Published in EMBO Mol Med on May 01, 2014
Cystic fibrosis genetics: from molecular understanding to clinical application. Nat Rev Genet (2014) 1.70
Nonsense-mediated mRNA decay: an intricate machinery that shapes transcriptomes. Nat Rev Mol Cell Biol (2015) 1.61
The unfolded protein response is shaped by the NMD pathway. EMBO Rep (2015) 1.05
Mechanism and regulation of the nonsense-mediated decay pathway. Nucleic Acids Res (2016) 0.99
Physiological and pathophysiological role of nonsense-mediated mRNA decay. Pflugers Arch (2016) 0.80
Inhibition of nonsense-mediated RNA decay by ER stress. RNA (2016) 0.77
Proteomic Analysis Reveals Branch-specific Regulation of the Unfolded Protein Response by Nonsense-mediated mRNA Decay. Mol Cell Proteomics (2016) 0.77
Control of gene expression through the nonsense-mediated RNA decay pathway. Cell Biosci (2017) 0.75
p38 MAPK Inhibits Nonsense-mediated RNA Decay in Response to Persistent DNA Damage in Non-cycling Cells. J Biol Chem (2017) 0.75
Strategies for the etiological therapy of cystic fibrosis. Cell Death Differ (2017) 0.75
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
Signal integration in the endoplasmic reticulum unfolded protein response. Nat Rev Mol Cell Biol (2007) 33.06
The unfolded protein response: from stress pathway to homeostatic regulation. Science (2011) 15.71
Stress signaling from the lumen of the endoplasmic reticulum: coordination of gene transcriptional and translational controls. Genes Dev (1999) 13.24
Ensembl 2013. Nucleic Acids Res (2012) 11.70
The nonsense-mediated decay RNA surveillance pathway. Annu Rev Biochem (2007) 8.94
From endoplasmic-reticulum stress to the inflammatory response. Nature (2008) 7.17
Nonsense-mediated mRNA decay in health and disease. Hum Mol Genet (1999) 6.90
PTC124 targets genetic disorders caused by nonsense mutations. Nature (2007) 6.67
Functional and quantitative proteomics using SILAC. Nat Rev Mol Cell Biol (2006) 6.25
Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat Genet (2004) 6.14
Interference of nonsense mutations with eukaryotic messenger RNA stability. Proc Natl Acad Sci U S A (1979) 5.70
XLF interacts with the XRCC4-DNA ligase IV complex to promote DNA nonhomologous end-joining. Cell (2006) 5.62
Cernunnos, a novel nonhomologous end-joining factor, is mutated in human immunodeficiency with microcephaly. Cell (2006) 5.33
Nonsense-mediated decay approaches the clinic. Nat Genet (2004) 5.12
Gentamicin-induced correction of CFTR function in patients with cystic fibrosis and CFTR stop mutations. N Engl J Med (2003) 4.43
Effectiveness of PTC124 treatment of cystic fibrosis caused by nonsense mutations: a prospective phase II trial. Lancet (2008) 4.35
Principles of ubiquitin and SUMO modifications in DNA repair. Nature (2009) 4.10
Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. Science (1996) 3.94
Separable roles for rent1/hUpf1 in altered splicing and decay of nonsense transcripts. Science (2002) 3.84
Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. Mol Cell Proteomics (2012) 3.57
SC35 autoregulates its expression by promoting splicing events that destabilize its mRNAs. EMBO J (2001) 3.55
RNA surveillance. Unforeseen consequences for gene expression, inherited genetic disorders and cancer. Trends Genet (1999) 3.43
Quantitative, high-resolution proteomics for data-driven systems biology. Annu Rev Biochem (2011) 3.19
Aminoglycoside antibiotics restore dystrophin function to skeletal muscles of mdx mice. J Clin Invest (1999) 3.06
The critical roles of endoplasmic reticulum chaperones and unfolded protein response in tumorigenesis and anticancer therapies. Oncogene (2012) 2.82
When the message goes awry: disease-producing mutations that influence mRNA content and performance. Cell (2001) 2.55
Organizing principles of mammalian nonsense-mediated mRNA decay. Annu Rev Genet (2013) 2.55
Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res (1994) 2.41
Applying nonsense-mediated mRNA decay research to the clinic: progress and challenges. Trends Mol Med (2006) 2.39
Mutations in UPF3B, a member of the nonsense-mediated mRNA decay complex, cause syndromic and nonsyndromic mental retardation. Nat Genet (2007) 2.35
Nonsense-mediated mRNA decay - mechanisms of substrate mRNA recognition and degradation in mammalian cells. Biochim Biophys Acta (2013) 2.30
Gentamicin treatment of Duchenne and Becker muscular dystrophy due to nonsense mutations. Ann Neurol (2001) 2.29
Domain interdependence in the biosynthetic assembly of CFTR. J Mol Biol (2006) 2.17
Safety, tolerability, and pharmacokinetics of PTC124, a nonaminoglycoside nonsense mutation suppressor, following single- and multiple-dose administration to healthy male and female adult volunteers. J Clin Pharmacol (2007) 2.16
