Published in Mar Drugs on July 29, 2010
Comparative proteogenomics of twelve Roseobacter exoproteomes reveals different adaptive strategies among these marine bacteria. Mol Cell Proteomics (2011) 1.11
Restricting fermentative potential by proteome remodeling: an adaptive strategy evidenced in Bacillus cereus. Mol Cell Proteomics (2012) 1.08
Proteomic insights into the lifestyle of an environmentally relevant marine bacterium. ISME J (2011) 1.03
High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade. BMC Genomics (2012) 0.98
Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes. ISME J (2015) 0.91
Exploring the functional soil-microbe interface and exoenzymes through soil metaexoproteomics. ISME J (2014) 0.85
Functional distinctness in the exoproteomes of marine Synechococcus. Environ Microbiol (2015) 0.82
The Aeromonas salmonicida subsp. salmonicida exoproteome: global analysis, moonlighting proteins and putative antigens for vaccination against furunculosis. Proteome Sci (2013) 0.81
"You produce while I clean up", a strategy revealed by exoproteomics during Synechococcus-Roseobacter interactions. Proteomics (2015) 0.81
Salt Stress Induced Changes in the Exoproteome of the Halotolerant Bacterium Tistlia consotensis Deciphered by Proteogenomics. PLoS One (2015) 0.80
Cytoplasmic and periplasmic proteomic signatures of exponentially growing cells of the psychrophilic bacterium Pseudoalteromonas haloplanktis TAC125. Appl Environ Microbiol (2010) 0.80
Comparative genomic, proteomic and exoproteomic analyses of three Pseudomonas strains reveals novel insights into the phosphorus scavenging capabilities of soil bacteria. Environ Microbiol (2016) 0.78
Assessing the exoproteome of marine bacteria, lesson from a RTX-toxin abundantly secreted by Phaeobacter strain DSM 17395. PLoS One (2014) 0.78
The Exposed Proteomes of Brachyspira hyodysenteriae and B. pilosicoli. Front Microbiol (2016) 0.75
GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes. Mol Cell Proteomics (2016) 0.75
Exoproteome Analysis of the Seaweed Pathogen Nautella italica R11 Reveals Temperature-Dependent Regulation of RTX-Like Proteins. Front Microbiol (2017) 0.75
Improved prediction of signal peptides: SignalP 3.0. J Mol Biol (2004) 48.40
Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc (2007) 19.50
A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem (2004) 19.20
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol (2007) 13.99
Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature (2004) 5.00
A proteomic view on genome-based signal peptide predictions. Genome Res (2001) 3.96
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The genomic basis of trophic strategy in marine bacteria. Proc Natl Acad Sci U S A (2009) 3.72
InBase: the Intein Database. Nucleic Acids Res (2002) 3.51
An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J Proteome Res (2008) 3.36
N-terminal processing: the methionine aminopeptidase and N alpha-acetyl transferase families. Trends Biochem Sci (1998) 3.14
Environmental biology of the marine Roseobacter lineage. Annu Rev Microbiol (2006) 3.05
A comprehensive assessment of N-terminal signal peptides prediction methods. BMC Bioinformatics (2009) 2.85
Ecological genomics of marine Roseobacters. Appl Environ Microbiol (2007) 2.68
The proteomics of N-terminal methionine cleavage. Mol Cell Proteomics (2006) 2.55
Diversity, ecology, and genomics of the Roseobacter clade: a short overview. Arch Microbiol (2008) 2.45
Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence. Curr Biol (2009) 2.35
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Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue. Trends Microbiol (2009) 2.14
Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments. Int J Syst Evol Microbiol (2003) 1.85
Does trypsin cut before proline? J Proteome Res (2007) 1.79
Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea. Genome Biol (2009) 1.69
Inteins: structure, function, and evolution. Annu Rev Microbiol (2002) 1.67
LocateP: genome-scale subcellular-location predictor for bacterial proteins. BMC Bioinformatics (2008) 1.64
Detection of secreted peptides by using hypothesis-driven multistage mass spectrometry. Proc Natl Acad Sci U S A (2003) 1.63
A toolbox for validation of mass spectrometry peptides identification and generation of database: IRMa. Bioinformatics (2009) 1.59
Environmental proteomics: a paradigm shift in characterizing microbial activities at the molecular level. Microbiol Mol Biol Rev (2009) 1.53
Protein secretion and membrane insertion systems in gram-negative bacteria. J Membr Biol (2007) 1.51
Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti. PLoS Genet (2009) 1.50
New knowledge from old: in silico discovery of novel protein domains in Streptomyces coelicolor. BMC Microbiol (2003) 1.33
