Published in Nat Cell Biol on June 20, 2004
Weighing in on ubiquitin: the expanding role of mass-spectrometry-based proteomics. Nat Cell Biol (2005) 2.62
Chemical genetics screen for enhancers of rapamycin identifies a specific inhibitor of an SCF family E3 ubiquitin ligase. Nat Biotechnol (2010) 1.71
Regulation of amino acid, nucleotide, and phosphate metabolism in Saccharomyces cerevisiae. Genetics (2012) 1.64
Loss of epigenetic modification driven by the Foxp3 transcription factor leads to regulatory T cell insufficiency. Immunity (2012) 1.61
Ubiquitin signals proteolysis-independent stripping of transcription factors. Mol Cell (2014) 1.49
The loop-less tmCdc34 E2 mutant defective in polyubiquitination in vitro and in vivo supports yeast growth in a manner dependent on Ubp14 and Cka2. Cell Div (2011) 1.48
The von Hippel-Lindau tumor suppressor protein and Egl-9-Type proline hydroxylases regulate the large subunit of RNA polymerase II in response to oxidative stress. Mol Cell Biol (2008) 1.43
Polyubiquitin binding and disassembly by deubiquitinating enzymes. Chem Rev (2009) 1.36
Balance of Yin and Yang: ubiquitylation-mediated regulation of p53 and c-Myc. Neoplasia (2006) 1.34
Inducible dissociation of SCF(Met30) ubiquitin ligase mediates a rapid transcriptional response to cadmium. EMBO J (2005) 1.29
Dissection of combinatorial control by the Met4 transcriptional complex. Mol Biol Cell (2009) 1.22
The yeast ubiquitin ligase SCFMet30: connecting environmental and intracellular conditions to cell division. Cell Div (2006) 1.21
APOBEC3G is degraded by the proteasomal pathway in a Vif-dependent manner without being polyubiquitylated. J Biol Chem (2008) 1.21
Polyubiquitylation of histone H2B. Mol Biol Cell (2008) 1.17
Salmonella type III secretion effector SlrP is an E3 ubiquitin ligase for mammalian thioredoxin. J Biol Chem (2009) 1.16
Improved identification of SUMO attachment sites using C-terminal SUMO mutants and tailored protease digestion strategies. J Proteome Res (2006) 1.14
Ubiquitin modifications. Cell Res (2016) 1.10
SCF(Pof1)-ubiquitin and its target Zip1 transcription factor mediate cadmium response in fission yeast. EMBO J (2005) 1.09
Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast. Mol Biol Cell (2011) 1.08
The yeast ubiquitin ligase SCFMet30 regulates heavy metal response. Mol Biol Cell (2005) 1.08
Heterochromatin assembly: a new twist on an old model. Chromosome Res (2006) 1.08
Global approaches to understanding ubiquitination. Genome Biol (2005) 1.03
Characterizing ubiquitination sites by peptide-based immunoaffinity enrichment. Mol Cell Proteomics (2012) 1.00
A transcriptional activator is part of an SCF ubiquitin ligase to control degradation of its cofactors. Mol Cell (2010) 0.98
The F-box protein Met30 is required for multiple steps in the budding yeast cell cycle. Mol Cell Biol (2005) 0.97
C-terminal UBA domains protect ubiquitin receptors by preventing initiation of protein degradation. Nat Commun (2011) 0.96
Repression of sulfate assimilation is an adaptive response of yeast to the oxidative stress of zinc deficiency. J Biol Chem (2009) 0.96
TRIM5α requires Ube2W to anchor Lys63-linked ubiquitin chains and restrict reverse transcription. EMBO J (2015) 0.93
Ubiquitin signalling: what's in a chain? Nat Cell Biol (2004) 0.92
A dominant suppressor mutation of the met30 cell cycle defect suggests regulation of the Saccharomyces cerevisiae Met4-Cbf1 transcription complex by Met32. J Biol Chem (2008) 0.89
SCFCdc4 enables mating type switching in yeast by cyclin-dependent kinase-mediated elimination of the Ash1 transcriptional repressor. Mol Cell Biol (2010) 0.88
Proteomics in neurodegeneration--disease driven approaches. J Neural Transm (Vienna) (2006) 0.85
Inhibiting K63 polyubiquitination abolishes no-go type stalled translation surveillance in Saccharomyces cerevisiae. PLoS Genet (2015) 0.82
Physiologically relevant and portable tandem ubiquitin-binding domain stabilizes polyubiquitylated proteins. Proc Natl Acad Sci U S A (2010) 0.82
Using the ubiquitin-modified proteome to monitor protein homeostasis function. Mol Cell Proteomics (2013) 0.82
The proteasome controls presynaptic differentiation through modulation of an on-site pool of polyubiquitinated conjugates. J Cell Biol (2016) 0.82
Ubiquitin and transcription: The SCF/Met4 pathway, a (protein-) complex issue. Transcription (2011) 0.80
Minireview: ubiquitination-regulated G protein-coupled receptor signaling and trafficking. Mol Endocrinol (2013) 0.80
Applications of proteomic technologies for understanding the premature proteolysis of CFTR. Expert Rev Proteomics (2010) 0.80
Identification of residues in the WD-40 repeat motif of the F-box protein Met30p required for interaction with its substrate Met4p. Mol Genet Genomics (2005) 0.80
The Deubiquitinase USP17 Regulates the Stability and Nuclear Function of IL-33. Int J Mol Sci (2015) 0.80
The 26S proteasome and initiation of gene transcription. Biomolecules (2014) 0.79
