Published in Mol Cell Proteomics on April 03, 2012
A new in vivo cross-linking mass spectrometry platform to define protein-protein interactions in living cells. Mol Cell Proteomics (2014) 1.18
RNA binding and core complexes constitute the U-insertion/deletion editosome. Mol Cell Biol (2014) 0.98
Developing new isotope-coded mass spectrometry-cleavable cross-linkers for elucidating protein structures. Anal Chem (2014) 0.90
Drosophila COP9 signalosome subunit 7 interacts with multiple genomic loci to regulate development. Nucleic Acids Res (2014) 0.89
Ubiquitin-like (UBX)-domain-containing protein, UBXN2A, promotes cell death by interfering with the p53-Mortalin interactions in colon cancer cells. Cell Death Dis (2014) 0.86
High-definition de novo sequencing of crustacean hyperglycemic hormone (CHH)-family neuropeptides. Mol Cell Proteomics (2012) 0.86
Characterization of Dynamic UbR-Proteasome Subcomplexes by In vivo Cross-linking (X) Assisted Bimolecular Tandem Affinity Purification (XBAP) and Label-free Quantitation. Mol Cell Proteomics (2016) 0.83
A pipeline for determining protein-protein interactions and proximities in the cellular milieu. Mol Cell Proteomics (2014) 0.81
Quantitative affinity purification mass spectrometry: a versatile technology to study protein-protein interactions. Front Genet (2015) 0.80
Ribosome-associated pentatricopeptide repeat proteins function as translational activators in mitochondria of trypanosomes. Mol Microbiol (2016) 0.79
Antisense Transcripts Delimit Exonucleolytic Activity of the Mitochondrial 3' Processome to Generate Guide RNAs. Mol Cell (2016) 0.79
Characterizing the dynamics of proteasome complexes by proteomics approaches. Antioxid Redox Signal (2014) 0.77
Akt Phosphorylates Wnt Coactivator and Chromatin Effector Pygo2 at Serine 48 to Antagonize Its Ubiquitin/Proteasome-mediated Degradation. J Biol Chem (2015) 0.76
Qualitative and quantitative top-down mass spectral analysis of crustacean hyperglycemic hormones in response to feeding. Proteomics (2014) 0.75
Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome. Mol Cell Proteomics (2017) 0.75
PPR polyadenylation factor defines mitochondrial mRNA identity and stability in trypanosomes. EMBO J (2017) 0.75
Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics (2002) 30.58
Function and regulation of cullin-RING ubiquitin ligases. Nat Rev Mol Cell Biol (2005) 14.42
RING domain E3 ubiquitin ligases. Annu Rev Biochem (2009) 12.55
Defining the human deubiquitinating enzyme interaction landscape. Cell (2009) 11.39
Recognition and processing of ubiquitin-protein conjugates by the proteasome. Annu Rev Biochem (2009) 8.83
The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res (2004) 8.79
Functional and quantitative proteomics using SILAC. Nat Rev Mol Cell Biol (2006) 6.25
A global protein kinase and phosphatase interaction network in yeast. Science (2010) 5.95
Mammalian cyclin-dependent kinases. Trends Biochem Sci (2005) 5.54
Proteasomes and their kin: proteases in the machine age. Nat Rev Mol Cell Biol (2004) 5.14
Role of predicted metalloprotease motif of Jab1/Csn5 in cleavage of Nedd8 from Cul1. Science (2002) 4.95
CORUM: the comprehensive resource of mammalian protein complexes--2009. Nucleic Acids Res (2009) 4.71
COP9 signalosome: a multifunctional regulator of SCF and other cullin-based ubiquitin ligases. Cell (2003) 4.25
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
SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nat Methods (2010) 3.50
Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors. Methods (2006) 3.37
Nedd8 on cullin: building an expressway to protein destruction. Oncogene (2004) 3.29
The COP9 signalosome. Annu Rev Cell Dev Biol (2003) 3.25
CORUM: the comprehensive resource of mammalian protein complexes. Nucleic Acids Res (2007) 3.23
Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics. Proc Natl Acad Sci U S A (2008) 3.23
Refinements to label free proteome quantitation: how to deal with peptides shared by multiple proteins. Anal Chem (2010) 3.07
The COP9 signalosome: more than a protease. Trends Biochem Sci (2008) 2.81
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
Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. Cell (2010) 2.59
Linking H3K79 trimethylation to Wnt signaling through a novel Dot1-containing complex (DotCom). Genes Dev (2010) 2.53
The COP9 signalosome: an assembly and maintenance platform for cullin ubiquitin ligases? Nat Cell Biol (2003) 2.50
Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat Rev Genet (2009) 2.44
