Published in J Proteome Res on April 20, 2007
Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics (2010) 42.80
ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes. Nucleic Acids Res (2007) 2.93
Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol. Genome Res (2008) 1.36
Profiling of N-acetylated protein termini provides in-depth insights into the N-terminal nature of the proteome. Mol Cell Proteomics (2010) 1.28
Genome information management and integrated data analysis with HaloLex. Arch Microbiol (2008) 1.26
Selecting protein N-terminal peptides by combined fractional diagonal chromatography. Nat Protoc (2011) 1.26
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 large scale characterization of plant versus mammal proteins reveals similar and idiosyncratic N-α-acetylation features. Mol Cell Proteomics (2012) 1.23
Proteogenomic analysis of bacteria and archaea: a 46 organism case study. PLoS One (2011) 1.16
Protein acetylation in archaea, bacteria, and eukaryotes. Archaea (2010) 1.15
Ser/Thr/Tyr protein phosphorylation in the archaeon Halobacterium salinarum--a representative of the third domain of life. PLoS One (2009) 1.10
A proteogenomic update to Yersinia: enhancing genome annotation. BMC Genomics (2010) 1.09
A statistics-based platform for quantitative N-terminome analysis and identification of protease cleavage products. Mol Cell Proteomics (2010) 1.05
Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels. BMC Genomics (2010) 1.05
Shotgun proteomics of the haloarchaeon Haloferax volcanii. J Proteome Res (2008) 1.02
The N-terminal penultimate residue of 20S proteasome alpha1 influences its N(alpha) acetylation and protein levels as well as growth rate and stress responses of Haloferax volcanii. J Bacteriol (2009) 1.01
Quantifying homologous replacement of loci between haloarchaeal species. Genome Biol Evol (2012) 1.00
Hydrophilic interaction liquid chromatography (HILIC) in proteomics. Anal Bioanal Chem (2008) 0.99
Mutation of an Arabidopsis NatB N-alpha-terminal acetylation complex component causes pleiotropic developmental defects. PLoS One (2013) 0.97
Evidence-based annotation of transcripts and proteins in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. J Bacteriol (2011) 0.96
S-layer glycoproteins and flagellins: reporters of archaeal posttranslational modifications. Archaea (2010) 0.96
Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline. Mol Cell Proteomics (2013) 0.94
Ubiquitin-Like Proteasome System Represents a Eukaryotic-Like Pathway for Targeted Proteolysis in Archaea. MBio (2016) 0.91
The biological functions of Naa10 - From amino-terminal acetylation to human disease. Gene (2015) 0.87
Genetic evidence for the importance of protein acetylation and protein deacetylation in the halophilic archaeon Haloferax volcanii. J Bacteriol (2008) 0.86
Deletion of cysteine cathepsins B or L yields differential impacts on murine skin proteome and degradome. Mol Cell Proteomics (2012) 0.86
Implications for the evolution of eukaryotic amino-terminal acetyltransferase (NAT) enzymes from the structure of an archaeal ortholog. Proc Natl Acad Sci U S A (2013) 0.85
Post-translation modification in Archaea: lessons from Haloferax volcanii and other haloarchaea. FEMS Microbiol Rev (2012) 0.83
A manual curation strategy to improve genome annotation: application to a set of haloarchael genomes. Life (Basel) (2015) 0.80
How many signal peptides are there in bacteria? Environ Microbiol (2013) 0.80
Abundant Lysine Methylation and N-Terminal Acetylation in Sulfolobus islandicus Revealed by Bottom-Up and Top-Down Proteomics. Mol Cell Proteomics (2016) 0.79
A proteogenomic analysis of Shigella flexneri using 2D LC-MALDI TOF/TOF. BMC Genomics (2011) 0.79
Sharpening Host Defenses during Infection: Proteases Cut to the Chase. Mol Cell Proteomics (2017) 0.78
Genomes of model organisms: know thy tools. Environ Microbiol (2008) 0.77