An alternative branch of the nonsense-mediated decay pathway. EMBO J (2007) 2.01
RNA sequence determinants for aminoglycoside binding to an A-site rRNA model oligonucleotide. J Mol Biol (1996) 1.92
Basis for prokaryotic specificity of action of aminoglycoside antibiotics. EMBO J (1999) 1.91
The ubiquitin landscape at DNA double-strand breaks. J Cell Biol (2009) 1.86
Autoregulation of the nonsense-mediated mRNA decay pathway in human cells. RNA (2011) 1.76
The protective and destructive roles played by molecular chaperones during ERAD (endoplasmic-reticulum-associated degradation). Biochem J (2007) 1.74
Nonsense-mediated mRNA decay affects nonsense transcript levels and governs response of cystic fibrosis patients to gentamicin. J Clin Invest (2007) 1.73
Suppression of a nonsense mutation in mammalian cells in vivo by the aminoglycoside antibiotics G-418 and paromomycin. Nucleic Acids Res (1985) 1.71
Ataluren (PTC124) induces cystic fibrosis transmembrane conductance regulator protein expression and activity in children with nonsense mutation cystic fibrosis. Am J Respir Crit Care Med (2010) 1.71
Correlation of sweat chloride concentration with classes of the cystic fibrosis transmembrane conductance regulator gene mutations. J Pediatr (1995) 1.70
Introducing sense into nonsense in treatments of human genetic diseases. Trends Genet (2008) 1.69
Hypoxic inhibition of nonsense-mediated RNA decay regulates gene expression and the integrated stress response. Mol Cell Biol (2008) 1.68
The unfolded protein response--a stress signaling pathway of the endoplasmic reticulum. J Chem Neuroanat (2004) 1.63
Aminoglycoside suppression at UAG, UAA and UGA codons in Escherichia coli and human tissue culture cells. Mol Gen Genet (1989) 1.59
Mutations in LPIN1 cause recurrent acute myoglobinuria in childhood. Am J Hum Genet (2008) 1.48
The efficiency of nonsense-mediated mRNA decay is an inherent character and varies among different cells. Eur J Hum Genet (2007) 1.48
Gentamicin administration in Duchenne patients with premature stop codon. Preliminary results. Acta Myol (2003) 1.48
Nonsense-mediated RNA decay regulation by cellular stress: implications for tumorigenesis. Mol Cancer Res (2010) 1.44
Sense from nonsense: therapies for premature stop codon diseases. Trends Mol Med (2012) 1.43
Inhibition of nonsense-mediated RNA decay by the tumor microenvironment promotes tumorigenesis. Mol Cell Biol (2011) 1.42
A pilot study of the effect of gentamicin on nasal potential difference measurements in cystic fibrosis patients carrying stop mutations. Am J Respir Crit Care Med (2000) 1.37
Eukaryotic ribosomal RNA determinants of aminoglycoside resistance and their role in translational fidelity. RNA (2007) 1.26
NMD: multitasking between mRNA surveillance and modulation of gene expression. Adv Genet (2008) 1.23
DHCR7 nonsense mutations and characterisation of mRNA nonsense mediated decay in Smith-Lemli-Opitz syndrome. J Med Genet (2005) 1.22
The unfolded protein response. Mol Biotechnol (2006) 1.16
How transmembrane proteins sense endoplasmic reticulum stress. Antioxid Redox Signal (2007) 1.14
Suppression of premature termination codons as a therapeutic approach. Crit Rev Biochem Mol Biol (2012) 1.13
Rescue of nonsense mutations by amlexanox in human cells. Orphanet J Rare Dis (2012) 1.13
The unfolded protein response in health and disease. Antioxid Redox Signal (2009) 1.10
Restoration of W1282X CFTR activity by enhanced expression. Am J Respir Cell Mol Biol (2007) 1.10
No detectable improvements in cystic fibrosis transmembrane conductance regulator by nasal aminoglycosides in patients with cystic fibrosis with stop mutations. Am J Respir Cell Mol Biol (2007) 1.08
Overexpression of the c-myc oncogene inhibits nonsense-mediated RNA decay in B lymphocytes. J Biol Chem (2011) 1.08
USP3 counteracts RNF168 via deubiquitinating H2A and γH2AX at lysine 13 and 15. Cell Cycle (2013) 1.07
The mechanism of cystic fibrosis transmembrane conductance regulator transcriptional repression during the unfolded protein response. J Biol Chem (2008) 1.06
Complementary cell-based high-throughput screens identify novel modulators of the unfolded protein response. J Biomol Screen (2011) 1.05
RNA surveillance is required for endoplasmic reticulum homeostasis. Proc Natl Acad Sci U S A (2012) 1.03
Gentamicin fails to increase dystrophin expression in dystrophin-deficient muscle. Muscle Nerve (2003) 1.02
Suppression of CFTR premature termination codons and rescue of CFTR protein and function by the synthetic aminoglycoside NB54. J Mol Med (Berl) (2011) 1.00
Cancer syndromes and therapy by stop-codon readthrough. Trends Mol Med (2012) 1.00
