

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

scientific article

Enigmatic, ultrasmall, uncultivated Archaea.

scientific article

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

scientific article published on November 11, 2010

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

scientific article

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

scientific article

Global molecular and morphological effects of 24-hour chromium(VI) exposure on Shewanella oneidensis MR-1.

scientific article

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

scientific article published on 16 December 2011

Heterotrophic archaea contribute to carbon cycling in low-pH, suboxic biofilm communities

scientific article

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

scientific article

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

scientific article published on 28 June 2007

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

scientific article

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

scientific article

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

scientific article published in December 2005

Mass spectrometric approaches for characterizing bacterial proteomes.

scientific article

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

scientific article published on 25 January 2012

Molecular dynamics of the Shewanella oneidensis response to chromate stress

scientific article published on 8 March 2006

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

scientific article (publication date: 2012)

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

scientific article published in October 2006

Proteogenomic approaches for the molecular characterization of natural microbial communities

scientific article

Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation

scientific article published on 28 August 2009

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

scientific article published on 25 April 2011

Proteomic analysis of Clostridium acetobutylicum in butanol production from lignocellulosic biomass

scientific article published on 13 September 2011

Shotgun metaproteomics of the human distal gut microbiota

article

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

scientific article published on 07 March 2012

Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria.

scientific article published on 7 March 2007

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

scientific article

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

scientific article published on September 2011

The probability distribution for a random match between an experimental-theoretical spectral pair in tandem mass spectrometry

scientific article published on 01 April 2005

Transcriptomic and proteomic characterization of the Fur modulon in the metal-reducing bacterium Shewanella oneidensis

scientific article

Twelve previously unknown phage genera are ubiquitous in global oceans

scientific article

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