Expanding the known repertoire of virulence factors produced by Bacillus cereus through early secretome profiling in three redox conditions. Mol Cell Proteomics (2010) 1.31
Control of protein life-span by N-terminal methionine excision. EMBO J (2003) 1.27
High abundance of virulence gene homologues in marine bacteria. Environ Microbiol (2009) 1.27
Proteomics-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons. Mol Cell Proteomics (2009) 1.24
The secretome of the plant pathogenic bacterium Erwinia chrysanthemi. Proteomics (2004) 1.22
Identification and characterization of a repeat-in-toxin gene cluster in Vibrio anguillarum. Infect Immun (2008) 1.22
A comparative study of Bacillus cereus, Bacillus thuringiensis and Bacillus anthracis extracellular proteomes. Proteomics (2005) 1.20
Transcriptional response of Silicibacter pomeroyi DSS-3 to dimethylsulfoniopropionate (DMSP). Environ Microbiol (2007) 1.17
A perfect genome annotation is within reach with the proteomics and genomics alliance. Curr Opin Microbiol (2009) 1.16
Profiling the secretomes of plant pathogenic Proteobacteria. FEMS Microbiol Rev (2005) 1.12
Comparative proteomic analysis of Botrytis cinerea secretome. J Proteome Res (2009) 1.04
Environmental proteomics: analysis of structure and function of microbial communities. Proteomics (2010) 1.03
Proteogenomics and systems biology: quest for the ultimate missing parts. Expert Rev Proteomics (2010) 0.99
Taxonomic evaluation of the genera Ruegeria and Silicibacter: a proposal to transfer the genus Silicibacter Petursdottir and Kristjansson 1999 to the genus Ruegeria Uchino et al. 1999. Int J Syst Evol Microbiol (2007) 0.93
Profiling the secretome of the marine bacterium Pseudoalteromonas tunicata using amine-specific isobaric tagging (iTRAQ). J Proteome Res (2007) 0.91
Evaluation of signal peptide prediction algorithms for identification of mycobacterial signal peptides using sequence data from proteomic methods. Microbiology (2009) 0.89
Crystal structure of a novel polyisoprenoid-binding protein from Thermus thermophilus HB8. Protein Sci (2005) 0.87
Proteomic analysis of the secretome of human umbilical vein endothelial cells using a combination of free-flow electrophoresis and nanoflow LC-MS/MS. Proteomics (2009) 0.87
Genetic or chemical protease inhibition causes significant changes in the Bacillus subtilis exoproteome. Proteomics (2008) 0.86
Insight into the core and variant exoproteomes of Listeria monocytogenes species by comparative subproteomic analysis. Proteomics (2009) 0.86
Identification and characterization of hemolysin-like proteins similar to RTX toxin in Pasteurella pneumotropica. J Bacteriol (2009) 0.85
Computational prediction and experimental validation of signal peptide cleavages in the extracellular proteome of a natural microbial community. J Proteome Res (2010) 0.85
Characterization of PaxA and its operon: a cohemolytic RTX toxin determinant from pathogenic Pasteurella aerogenes. Infect Immun (2000) 0.81
Marine molecular biology: an emerging field of biological sciences. Biotechnol Adv (2008) 0.80
Application of proteomics in biotechnology--microbial proteomics. Biotechnol J (2008) 0.79
Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea. Genome Biol (2009) 1.69
Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti. PLoS Genet (2009) 1.50
A role for GPN-loop GTPase yGPN1 in sister chromatid cohesion. Cell Cycle (2011) 1.41
Expanding the known repertoire of virulence factors produced by Bacillus cereus through early secretome profiling in three redox conditions. Mol Cell Proteomics (2010) 1.31
Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea. Mol Biol Evol (2010) 1.28
Proteomics-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons. Mol Cell Proteomics (2009) 1.24
Comparative proteogenomics of twelve Roseobacter exoproteomes reveals different adaptive strategies among these marine bacteria. Mol Cell Proteomics (2011) 1.11
Restricting fermentative potential by proteome remodeling: an adaptive strategy evidenced in Bacillus cereus. Mol Cell Proteomics (2012) 1.08
Taking the shortcut for high-throughput shotgun proteomic analysis of bacteria. Methods Mol Biol (2014) 1.06
THUMP from archaeal tRNA:m22G10 methyltransferase, a genuine autonomously folding domain. Nucleic Acids Res (2006) 1.04
Proteomic insights into the lifestyle of an environmentally relevant marine bacterium. ISME J (2011) 1.03
Revisiting iodination sites in thyroglobulin with an organ-oriented shotgun strategy. J Biol Chem (2010) 1.00
N-terminomics and proteogenomics, getting off to a good start. Proteomics (2014) 0.99
High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade. BMC Genomics (2012) 0.98
Structural insights into a new homodimeric self-activated GTPase family. EMBO Rep (2007) 0.97
4-Demethylwyosine synthase from Pyrococcus abyssi is a radical-S-adenosyl-L-methionine enzyme with an additional [4Fe-4S](+2) cluster that interacts with the pyruvate co-substrate. J Biol Chem (2012) 0.96
