Published in PLoS Genet on June 19, 2009
Modelling and simulating generic RNA-Seq experiments with the flux simulator. Nucleic Acids Res (2012) 4.81
Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Res (2011) 2.26
The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus. Cell (2012) 1.88
Autoregulation of the nonsense-mediated mRNA decay pathway in human cells. RNA (2011) 1.76
Interplay between gene expression noise and regulatory network architecture. Trends Genet (2012) 1.61
Evidence of abundant stop codon readthrough in Drosophila and other metazoa. Genome Res (2011) 1.60
Smg1 is required for embryogenesis and regulates diverse genes via alternative splicing coupled to nonsense-mediated mRNA decay. Proc Natl Acad Sci U S A (2010) 1.59
Statistical Modeling of RNA-Seq Data. Stat Sci (2011) 1.49
The function of introns. Front Genet (2012) 1.42
Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay. Genome Res (2013) 1.39
The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels. PLoS Genet (2012) 1.25
Nonsense-mediated decay enables intron gain in Drosophila. PLoS Genet (2010) 1.17
Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function. Mol Biol Evol (2012) 1.12
Expression proteomics of UPF1 knockdown in HeLa cells reveals autoregulation of hnRNP A2/B1 mediated by alternative splicing resulting in nonsense-mediated mRNA decay. BMC Genomics (2010) 1.07
The origins, evolution, and functional potential of alternative splicing in vertebrates. Mol Biol Evol (2011) 1.05
Genome-wide analysis of Staufen-associated mRNAs identifies secondary structures that confer target specificity. Nucleic Acids Res (2013) 1.04
Genome-wide detection of condition-sensitive alternative splicing in Arabidopsis roots. Plant Physiol (2013) 1.03
Cytoplasmic and nuclear quality control and turnover of single-stranded RNA modulate post-transcriptional gene silencing in plants. Nucleic Acids Res (2013) 1.00
Widespread polymorphism in the positions of stop codons in Drosophila melanogaster. Genome Biol Evol (2011) 0.91
Regulation of splicing factors by alternative splicing and NMD is conserved between kingdoms yet evolutionarily flexible. Mol Biol Evol (2015) 0.89
Nonsense-mediated RNA decay--a switch and dial for regulating gene expression. Bioessays (2015) 0.89
DHX34 and NBAS form part of an autoregulatory NMD circuit that regulates endogenous RNA targets in human cells, zebrafish and Caenorhabditis elegans. Nucleic Acids Res (2013) 0.89
Global transcriptome analysis of the scorpion Centruroides noxius: new toxin families and evolutionary insights from an ancestral scorpion species. PLoS One (2012) 0.89
RNA secondary structure mediates alternative 3'ss selection in Saccharomyces cerevisiae. RNA (2012) 0.88
Polypyrimidine tract binding protein 1 protects mRNAs from recognition by the nonsense-mediated mRNA decay pathway. Elife (2016) 0.88
Is there a classical nonsense-mediated decay pathway in trypanosomes? PLoS One (2011) 0.88
Regulation of natural mRNAs by the nonsense-mediated mRNA decay pathway. Eukaryot Cell (2014) 0.88
The importance of identifying alternative splicing in vertebrate genome annotation. Database (Oxford) (2012) 0.87
Diverse forms of RPS9 splicing are part of an evolving autoregulatory circuit. PLoS Genet (2012) 0.87
In vivo determination of direct targets of the nonsense-mediated decay pathway in Drosophila. G3 (Bethesda) (2014) 0.86
A mild form of SLC29A3 disorder: a frameshift deletion leads to the paradoxical translation of an otherwise noncoding mRNA splice variant. PLoS One (2012) 0.85
Intron retention in the Drosophila melanogaster Rieske Iron Sulphur Protein gene generated a new protein. Nat Commun (2011) 0.83
The role of canonical and noncanonical pre-mRNA splicing in plant stress responses. Biomed Res Int (2012) 0.80
Effects of premature termination codon polymorphisms in the Drosophila pseudoobscura subclade. J Mol Evol (2012) 0.80
Evolutionarily conserved autoregulation of alternative pre-mRNA splicing by ribosomal protein L10a. Nucleic Acids Res (2016) 0.77
Non-coding functions of alternative pre-mRNA splicing in development. Semin Cell Dev Biol (2015) 0.77
A role for the membrane protein M6 in the Drosophila visual system. BMC Neurosci (2012) 0.76
Drosophila intersex orthologue in the silkworm, Bombyx mori and related species. Genetica (2010) 0.76
How do RNA sequence, DNA sequence, and chromatin properties regulate splicing? F1000 Biol Rep (2010) 0.76