Mass spectrometric characterization of the affinity-purified human 26S proteasome complex. Biochemistry (2007) 2.43
A novel protein complex involved in signal transduction possessing similarities to 26S proteasome subunits. FASEB J (1998) 2.43
Symmetrical modularity of the COP9 signalosome complex suggests its multifunctionality. Structure (2009) 2.30
Characterization of the proteasome interaction network using a QTAX-based tag-team strategy and protein interaction network analysis. Proc Natl Acad Sci U S A (2008) 1.76
Chemical genetics screen for enhancers of rapamycin identifies a specific inhibitor of an SCF family E3 ubiquitin ligase. Nat Biotechnol (2010) 1.71
The emerging role of the COP9 signalosome in cancer. Mol Cancer Res (2005) 1.57
The zinc finger of the CSN-associated deubiquitinating enzyme USP15 is essential to rescue the E3 ligase Rbx1. Curr Biol (2005) 1.55
Protein kinase CK2 and protein kinase D are associated with the COP9 signalosome. EMBO J (2003) 1.53
Dual function of eIF3j/Hcr1p in processing 20 S pre-rRNA and translation initiation. J Biol Chem (2001) 1.50
REGgamma, a proteasome activator and beyond? Cell Mol Life Sci (2008) 1.43
Consequences of COP9 signalosome and 26S proteasome interaction. FEBS J (2005) 1.24
An interaction network of the mammalian COP9 signalosome identifies Dda1 as a core subunit of multiple Cul4-based E3 ligases. J Cell Sci (2009) 1.23
Behind the wheel and under the hood: functions of cyclin-dependent kinases in response to DNA damage. DNA Repair (Amst) (2009) 1.23
Characterization of the human COP9 signalosome complex using affinity purification and mass spectrometry. J Proteome Res (2008) 1.20
Temporal profiling of the adipocyte proteome during differentiation using a five-plex SILAC based strategy. J Proteome Res (2009) 1.15
Characterization of cell cycle specific protein interaction networks of the yeast 26S proteasome complex by the QTAX strategy. J Proteome Res (2010) 1.14
Profiling of protein interaction networks of protein complexes using affinity purification and quantitative mass spectrometry. Mol Cell Proteomics (2010) 1.13
The COP9 signalosome: an alternative lid for the 26S proteasome? Trends Cell Biol (2003) 1.11
Roles for CSN5 in control of p53/MDM2 activities. J Cell Biochem (2008) 1.10
CSN5 isopeptidase activity links COP9 signalosome activation to breast cancer progression. Cancer Res (2008) 1.01
The transmembrane segment of a tail-anchored protein determines its degradative fate through dislocation from the endoplasmic reticulum. J Biol Chem (2010) 1.01
Determining protein complex connectivity using a probabilistic deletion network derived from quantitative proteomics. PLoS One (2009) 0.96
INT6--a link between the proteasome and tumorigenesis. Cell Cycle (2003) 0.90
Arabidopsis eIF3e is regulated by the COP9 signalosome and has an impact on development and protein translation. Plant J (2007) 0.89
Arabidopsis eIF3e interacts with subunits of the ribosome, Cop9 signalosome and proteasome. Plant Signal Behav (2008) 0.83
Novel anti-angiogenic compounds for application in tumor therapy - COP9 signalosome-associated kinases as possible targets. Mini Rev Med Chem (2008) 0.80
The AIM2 inflammasome is critical for innate immunity to Francisella tularensis. Nat Immunol (2010) 5.79
Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins (2002) 5.29
An elliptic spatial scan statistic. Stat Med (2006) 5.09
An enhanced MITOMAP with a global mtDNA mutational phylogeny. Nucleic Acids Res (2006) 4.51
Global landscape of recent inferred Darwinian selection for Homo sapiens. Proc Natl Acad Sci U S A (2005) 3.77
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
Profiling the humoral immune response to infection by using proteome microarrays: high-throughput vaccine and diagnostic antigen discovery. Proc Natl Acad Sci U S A (2005) 3.59
MITOMAP: a human mitochondrial genome database--2004 update. Nucleic Acids Res (2005) 3.35
Prediction of protein stability changes for single-site mutations using support vector machines. Proteins (2006) 3.00
A prospective analysis of the Ab response to Plasmodium falciparum before and after a malaria season by protein microarray. Proc Natl Acad Sci U S A (2010) 2.90
Prediction of coordination number and relative solvent accessibility in proteins. Proteins (2002) 2.66
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
Mass spectrometric characterization of the affinity-purified human 26S proteasome complex. Biochemistry (2007) 2.43