ApoFnr binds as a monomer to promoters regulating the expression of enterotoxin genes of Bacillus cereus. J Bacteriol (2008) 0.96
ResDE-dependent regulation of enterotoxin gene expression in Bacillus cereus: evidence for multiple modes of binding for ResD and interaction with Fnr. J Bacteriol (2009) 0.95
Structure of a [2Fe-2S] ferredoxin from Rhodobacter capsulatus likely involved in Fe-S cluster biogenesis and conformational changes observed upon reduction. J Biol Inorg Chem (2006) 0.94
Identity elements required for enzymatic formation of N2,N2-dimethylguanosine from N2-monomethylated derivative and its possible role in avoiding alternative conformations in archaeal tRNA. J Mol Biol (2006) 0.94
Ribosomal proteins as biomarkers for bacterial identification by mass spectrometry in the clinical microbiology laboratory. J Microbiol Methods (2013) 0.90
Shotgun proteomics suggests involvement of additional enzymes in dioxin degradation by Sphingomonas wittichii RW1. Environ Microbiol (2013) 0.90
The Deinococcus radiodurans DR1245 protein, a DdrB partner homologous to YbjN proteins and reminiscent of type III secretion system chaperones. PLoS One (2013) 0.89
Assessment of solvent residues accessibility using three Sulfo-NHS-biotin reagents in parallel: application to footprint changes of a methyltransferase upon binding its substrate. J Mass Spectrom (2008) 0.89
RNA sequencing and proteogenomics reveal the importance of leaderless mRNAs in the radiation-tolerant bacterium Deinococcus deserti. Genome Biol Evol (2014) 0.87
Expression, purification, crystallization and preliminary crystallographic analysis of the PAB0955 gene product. Acta Crystallogr Sect F Struct Biol Cryst Commun (2005) 0.86
OhrRA functions as a redox-responsive system controlling toxinogenesis in Bacillus cereus. J Proteomics (2013) 0.86
Comparative proteomics reveals key proteins recruited at the nucleoid of Deinococcus after irradiation-induced DNA damage. Proteomics (2013) 0.85
Next-generation proteomics: toward customized biomarkers for environmental biomonitoring. Environ Sci Technol (2014) 0.83
Determination of estrogen presence in water by SPR using estrogen receptor dimerization. Anal Bioanal Chem (2007) 0.83
Analytical constraints for the analysis of human cell line secretomes by shotgun proteomics. J Proteomics (2011) 0.82
Ferredoxin-mediated reactivation of the chlorocatechol 2,3-dioxygenase from Pseudomonas putida GJ31. Arch Microbiol (2002) 0.81
In vitro assessment of cobalt oxide particle toxicity: identifying and circumventing interference. Toxicol In Vitro (2013) 0.79
Proteogenomic biomarkers for identification of Francisella species and subspecies by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry. Anal Chem (2014) 0.79
Shotgun nanoLC-MS/MS proteogenomics to document MALDI-TOF biomarkers for screening new members of the Ruegeria genus. Environ Microbiol (2012) 0.79
Nutriproteomics and Proteogenomics: Cultivating Two Novel Hybrid Fields of Personalized Medicine with Added Societal Value. Curr Pharmacogenomics Person Med (2010) 0.78
Proteogenomic definition of biomarkers for the large Roseobacter clade and application for a quick screening of new environmental isolates. J Proteome Res (2013) 0.78
A comparative proteomic approach to better define Deinococcus nucleoid specificities. J Proteomics (2012) 0.78
Eukaryotic GPN-loop GTPases paralogs use a dimeric assembly reminiscent of archeal GPN. Cell Cycle (2013) 0.78
Magnetic immunoaffinity enrichment for selective capture and MS/MS analysis of N-terminal-TMPP-labeled peptides. J Proteome Res (2013) 0.77
N-Terminal-oriented proteogenomics of the marine bacterium roseobacter denitrificans Och114 using N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) labeling and diagonal chromatography. Mol Cell Proteomics (2014) 0.77
Proteomic investigation of male Gammarus fossarum, a freshwater crustacean, in response to endocrine disruptors. J Proteome Res (2014) 0.77
Prioritizing targets for structural biology through the lens of proteomics: the archaeal protein TGAM_1934 from Thermococcus gammatolerans. Proteomics (2015) 0.77
Major soluble proteome changes in Deinococcus deserti over the earliest stages following gamma-ray irradiation. Proteome Sci (2013) 0.76
Subcellular localization and interaction network of the mRNA decay activator Pat1 upon UV stress. Yeast (2013) 0.75
Ecotoxico-proteomics for aquatic environmental monitoring: first in situ application of a new proteomics-based multibiomarker assay using caged amphipods. Environ Sci Technol (2017) 0.75
Microbiomes - Embracing complexity. Proteomics (2015) 0.75
Multiple phosphorylable sites in the Zaire Ebolavirus nucleoprotein evidenced by high resolution tandem mass spectrometry. J Virol Methods (2012) 0.75