20-hydroxyecdysone mediates non-canonical regulation of mosquito vitellogenins through alternative splicing. Insect Mol Biol (2014) 0.75
Androgen Receptor Splice Variants Are Not Substrates of Nonsense-Mediated Decay. Prostate (2017) 0.75
The role of nucleotide composition in premature termination codon recognition. BMC Bioinformatics (2016) 0.75
Transcriptome-wide identification of NMD-targeted human mRNAs reveals extensive redundancy between SMG6- and SMG7-mediated degradation pathways. RNA (2016) 0.75
Bioconductor: open software development for computational biology and bioinformatics. Genome Biol (2004) 143.19
Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol (1994) 37.96
The scanning model for translation: an update. J Cell Biol (1989) 31.23
Predictive identification of exonic splicing enhancers in human genes. Science (2002) 16.86
AmiGO: online access to ontology and annotation data. Bioinformatics (2008) 10.77
Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc Natl Acad Sci U S A (2002) 10.28
A rule for termination-codon position within intron-containing genes: when nonsense affects RNA abundance. Trends Biochem Sci (1998) 9.06
A comparison of background correction methods for two-colour microarrays. Bioinformatics (2007) 8.59
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res (2006) 8.36
The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions. EMBO J (2000) 7.54
Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature (2007) 7.12
Pushing the limits of the scanning mechanism for initiation of translation. Gene (2002) 6.47
Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat Genet (2004) 6.14
Genes required for mitotic spindle assembly in Drosophila S2 cells. Science (2007) 5.58
A gene expression map for the euchromatic genome of Drosophila melanogaster. Science (2004) 5.38
Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function. Genes Dev (2007) 4.97
Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes Dev (2007) 4.75
The RNA binding protein Pub1 modulates the stability of transcripts containing upstream open reading frames. Cell (2000) 4.59
Sex-lethal, a Drosophila sex determination switch gene, exhibits sex-specific RNA splicing and sequence similarity to RNA binding proteins. Cell (1988) 4.52
Autoregulation of polypyrimidine tract binding protein by alternative splicing leading to nonsense-mediated decay. Mol Cell (2004) 4.13
Mammalian Staufen1 recruits Upf1 to specific mRNA 3'UTRs so as to elicit mRNA decay. Cell (2005) 4.02
Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways. EMBO J (2003) 3.68
SC35 autoregulates its expression by promoting splicing events that destabilize its mRNAs. EMBO J (2001) 3.55
Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression. Genes Dev (2006) 3.18
Alternative splicing resulting in nonsense-mediated mRNA decay: what is the meaning of nonsense? Trends Biochem Sci (2008) 2.64
Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets. RNA (2005) 2.59
Identification and characterization of a sequence motif involved in nonsense-mediated mRNA decay. Mol Cell Biol (1995) 2.31
Regulation of multiple core spliceosomal proteins by alternative splicing-coupled nonsense-mediated mRNA decay. Mol Cell Biol (2008) 2.25
Dscam diversity is essential for neuronal wiring and self-recognition. Nature (2007) 2.18
Staufen1 regulates diverse classes of mammalian transcripts. EMBO J (2007) 2.18
A conserved role for cytoplasmic poly(A)-binding protein 1 (PABPC1) in nonsense-mediated mRNA decay. EMBO J (2007) 2.11
Nonsense-mediated mRNA decay: Target genes and functional diversification of effectors. Trends Biochem Sci (2006) 2.07
Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila. Genes Dev (2005) 2.03
Looking at mRNA decay pathways through the window of molecular evolution. Curr Opin Genet Dev (2003) 1.86
Widespread impact of nonsense-mediated mRNA decay on the yeast intronome. Mol Cell (2008) 1.72
Inferring global levels of alternative splicing isoforms using a generative model of microarray data. Bioinformatics (2006) 1.72
mRNA surveillance mitigates genetic dominance in Caenorhabditis elegans. Mol Gen Genet (1998) 1.58
Sex-specific expression of alternative transcripts in Drosophila. Genome Biol (2006) 1.53
Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members. Mol Cell (2009) 1.52
Alternative splicing and nonsense-mediated mRNA decay regulate mammalian ribosomal gene expression. Nucleic Acids Res (2005) 1.48
