Published in BMC Genomics on February 15, 2012
An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3. Stand Genomic Sci (2014) 1.41
Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline. Mol Cell Proteomics (2013) 0.94
Re-annotation of the Saccharopolyspora erythraea genome using a systems biology approach. BMC Genomics (2013) 0.88
Proteogenomics of Gammarus fossarum to document the reproductive system of amphipods. Mol Cell Proteomics (2014) 0.88
Data for comparative proteomics of ovaries from five non-model, crustacean amphipods. Data Brief (2015) 0.81
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
Environmental Pressure May Change the Composition Protein Disorder in Prokaryotes. PLoS One (2015) 0.76
Tissue-specific Proteogenomic Analysis of Plutella xylostella Larval Midgut Using a Multialgorithm Pipeline. Mol Cell Proteomics (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
Ovary and embryo proteogenomic dataset revealing diversity of vitellogenins in the crustacean Gammarus fossarum. Data Brief (2016) 0.75
Identification of new protein-coding genes with a potential role in the virulence of the plant pathogen Xanthomonas euvesicatoria. BMC Genomics (2017) 0.75
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science (1995) 68.34
Improved prediction of signal peptides: SignalP 3.0. J Mol Biol (2004) 48.40
Artemis: sequence visualization and annotation. Bioinformatics (2000) 46.68
Annotating genomes with massive-scale RNA sequencing. Genome Biol (2008) 7.73
Overview of the marine roseobacter lineage. Appl Environ Microbiol (2005) 5.79
Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature (2004) 5.00
Large-scale prokaryotic gene prediction and comparison to genome annotation. Bioinformatics (2005) 4.25
Bacterial carbon processing by generalist species in the coastal ocean. Nature (2008) 3.37
The complete genome and proteome of Mycoplasma mobile. Genome Res (2004) 3.36
Genome characteristics of a generalist marine bacterial lineage. ISME J (2010) 3.11
Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream. Nat Biotechnol (2009) 3.08
Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases. Anal Chem (1995) 2.86
Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res (2007) 2.67
Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat Rev Genet (2009) 2.44
RTX proteins: a highly diverse family secreted by a common mechanism. FEMS Microbiol Rev (2010) 2.13
The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea. ISME J (2009) 2.00
Using comparative genome analysis to identify problems in annotated microbial genomes. Microbiology (2010) 1.77
Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea. Genome Biol (2009) 1.69
Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes. Genome Res (2008) 1.68
Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models. Genome Res (2010) 1.66
A toolbox for validation of mass spectrometry peptides identification and generation of database: IRMa. Bioinformatics (2009) 1.59
Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti. PLoS Genet (2009) 1.50
Recoding in bacteriophages and bacterial IS elements. Trends Genet (2006) 1.43
Structural and operational complexity of the Geobacter sulfurreducens genome. Genome Res (2010) 1.37
Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol. Genome Res (2008) 1.36
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
Generating and navigating proteome maps using mass spectrometry. Nat Rev Mol Cell Biol (2010) 1.29
Transterm: a database to aid the analysis of regulatory sequences in mRNAs. Nucleic Acids Res (2008) 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
A perfect genome annotation is within reach with the proteomics and genomics alliance. Curr Opin Microbiol (2009) 1.16
Comparative proteogenomics of twelve Roseobacter exoproteomes reveals different adaptive strategies among these marine bacteria. Mol Cell Proteomics (2011) 1.11
A proteogenomic update to Yersinia: enhancing genome annotation. BMC Genomics (2010) 1.09
Interrupted coding sequences in Mycobacterium smegmatis: authentic mutations or sequencing errors? Genome Biol (2007) 1.07
Proteomic insights into the lifestyle of an environmentally relevant marine bacterium. ISME J (2011) 1.03
Identification, purification, and characterization of an eukaryotic-like phosphopantetheine adenylyltransferase (coenzyme A biosynthetic pathway) in the hyperthermophilic archaeon Pyrococcus abyssi. J Biol Chem (2003) 1.01
In-depth analysis of exoproteomes from marine bacteria by shotgun liquid chromatography-tandem mass spectrometry: the Ruegeria pomeroyi DSS-3 case-study. Mar Drugs (2010) 0.99
Proteogenomics and systems biology: quest for the ultimate missing parts. Expert Rev Proteomics (2010) 0.99
Genome sequences of Oceanicola granulosus HTCC2516(T) and Oceanicola batsensis HTCC2597(TDelta). J Bacteriol (2010) 0.96
Functional characterization and high-throughput proteomic analysis of interrupted genes in the archaeon Sulfolobus solfataricus. J Proteome Res (2010) 0.90
Genome sequences of Pelagibaca bermudensis HTCC2601T and Maritimibacter alkaliphilus HTCC2654T, the type strains of two marine Roseobacter genera. J Bacteriol (2010) 0.83
Genome sequence of the marine alphaproteobacterium HTCC2150, assigned to the Roseobacter clade. J Bacteriol (2010) 0.79
Genome sequence of strain HTCC2083, a novel member of the marine clade Roseobacter. J Bacteriol (2010) 0.78
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
In-depth analysis of exoproteomes from marine bacteria by shotgun liquid chromatography-tandem mass spectrometry: the Ruegeria pomeroyi DSS-3 case-study. Mar Drugs (2010) 0.99
N-terminomics and proteogenomics, getting off to a good start. Proteomics (2014) 0.99
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