Characterizing the roles of Met31 and Met32 in coordinating Met4-activated transcription in the absence of Met30. Mol Biol Cell (2012) 0.79
The emerging regulatory potential of SCFMet30 -mediated polyubiquitination and proteolysis of the Met4 transcriptional activator. Cell Div (2008) 0.78
SAGA DUB-Ubp8 Deubiquitylates Centromeric Histone Variant Cse4. G3 (Bethesda) (2015) 0.75
Skp1 Independent Function of Cdc53/Cul1 in F-box Protein Homeostasis. PLoS Genet (2015) 0.75
Structural insights into Parkin substrate lysine targeting from minimal Miro substrates. Sci Rep (2016) 0.75
A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem (2004) 19.20
Wnt proteins are lipid-modified and can act as stem cell growth factors. Nature (2003) 12.54
DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J Proteome Res (2003) 12.31
A proteomic view of the Plasmodium falciparum life cycle. Nature (2002) 10.65
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24
Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature (2002) 8.92
An endogenous small interfering RNA pathway in Drosophila. Nature (2008) 7.88
A role for the P-body component GW182 in microRNA function. Nat Cell Biol (2005) 7.54
Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Science (2002) 7.49
The human CENP-A centromeric nucleosome-associated complex. Nat Cell Biol (2006) 6.85
Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science (2006) 6.74
A method for the comprehensive proteomic analysis of membrane proteins. Nat Biotechnol (2003) 6.32
A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science (2005) 5.99
Phospho-regulation of kinetochore-microtubule attachments by the Aurora kinase Ipl1p. Cell (2002) 5.91
A conserved protein network controls assembly of the outer kinetochore and its ability to sustain tension. Genes Dev (2004) 5.23
Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation. Nature (2005) 5.15
Human SLX4 is a Holliday junction resolvase subunit that binds multiple DNA repair/recombination endonucleases. Cell (2009) 5.05
Hsp90 cochaperone Aha1 downregulation rescues misfolding of CFTR in cystic fibrosis. Cell (2006) 5.01
Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions. Science (2004) 4.97
The CREB coactivator TORC2 functions as a calcium- and cAMP-sensitive coincidence detector. Cell (2004) 4.91
The CENP-H-I complex is required for the efficient incorporation of newly synthesized CENP-A into centromeres. Nat Cell Biol (2006) 4.89
MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. Rapid Commun Mass Spectrom (2004) 4.76
Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat Methods (2004) 4.62
Analysis of the myosin-II-responsive focal adhesion proteome reveals a role for β-Pix in negative regulation of focal adhesion maturation. Nat Cell Biol (2011) 4.59
Assigning function to yeast proteins by integration of technologies. Mol Cell (2003) 4.58
Mammalian miRNA RISC recruits CAF1 and PABP to affect PABP-dependent deadenylation. Mol Cell (2009) 4.57
Neural palmitoyl-proteomics reveals dynamic synaptic palmitoylation. Nature (2008) 4.52
Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways. Cell (2006) 4.50
Global analysis of protein palmitoylation in yeast. Cell (2006) 4.43
PRAK is essential for ras-induced senescence and tumor suppression. Cell (2007) 4.30
The biological impact of mass-spectrometry-based proteomics. Nature (2007) 4.24
Systematic identification of C. elegans miRISC proteins, miRNAs, and mRNA targets by their interactions with GW182 proteins AIN-1 and AIN-2. Mol Cell (2007) 4.22
Centromere-specific assembly of CENP-a nucleosomes is mediated by HJURP. Cell (2009) 4.22
Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21
Asymmetric CLASP-dependent nucleation of noncentrosomal microtubules at the trans-Golgi network. Dev Cell (2007) 4.17
The Set2 histone methyltransferase functions through the phosphorylated carboxyl-terminal domain of RNA polymerase II. J Biol Chem (2003) 4.13
Probability-based validation of protein identifications using a modified SEQUEST algorithm. Anal Chem (2002) 3.86
Bora and the kinase Aurora a cooperatively activate the kinase Plk1 and control mitotic entry. Science (2008) 3.77
Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. J Proteome Res (2009) 3.77
Shotgun identification of protein modifications from protein complexes and lens tissue. Proc Natl Acad Sci U S A (2002) 3.70
Nuclear membrane proteins with potential disease links found by subtractive proteomics. Science (2003) 3.64
Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res (2004) 3.63
A tandem affinity tag for two-step purification under fully denaturing conditions: application in ubiquitin profiling and protein complex identification combined with in vivocross-linking. Mol Cell Proteomics (2006) 3.62
Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book. Nat Methods (2004) 3.62
Cln3 activates G1-specific transcription via phosphorylation of the SBF bound repressor Whi5. Cell (2004) 3.60
A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat Biotechnol (2003) 3.57