Alternative splicing regulation during C. elegans development: splicing factors as regulated targets. PLoS Genet (2008) 1.41
Auto- and cross-regulation of the hnRNP L proteins by alternative splicing. Mol Cell Biol (2009) 1.41
Identification of Drosophila mitotic genes by combining co-expression analysis and RNA interference. PLoS Genet (2008) 1.41
The odyssey of a regulated transcript. RNA (2000) 1.17
Polyamine-regulated unproductive splicing and translation of spermidine/spermine N1-acetyltransferase. RNA (2006) 1.07
Overexpression of poly(A)-binding protein down-regulates the translation or the abundance of its own mRNA. FEBS Lett (1999) 1.03
Technologies for the global discovery and analysis of alternative splicing. Adv Exp Med Biol (2007) 0.99
A Hox gene mutation that triggers nonsense-mediated RNA decay and affects alternative splicing during Drosophila development. Nucleic Acids Res (2003) 0.90
The SR family proteins B52 and dASF/SF2 modulate development of the Drosophila visual system by regulating specific RNA targets. Mol Cell Biol (2007) 0.89
Bioconductor: open software development for computational biology and bioinformatics. Genome Biol (2004) 143.19
WebLogo: a sequence logo generator. Genome Res (2004) 59.58
The Bioperl toolkit: Perl modules for the life sciences. Genome Res (2002) 58.63
Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res (2002) 40.03
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics (2010) 19.86
SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res (2002) 18.11
SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res (2004) 15.21
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol (2007) 13.99
Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res (2007) 13.44
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
The developmental transcriptome of Drosophila melanogaster. Nature (2010) 11.85
Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell (2011) 10.56
Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc Natl Acad Sci U S A (2002) 10.28
The ASTRAL Compendium in 2004. Nucleic Acids Res (2004) 10.03
Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat Rev Genet (2011) 9.79
Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res (2010) 9.08
Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature (2010) 8.99
mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. Genes Dev (2006) 8.78
Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res (2011) 8.38
P bodies: at the crossroads of post-transcriptional pathways. Nat Rev Mol Cell Biol (2007) 7.96
A high-coverage genome sequence from an archaic Denisovan individual. Science (2012) 7.89
Getting to the root of miRNA-mediated gene silencing. Cell (2008) 7.17
Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature (2007) 7.12
Diversity, topographic differentiation, and positional memory in human fibroblasts. Proc Natl Acad Sci U S A (2002) 6.98
Gene expression patterns in human liver cancers. Mol Biol Cell (2002) 6.93
Patterns of damage in genomic DNA sequences from a Neandertal. Proc Natl Acad Sci U S A (2007) 6.12
A fine-scale linkage-disequilibrium measure based on length of haplotype sharing. Am J Hum Genet (2006) 6.02
Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science (2009) 5.79
GW182 interaction with Argonaute is essential for miRNA-mediated translational repression and mRNA decay. Nat Struct Mol Biol (2008) 5.57
The impact of structural genomics: expectations and outcomes. Science (2006) 5.30
A crucial role for GW182 and the DCP1:DCP2 decapping complex in miRNA-mediated gene silencing. RNA (2005) 5.15
Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain. Nature (2003) 4.92
P-body formation is a consequence, not the cause, of RNA-mediated gene silencing. Mol Cell Biol (2007) 4.90
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
Nonsense-mediated mRNA decay: molecular insights and mechanistic variations across species. Curr Opin Cell Biol (2005) 4.45
ASTRAL compendium enhancements. Nucleic Acids Res (2002) 4.43
Nucleic acid 3'-end recognition by the Argonaute2 PAZ domain. Nat Struct Mol Biol (2004) 4.38
GenomeGraphs: integrated genomic data visualization with R. BMC Bioinformatics (2009) 4.16
Deadenylation is a widespread effect of miRNA regulation. RNA (2008) 3.98
Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing. Genes Dev (2007) 3.92
GC-content normalization for RNA-Seq data. BMC Bioinformatics (2011) 3.89
Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proc Natl Acad Sci U S A (2002) 3.85