Aldehyde dehydrogenase of the haloalkaliphilic archaeon Natronomonas pharaonis and its function in ethanol metabolism. Extremophiles (2008) 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
Antagonizing effects of membrane-acting androgens on the eicosanoid receptor OXER1 in prostate cancer. Sci Rep (2017) 0.75
Extreme challenges and advances in archaeal proteomics. Curr Opin Microbiol (2012) 0.75
ERCC1-XPF cooperates with CTCF and cohesin to facilitate the developmental silencing of imprinted genes. Nat Cell Biol (2017) 0.75
In vivo activation of the p53 pathway by small-molecule antagonists of MDM2. Science (2004) 24.42
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24
PRIDE: the proteomics identifications database. Proteomics (2005) 7.52
A guide to the Proteomics Identifications Database proteomics data repository. Proteomics (2009) 5.63
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. Nucleic Acids Res (2008) 4.73
The Proteomics Identifications database: 2010 update. Nucleic Acids Res (2009) 4.47
PRIDE: new developments and new datasets. Nucleic Acids Res (2007) 4.42
Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21
PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res (2006) 4.19
Proteomics analyses reveal the evolutionary conservation and divergence of N-terminal acetyltransferases from yeast and humans. Proc Natl Acad Sci U S A (2009) 4.09
The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases. BMC Bioinformatics (2007) 3.97
Morphological and biochemical characterization of a human liver in a uPA-SCID mouse chimera. Hepatology (2005) 3.72
Improved visualization of protein consensus sequences by iceLogo. Nat Methods (2009) 3.64
PRIDE Converter: making proteomics data-sharing easy. Nat Biotechnol (2009) 3.22
Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat Biotechnol (2003) 3.10
STAT3 is required for IL-6-gp130-dependent activation of hepcidin in vivo. Gastroenterology (2006) 3.05
The complete genome sequence of Haloferax volcanii DS2, a model archaeon. PLoS One (2010) 2.84
Caspase-14 protects against epidermal UVB photodamage and water loss. Nat Cell Biol (2007) 2.82
Interleukin 6/gp130-dependent pathways are protective during chronic liver diseases. Hepatology (2003) 2.68
Targeted peptidecentric proteomics reveals caspase-7 as a substrate of the caspase-1 inflammasomes. Mol Cell Proteomics (2008) 2.64
Target binding properties and cellular activity of afatinib (BIBW 2992), an irreversible ErbB family blocker. J Pharmacol Exp Ther (2012) 2.63
Listeria monocytogenes impairs SUMOylation for efficient infection. Nature (2010) 2.57
LRRK2 controls an EndoA phosphorylation cycle in synaptic endocytosis. Neuron (2012) 2.49
The genome of the square archaeon Haloquadratum walsbyi : life at the limits of water activity. BMC Genomics (2006) 2.48
The first comprehensive and quantitative analysis of human platelet protein composition allows the comparative analysis of structural and functional pathways. Blood (2012) 2.47
LNCipedia: a database for annotated human lncRNA transcript sequences and structures. Nucleic Acids Res (2012) 2.40
The miR-17-92 microRNA cluster regulates multiple components of the TGF-β pathway in neuroblastoma. Mol Cell (2010) 2.38
Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis. Nat Methods (2005) 2.33
The Ontology Lookup Service: bigger and better. Nucleic Acids Res (2010) 2.27
Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster. PLoS Biol (2009) 2.25
Living with two extremes: conclusions from the genome sequence of Natronomonas pharaonis. Genome Res (2005) 2.22
Protein N-terminal acetyltransferases: when the start matters. Trends Biochem Sci (2012) 2.19
Epitope characterization and crystal structure of GA101 provide insights into the molecular basis for type I/II distinction of CD20 antibodies. Blood (2011) 2.13
The effect of alpha-amanitin on the Arabidopsis seed proteome highlights the distinct roles of stored and neosynthesized mRNAs during germination. Plant Physiol (2004) 2.12