Molecular architecture of the human pre-mRNA 3' processing complex. Mol Cell (2009) 3.52
Quantitative mass spectrometry identifies insulin signaling targets in C. elegans. Science (2007) 3.46
Aurora B phosphorylates spatially distinct targets to differentially regulate the kinetochore-microtubule interface. Mol Cell (2010) 3.44
Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline. Mol Cell (2009) 3.43
A quantitative analysis software tool for mass spectrometry-based proteomics. Nat Methods (2008) 3.35
Determination and comparison of the baseline proteomes of the versatile microbe Rhodopseudomonas palustris under its major metabolic states. J Proteome Res (2006) 3.32
A complex containing the Sm protein CAR-1 and the RNA helicase CGH-1 is required for embryonic cytokinesis in Caenorhabditis elegans. J Cell Biol (2005) 3.18
Chemical and biological approaches synergize to ameliorate protein-folding diseases. Cell (2008) 3.11
Functional specialization of beta-arrestin interactions revealed by proteomic analysis. Proc Natl Acad Sci U S A (2007) 3.08
Arginylation of beta-actin regulates actin cytoskeleton and cell motility. Science (2006) 3.05
A streamlined platform for high-content functional proteomics of primary human specimens. Nat Methods (2005) 3.00
Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture. Nat Biotechnol (2004) 2.98
Analysis of quantitative proteomic data generated via multidimensional protein identification technology. Anal Chem (2002) 2.94
Architecture of the budding yeast kinetochore reveals a conserved molecular core. J Cell Biol (2003) 2.92
A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases. Anal Chem (2003) 2.91
Mass spectrometry in high-throughput proteomics: ready for the big time. Nat Methods (2010) 2.91
A correlation algorithm for the automated quantitative analysis of shotgun proteomics data. Anal Chem (2003) 2.89
Proteomic analysis of isolated chlamydomonas centrioles reveals orthologs of ciliary-disease genes. Curr Biol (2005) 2.86
TOR complex 2 integrates cell movement during chemotaxis and signal relay in Dictyostelium. Mol Biol Cell (2005) 2.76
GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model. Anal Chem (2003) 2.74
Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2003) 2.73
Automatic quality assessment of peptide tandem mass spectra. Bioinformatics (2004) 2.70
Reduced histone deacetylase 7 activity restores function to misfolded CFTR in cystic fibrosis. Nat Chem Biol (2009) 2.70
Tea4p links microtubule plus ends with the formin for3p in the establishment of cell polarity. Dev Cell (2005) 2.65
An integrated mass spectrometry-based proteomic approach: quantitative analysis of tandem affinity-purified in vivo cross-linked protein complexes (QTAX) to decipher the 26 S proteasome-interacting network. Mol Cell Proteomics (2005) 2.62
The application of mass spectrometry to membrane proteomics. Nat Biotechnol (2003) 2.61
Control of iron homeostasis by an iron-regulated ubiquitin ligase. Science (2009) 2.60
Global analysis of protein sumoylation in Saccharomyces cerevisiae. J Biol Chem (2004) 2.60
LRRTM2 interacts with Neurexin1 and regulates excitatory synapse formation. Neuron (2009) 2.60
Swi1 and Swi3 are components of a replication fork protection complex in fission yeast. Mol Cell Biol (2004) 2.55
Code developments to improve the efficiency of automated MS/MS spectra interpretation. J Proteome Res (2003) 2.53
The proteomes of human parotid and submandibular/sublingual gland salivas collected as the ductal secretions. J Proteome Res (2008) 2.53
RNA-dependent cysteine biosynthesis in archaea. Science (2005) 2.50
Deubiquitination of histone H2B by a yeast acetyltransferase complex regulates transcription. J Biol Chem (2003) 2.48
Digestion and depletion of abundant proteins improves proteomic coverage. Nat Methods (2012) 2.48
MMS19 assembles iron-sulfur proteins required for DNA metabolism and genomic integrity. Science (2012) 2.46
Mass spectrometric characterization of the affinity-purified human 26S proteasome complex. Biochemistry (2007) 2.43
Replication-independent histone deposition by the HIR complex and Asf1. Curr Biol (2005) 2.40
Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis. Anal Chem (2004) 2.40
Target identification using drug affinity responsive target stability (DARTS). Proc Natl Acad Sci U S A (2009) 2.40
The deubiquitinating enzyme BAP1 regulates cell growth via interaction with HCF-1. J Biol Chem (2009) 2.40
Identification of Plasmodium falciparum antigens by antigenic analysis of genomic and proteomic data. Proc Natl Acad Sci U S A (2003) 2.38
Validation of tandem mass spectrometry database search results using DTASelect. Curr Protoc Bioinformatics (2007) 2.37
Jmjd6 catalyses lysyl-hydroxylation of U2AF65, a protein associated with RNA splicing. Science (2009) 2.37
ZW10 links mitotic checkpoint signaling to the structural kinetochore. J Cell Biol (2005) 2.36
Human-specific transcriptional regulation of CNS development genes by FOXP2. Nature (2009) 2.33