Genome-wide analysis of mRNAs regulated by Drosha and Argonaute proteins in Drosophila melanogaster. Mol Cell Biol (2006) 3.80
Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species. PLoS Genet (2008) 3.69
Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways. EMBO J (2003) 3.68
The RNA Ontology Consortium: an open invitation to the RNA community. RNA (2006) 3.60
The derived FOXP2 variant of modern humans was shared with Neandertals. Curr Biol (2007) 3.39
Protein molecular function prediction by Bayesian phylogenomics. PLoS Comput Biol (2005) 3.14
Decay of mRNAs targeted by RISC requires XRN1, the Ski complex, and the exosome. RNA (2005) 3.11
Aicardi-Goutieres syndrome and related phenotypes: linking nucleic acid metabolism with autoimmunity. Hum Mol Genet (2009) 3.07
SMG7 acts as a molecular link between mRNA surveillance and mRNA decay. Mol Cell (2004) 3.05
The evolving roles of alternative splicing. Curr Opin Struct Biol (2004) 2.99
An eIF4AIII-containing complex required for mRNA localization and nonsense-mediated mRNA decay. Nature (2004) 2.95
Survival ensembles. Biostatistics (2005) 2.88
GW182 proteins directly recruit cytoplasmic deadenylase complexes to miRNA targets. Mol Cell (2011) 2.80
Nonsense-mediated messenger RNA decay is initiated by endonucleolytic cleavage in Drosophila. Nature (2004) 2.80
SCOR: a Structural Classification of RNA database. Nucleic Acids Res (2002) 2.79
PatMaN: rapid alignment of short sequences to large databases. Bioinformatics (2008) 2.77
Drosophila melanogaster MNK/Chk2 and p53 regulate multiple DNA repair and apoptotic pathways following DNA damage. Mol Cell Biol (2004) 2.75
SMG7 is a 14-3-3-like adaptor in the nonsense-mediated mRNA decay pathway. Mol Cell (2005) 2.71
Genome-wide analysis of mRNAs regulated by the THO complex in Drosophila melanogaster. Nat Struct Mol Biol (2004) 2.70
The structural basis for the interaction between nonsense-mediated mRNA decay factors UPF2 and UPF3. Nat Struct Mol Biol (2004) 2.65
The shaping of modern human immune systems by multiregional admixture with archaic humans. Science (2011) 2.63
Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets. RNA (2005) 2.59
REF1/Aly and the additional exon junction complex proteins are dispensable for nuclear mRNA export. J Cell Biol (2002) 2.55
SMG6 is the catalytic endonuclease that cleaves mRNAs containing nonsense codons in metazoan. RNA (2008) 2.54
Stage II colon cancer prognosis prediction by tumor gene expression profiling. J Clin Oncol (2006) 2.49
Targeted investigation of the Neandertal genome by array-based sequence capture. Science (2010) 2.49
Conservation of an RNA regulatory map between Drosophila and mammals. Genome Res (2010) 2.43
The GW182 protein family in animal cells: new insights into domains required for miRNA-mediated gene silencing. RNA (2009) 2.37
Activation of MDA5 requires higher-order RNA structures generated during virus infection. J Virol (2009) 2.37
The superhelical TPR-repeat domain of O-linked GlcNAc transferase exhibits structural similarities to importin alpha. Nat Struct Mol Biol (2004) 2.36
An unappreciated role for RNA surveillance. Genome Biol (2004) 2.28
The silencing domain of GW182 interacts with PABPC1 to promote translational repression and degradation of microRNA targets and is required for target release. Mol Cell Biol (2009) 2.28
Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature (2005) 2.27
Planning the human variome project: the Spain report. Hum Mutat (2009) 2.22
mRNA quality control: an ancient machinery recognizes and degrades mRNAs with nonsense codons. FEBS Lett (2007) 2.22
SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures. Nucleic Acids Res (2013) 2.22
Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears. Mol Ecol (2015) 2.19
SAMHD1 is mutated recurrently in chronic lymphocytic leukemia and is involved in response to DNA damage. Blood (2013) 2.18
Structures of the PIN domains of SMG6 and SMG5 reveal a nuclease within the mRNA surveillance complex. EMBO J (2006) 2.16
A conserved role for cytoplasmic poly(A)-binding protein 1 (PABPC1) in nonsense-mediated mRNA decay. EMBO J (2007) 2.11
A novel mode of RBD-protein recognition in the Y14-Mago complex. Nat Struct Biol (2003) 2.11
The C-terminal domains of human TNRC6A, TNRC6B, and TNRC6C silence bound transcripts independently of Argonaute proteins. RNA (2009) 2.11
A C-terminal silencing domain in GW182 is essential for miRNA function. RNA (2009) 2.10