Profiling humoral immune responses to P. falciparum infection with protein microarrays. Proteomics (2008) 2.43
Phospho-dependent functional modulation of GABA(B) receptors by the metabolic sensor AMP-dependent protein kinase. Neuron (2007) 2.38
Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR. J Biol Chem (2003) 2.32
Quantitative analysis of global ubiquitination in HeLa cells by mass spectrometry. J Proteome Res (2008) 2.27
Coordination of the transcriptome and metabolome by the circadian clock. Proc Natl Acad Sci U S A (2012) 2.22
Lung microvascular endothelium is enriched with progenitor cells that exhibit vasculogenic capacity. Am J Physiol Lung Cell Mol Physiol (2007) 2.21
ChemDB: a public database of small molecules and related chemoinformatics resources. Bioinformatics (2005) 2.16
IKK phosphorylates Huntingtin and targets it for degradation by the proteasome and lysosome. J Cell Biol (2009) 2.16
A genome-wide proteome array reveals a limited set of immunogens in natural infections of humans and white-footed mice with Borrelia burgdorferi. Infect Immun (2008) 2.15
A Burkholderia pseudomallei protein microarray reveals serodiagnostic and cross-reactive antigens. Proc Natl Acad Sci U S A (2009) 2.10
Pentatricopeptide repeat proteins stimulate mRNA adenylation/uridylation to activate mitochondrial translation in trypanosomes. Mol Cell (2011) 2.10
Improved residue contact prediction using support vector machines and a large feature set. BMC Bioinformatics (2007) 2.03
Identifying dynamic interactors of protein complexes by quantitative mass spectrometry. Mol Cell Proteomics (2007) 2.02
Data structures and compression algorithms for genomic sequence data. Bioinformatics (2009) 1.96
Circulating angiogenic precursors in idiopathic pulmonary arterial hypertension. Am J Pathol (2008) 1.90
An essential role for stromal interaction molecule 1 in neointima formation following arterial injury. Cardiovasc Res (2008) 1.87
Bayesian surprise attracts human attention. Vision Res (2008) 1.86
Bounds and algorithms for fast exact searches of chemical fingerprints in linear and sublinear time. J Chem Inf Model (2007) 1.86
Graph kernels for chemical informatics. Neural Netw (2005) 1.86
Immunodominant Francisella tularensis antigens identified using proteome microarray. Proteomics (2007) 1.85
ChemDB update--full-text search and virtual chemical space. Bioinformatics (2007) 1.83
Fus3-regulated Tec1 degradation through SCFCdc4 determines MAPK signaling specificity during mating in yeast. Cell (2004) 1.83
The mammalian retromer regulates transcytosis of the polymeric immunoglobulin receptor. Nat Cell Biol (2004) 1.80
PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure. Bioinformatics (2008) 1.78
Characterization of the proteasome interaction network using a QTAX-based tag-team strategy and protein interaction network analysis. Proc Natl Acad Sci U S A (2008) 1.76
A machine learning information retrieval approach to protein fold recognition. Bioinformatics (2006) 1.75
Guide RNA-binding complex from mitochondria of trypanosomatids. Mol Cell (2008) 1.75
A targeted proteomic analysis of the ubiquitin-like modifier nedd8 and associated proteins. J Proteome Res (2008) 1.74
MotifMap: a human genome-wide map of candidate regulatory motif sites. Bioinformatics (2008) 1.73
Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA. J Biol Chem (2005) 1.73
Chemical genetics screen for enhancers of rapamycin identifies a specific inhibitor of an SCF family E3 ubiquitin ligase. Nat Biotechnol (2010) 1.71
Global gene expression profiling in Escherichia coli K12. The effects of leucine-responsive regulatory protein. J Biol Chem (2002) 1.69
A scan statistic for continuous data based on the normal probability model. Int J Health Geogr (2009) 1.68
From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis. Bioinformatics (2007) 1.68
miR-34a, a microRNA up-regulated in a double transgenic mouse model of Alzheimer's disease, inhibits bcl2 translation. Brain Res Bull (2009) 1.66
A technique for retrograde intubation in mice. Lab Anim (NY) (2006) 1.65
Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques. Bioinformatics (2006) 1.65
Renal D3 dopamine receptor stimulation induces natriuresis by endothelin B receptor interactions. Kidney Int (2008) 1.63
Development of a novel cross-linking strategy for fast and accurate identification of cross-linked peptides of protein complexes. Mol Cell Proteomics (2010) 1.61
Stress-inducible protein 1 is a cell surface ligand for cellular prion that triggers neuroprotection. EMBO J (2002) 1.58