The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium. Mol Cell Proteomics (2012) 2.10
PRIDE Inspector: a tool to visualize and validate MS proteomics data. Nat Biotechnol (2012) 2.10
Discovery of two novel families of proteins that are proposed to interact with prokaryotic SMC proteins, and characterization of the Bacillus subtilis family members ScpA and ScpB. Mol Microbiol (2002) 2.06
PIP(2)-PDZ domain binding controls the association of syntenin with the plasma membrane. Mol Cell (2002) 2.04
Chlamydia causes fragmentation of the Golgi compartment to ensure reproduction. Nature (2008) 2.04
Analysis of protein processing by N-terminal proteomics reveals novel species-specific substrate determinants of granzyme B orthologs. Mol Cell Proteomics (2008) 2.01
Global analysis of the mitochondrial N-proteome identifies a processing peptidase critical for protein stability. Cell (2009) 1.96
jmzML, an open-source Java API for mzML, the PSI standard for MS data. Proteomics (2010) 1.96
WT p53, but not tumor-derived mutants, bind to Bcl2 via the DNA binding domain and induce mitochondrial permeabilization. J Biol Chem (2006) 1.94
Caspase-14 is required for filaggrin degradation to natural moisturizing factors in the skin. J Invest Dermatol (2011) 1.93
Immunoglobulin domain crossover as a generic approach for the production of bispecific IgG antibodies. Proc Natl Acad Sci U S A (2011) 1.85
Angiopoietin-2 differentially regulates angiogenesis through TIE2 and integrin signaling. J Clin Invest (2012) 1.85
Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC). Proteomics (2008) 1.81
An archaeal immune system can detect multiple protospacer adjacent motifs (PAMs) to target invader DNA. J Biol Chem (2012) 1.77
p53 contains large unstructured regions in its native state. J Mol Biol (2002) 1.75
Metabolism of halophilic archaea. Extremophiles (2008) 1.75
BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison. Bioinformatics (2004) 1.73
Integral quantification accuracy estimation for reporter ion-based quantitative proteomics (iQuARI). J Proteome Res (2012) 1.72
Involvement of sialoadhesin in entry of porcine reproductive and respiratory syndrome virus into porcine alveolar macrophages. J Virol (2003) 1.72
A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581 T. Environ Microbiol (2010) 1.70
TraML--a standard format for exchange of selected reaction monitoring transition lists. Mol Cell Proteomics (2011) 1.65
Absolute SILAC for accurate quantitation of proteins in complex mixtures down to the attomole level. J Proteome Res (2008) 1.64
Bupropion and 4-OH-bupropion pharmacokinetics in relation to genetic polymorphisms in CYP2B6. Pharmacogenetics (2003) 1.63
SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches. Proteomics (2011) 1.63
The PSI semantic validator: a framework to check MIAPE compliance of proteomics data. Proteomics (2009) 1.62
The N-terminal domain of p53 is natively unfolded. J Mol Biol (2003) 1.62
Stability of bacteriorhodopsin alpha-helices and loops analyzed by single-molecule force spectroscopy. Biophys J (2002) 1.60
Preclinical activity of the type II CD20 antibody GA101 (obinutuzumab) compared with rituximab and ofatumumab in vitro and in xenograft models. Mol Cancer Ther (2013) 1.60
NatF contributes to an evolutionary shift in protein N-terminal acetylation and is important for normal chromosome segregation. PLoS Genet (2011) 1.57
Comparison of the in vitro effects of the anti-CD20 antibodies rituximab and GA101 on chronic lymphocytic leukaemia cells. Br J Haematol (2010) 1.57
Proteomics of Arabidopsis seed germination. A comparative study of wild-type and gibberellin-deficient seeds. Plant Physiol (2002) 1.56
Proteomics of Medicago truncatula seed development establishes the time frame of diverse metabolic processes related to reserve accumulation. Plant Physiol (2003) 1.53
Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering. Proteomics (2006) 1.52