Transcriptional induction of the human asparagine synthetase gene during the unfolded protein response does not require the ATF6 and IRE1/XBP1 arms of the pathway. Biochem J (2009) 0.99
Readthrough of premature termination codons in the adenomatous polyposis coli gene restores its biological activity in human cancer cells. PLoS One (2011) 0.98
Airway epithelial inflammation-induced endoplasmic reticulum Ca2+ store expansion is mediated by X-box binding protein-1. J Biol Chem (2009) 0.95
Repair of UV photolesions in xeroderma pigmentosum group C cells induced by translational readthrough of premature termination codons. Proc Natl Acad Sci U S A (2013) 0.93
Role of endoplasmic reticulum stress in cystic fibrosis-related airway inflammatory responses. Proc Am Thorac Soc (2010) 0.89
SnapShot: Nonsense-mediated mRNA decay. Cell (2011) 0.88
R-domain interactions with distal regions of CFTR lead to phosphorylation and activation. Biochemistry (2000) 0.82
A novel therapeutic approach for genetic diseases by introduction of suppressor tRNA. Nucleic Acids Symp Ser (Oxf) (2006) 0.79
Activation of the unfolded protein response and alternative splicing of ATF6alpha in HLA-B27 positive lymphocytes. FEBS Lett (2007) 0.78
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol (2008) 38.00
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature (2002) 37.66
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
Mass spectrometry-based proteomics. Nature (2003) 28.94
Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell (2006) 20.92
Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science (2009) 20.49
miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev (2002) 19.24
Universal sample preparation method for proteome analysis. Nat Methods (2009) 16.88
In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc (2006) 16.56
Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res (2011) 14.82
Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal Chem (2003) 13.58
Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc (2007) 10.71
Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics (2005) 10.67
Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol Cell Proteomics (2005) 10.60
Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature (2008) 10.28
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24
Proteomic characterization of the human centrosome by protein correlation profiling. Nature (2003) 8.74
A CFTR potentiator in patients with cystic fibrosis and the G551D mutation. N Engl J Med (2011) 8.73
Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal (2010) 8.61
Cystic fibrosis. N Engl J Med (2005) 8.09
Mass spectrometry-based proteomics turns quantitative. Nat Chem Biol (2005) 7.52
Nucleolar proteome dynamics. Nature (2005) 7.32
Directed proteomic analysis of the human nucleolus. Curr Biol (2002) 7.04
Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics. Proc Natl Acad Sci U S A (2003) 6.87
Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell (2003) 6.77
Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell (2007) 6.62
Mechanism of regulation of WAVE1-induced actin nucleation by Rac1 and Nck. Nature (2002) 6.26
Effect of VX-770 in persons with cystic fibrosis and the G551D-CFTR mutation. N Engl J Med (2010) 6.23
Large-scale proteomic analysis of the human spliceosome. Genome Res (2002) 5.75
Specificity in Toll-like receptor signalling through distinct effector functions of TRAF3 and TRAF6. Nature (2005) 5.72
Lumacaftor-Ivacaftor in Patients with Cystic Fibrosis Homozygous for Phe508del CFTR. N Engl J Med (2015) 5.51
Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature (2002) 5.48
Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol (2011) 5.48
Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle. Mol Cell (2008) 5.38
Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat Biotechnol (2004) 5.22
A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat Protoc (2006) 5.21
Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol Cell Proteomics (2005) 5.07
Higher-energy C-trap dissociation for peptide modification analysis. Nat Methods (2007) 5.04
SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell (2008) 5.02
Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors. Proc Natl Acad Sci U S A (2003) 4.87
A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics. Nat Protoc (2009) 4.84
Nucleotide deficiency promotes genomic instability in early stages of cancer development. Cell (2011) 4.83
Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol Cell Proteomics (2004) 4.79
Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli. Cell (2005) 4.78
A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed. Mol Cell Proteomics (2009) 4.75
PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. Genome Biol (2007) 4.66
A mammalian organelle map by protein correlation profiling. Cell (2006) 4.54
Gentamicin-induced correction of CFTR function in patients with cystic fibrosis and CFTR stop mutations. N Engl J Med (2003) 4.43
A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Mol Cell Proteomics (2011) 4.40
Effectiveness of PTC124 treatment of cystic fibrosis caused by nonsense mutations: a prospective phase II trial. Lancet (2008) 4.35
Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell (2010) 4.31
The ABC's (and XYZ's) of peptide sequencing. Nat Rev Mol Cell Biol (2004) 4.24
Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21
Paraspeckles: a novel nuclear domain. Curr Biol (2002) 4.19
Quantitative proteomics reveals subset-specific viral recognition in dendritic cells. Immunity (2010) 4.03
Axin-mediated CKI phosphorylation of beta-catenin at Ser 45: a molecular switch for the Wnt pathway. Genes Dev (2002) 3.80
The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins. Genome Biol (2006) 3.79
Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics (2008) 3.78
Decoding signalling networks by mass spectrometry-based proteomics. Nat Rev Mol Cell Biol (2010) 3.78
Proteome analysis of separated male and female gametocytes reveals novel sex-specific Plasmodium biology. Cell (2005) 3.77
Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer. Mol Cell Proteomics (2011) 3.75
Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. J Cell Biol (2010) 3.61
Precision mapping of an in vivo N-glycoproteome reveals rigid topological and sequence constraints. Cell (2010) 3.60
Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5,111 proteins. Mol Cell Proteomics (2007) 3.60
Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. Mol Cell Proteomics (2012) 3.57
Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome. J Proteome Res (2009) 3.56
Analysis of nucleolar protein dynamics reveals the nuclear degradation of ribosomal proteins. Curr Biol (2007) 3.55
A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat Biotechnol (2003) 3.54
A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility. Cell (2013) 3.53
More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J Proteome Res (2011) 3.53
System-wide changes to SUMO modifications in response to heat shock. Sci Signal (2009) 3.50
Phosphotyrosine interactome of the ErbB-receptor kinase family. Mol Syst Biol (2005) 3.48
Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc Natl Acad Sci U S A (2004) 3.43
Mass spectrometric-based approaches in quantitative proteomics. Methods (2003) 3.38
Mechanism of divergent growth factor effects in mesenchymal stem cell differentiation. Science (2005) 3.37
Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. Genome Biol (2006) 3.34
Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation. Nature (2007) 3.32
Nucleosome-interacting proteins regulated by DNA and histone methylation. Cell (2010) 3.25
Quantitative, high-resolution proteomics for data-driven systems biology. Annu Rev Biochem (2011) 3.19
Chromatin-Remodeling Components of the BAF Complex Facilitate Reprogramming. Cell (2010) 3.08
Human chromosome 7: DNA sequence and biology. Science (2003) 3.02
ERCC1/XPF removes the 3' overhang from uncapped telomeres and represses formation of telomeric DNA-containing double minute chromosomes. Mol Cell (2003) 3.01
Defining the transcriptome and proteome in three functionally different human cell lines. Mol Syst Biol (2010) 3.00
Regulation of ubiquitin-binding proteins by monoubiquitination. Nat Cell Biol (2006) 2.99
Decoding human cytomegalovirus. Science (2012) 2.98
Super-SILAC mix for quantitative proteomics of human tumor tissue. Nat Methods (2010) 2.95
Is proteomics the new genomics? Cell (2007) 2.92
Mass spectrometry in high-throughput proteomics: ready for the big time. Nat Methods (2010) 2.91
Results of a phase IIa study of VX-809, an investigational CFTR corrector compound, in subjects with cystic fibrosis homozygous for the F508del-CFTR mutation. Thorax (2011) 2.84
Robust Salmonella metabolism limits possibilities for new antimicrobials. Nature (2006) 2.78
System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap. Mol Cell Proteomics (2011) 2.77
Peptide separation with immobilized pI strips is an attractive alternative to in-gel protein digestion for proteome analysis. Proteomics (2008) 2.76
On the proper use of mass accuracy in proteomics. Mol Cell Proteomics (2006) 2.76
From genomics to proteomics. Nature (2003) 2.70
Reduced histone deacetylase 7 activity restores function to misfolded CFTR in cystic fibrosis. Nat Chem Biol (2009) 2.70