Cyber-T web server: differential analysis of high-throughput data. Nucleic Acids Res (2012) 1.58
C-reactive protein upregulates receptor for advanced glycation end products expression and alters antioxidant defenses in rat endothelial progenitor cells. J Cardiovasc Pharmacol (2009) 1.57
COBEpro: a novel system for predicting continuous B-cell epitopes. Protein Eng Des Sel (2008) 1.54
Sterile protective immunity to malaria is associated with a panel of novel P. falciparum antigens. Mol Cell Proteomics (2011) 1.53
Histone acetylation and deacetylation: identification of acetylation and methylation sites of HeLa histone H4 by mass spectrometry. Mol Cell Proteomics (2002) 1.52
Oxidative stress-mediated regulation of proteasome complexes. Mol Cell Proteomics (2011) 1.50
Regulation of the 26S proteasome complex during oxidative stress. Sci Signal (2010) 1.48
Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity. Bioinformatics (2005) 1.47
Deep architectures for protein contact map prediction. Bioinformatics (2012) 1.44
Differential analysis of DNA microarray gene expression data. Mol Microbiol (2003) 1.43
Structure-based inhibitor design of AccD5, an essential acyl-CoA carboxylase carboxyltransferase domain of Mycobacterium tuberculosis. Proc Natl Acad Sci U S A (2006) 1.42
Large-scale prediction of disulphide bridges using kernel methods, two-dimensional recursive neural networks, and weighted graph matching. Proteins (2006) 1.41
Value of myocardial regional perfusion on long-term function in collateral-dependent myocardium. South Med J (2008) 1.40
Assessment of predictions submitted for the CASP7 domain prediction category. Proteins (2007) 1.39
Retroviruses and yeast retrotransposons use overlapping sets of host genes. Genome Res (2005) 1.38
Deciphering networks of protein interactions at the nuclear pore complex. Mol Cell Proteomics (2002) 1.37
Activation of D3 dopamine receptor decreases angiotensin II type 1 receptor expression in rat renal proximal tubule cells. Circ Res (2006) 1.36
The neuron-specific chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory. Nat Neurosci (2013) 1.36
Phosphorylation of threonine 3: implications for Huntingtin aggregation and neurotoxicity. J Biol Chem (2009) 1.34
Leptin engages a hypothalamic neurocircuitry to permit survival in the absence of insulin. Cell Metab (2013) 1.32
Data structures and compression algorithms for high-throughput sequencing technologies. BMC Bioinformatics (2010) 1.31
Novel avian-origin human influenza A(H7N9) can be transmitted between ferrets via respiratory droplets. J Infect Dis (2013) 1.28
In vitro combination characterization of the new anticancer plant drug beta-elemene with taxanes against human lung carcinoma. Int J Oncol (2007) 1.26
Distribution patterns of over-represented k-mers in non-coding yeast DNA. Bioinformatics (2002) 1.25
The stability and complexity of antibody responses to the major surface antigen of Plasmodium falciparum are associated with age in a malaria endemic area. Mol Cell Proteomics (2011) 1.24
Why are complementary DNA strands symmetric? Bioinformatics (2002) 1.23
GM130-dependent control of Cdc42 activity at the Golgi regulates centrosome organization. Mol Biol Cell (2008) 1.23
HB tag modules for PCR-based gene tagging and tandem affinity purification in Saccharomyces cerevisiae. Yeast (2006) 1.23
A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval. Bioinformatics (2010) 1.20
Census and geographic differences between respondents and nonrespondents in a case-control study of non-Hodgkin lymphoma. Am J Epidemiol (2007) 1.20
Characterization of the human COP9 signalosome complex using affinity purification and mass spectrometry. J Proteome Res (2008) 1.20
Comparison of tests for spatial heterogeneity on data with global clustering patterns and outliers. Int J Health Geogr (2009) 1.20
Advanced glycation endproducts alter functions and promote apoptosis in endothelial progenitor cells through receptor for advanced glycation endproducts mediate overpression of cell oxidant stress. Mol Cell Biochem (2009) 1.19
miR-106b aberrantly expressed in a double transgenic mouse model for Alzheimer's disease targets TGF-β type II receptor. Brain Res (2010) 1.18
Bayesian Variable Selection and Computation for Generalized Linear Models with Conjugate Priors. Bayesian Anal (2008) 1.17
Two distinct coactivators, DRIP/mediator and SRC/p160, are differentially involved in vitamin D receptor transactivation during keratinocyte differentiation. Mol Endocrinol (2003) 1.17