Published in Nucleic Acids Res on May 22, 2015
Translation of poly(A) tails leads to precise mRNA cleavage. RNA (2017) 0.77
RNA damage in biological conflicts and the diversity of responding RNA repair systems. Nucleic Acids Res (2016) 0.75
Putative RNA-Directed Adaptive Mutations in Cancer Evolution. Transcription (2016) 0.75
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics (2010) 53.23
Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63
The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99
Signal integration in the endoplasmic reticulum unfolded protein response. Nat Rev Mol Cell Biol (2007) 33.06
Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods (2010) 9.09
Decay of endoplasmic reticulum-localized mRNAs during the unfolded protein response. Science (2006) 6.75
The UCSC Genome Browser database: 2014 update. Nucleic Acids Res (2013) 6.54
The transmembrane kinase Ire1p is a site-specific endonuclease that initiates mRNA splicing in the unfolded protein response. Cell (1997) 6.26
Genome-wide measurement of RNA secondary structure in yeast. Nature (2010) 5.74
Relationship between internucleotide linkage geometry and the stability of RNA. RNA (1999) 5.01
tRNA ligase is required for regulated mRNA splicing in the unfolded protein response. Cell (1996) 4.93
Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation. Nature (2006) 4.89
The tails of ubiquitin precursors are ribosomal proteins whose fusion to ubiquitin facilitates ribosome biogenesis. Nature (1989) 4.70
The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc (2012) 4.41
S. cerevisiae encodes an essential protein homologous in sequence and function to mammalian BiP. Cell (1989) 4.28
Counting absolute numbers of molecules using unique molecular identifiers. Nat Methods (2011) 4.18
Mechanism of action of a yeast RNA ligase in tRNA splicing. Cell (1983) 3.78
Synthetic spike-in standards for RNA-seq experiments. Genome Res (2011) 3.58
A ribosome-bound quality control complex triggers degradation of nascent peptides and signals translation stress. Cell (2012) 3.27
The human RNA kinase hClp1 is active on 3' transfer RNA exons and short interfering RNAs. Nature (2007) 2.84
Mechanism of non-spliceosomal mRNA splicing in the unfolded protein response pathway. EMBO J (1999) 2.84
Processing of the precursors to small nucleolar RNAs and rRNAs requires common components. Mol Cell Biol (1998) 2.80
The RNase Rny1p cleaves tRNAs and promotes cell death during oxidative stress in Saccharomyces cerevisiae. J Cell Biol (2009) 2.61
Saccharomyces cerevisiae tRNA ligase. Purification of the protein and isolation of the structural gene. J Biol Chem (1986) 2.42
Dom34 rescues ribosomes in 3' untranslated regions. Cell (2014) 2.38
Human pre-mRNA cleavage factor II(m) contains homologs of yeast proteins and bridges two other cleavage factors. EMBO J (2000) 2.33
Electrostatics in the ribosomal tunnel modulate chain elongation rates. J Mol Biol (2008) 2.32
Nascent peptide-dependent translation arrest leads to Not4p-mediated protein degradation by the proteasome. J Biol Chem (2009) 2.25
The yeast tRNA splicing endonuclease: a tetrameric enzyme with two active site subunits homologous to the archaeal tRNA endonucleases. Cell (1997) 2.12
Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome. Nat Protoc (2009) 2.12
Translation of the poly(A) tail plays crucial roles in nonstop mRNA surveillance via translation repression and protein destabilization by proteasome in yeast. Genes Dev (2007) 2.04
Translation drives mRNA quality control. Nat Struct Mol Biol (2012) 1.97
Small self-cleaving ribozymes. Cold Spring Harb Perspect Biol (2010) 1.79
The final step in the formation of 25S rRNA in Saccharomyces cerevisiae is performed by 5'-->3' exonucleases. RNA (2000) 1.65
Dom34:hbs1 plays a general role in quality-control systems by dissociation of a stalled ribosome at the 3' end of aberrant mRNA. Mol Cell (2012) 1.61
CapSeq and CIP-TAP identify Pol II start sites and reveal capped small RNAs as C. elegans piRNA precursors. Cell (2012) 1.61
Novel mechanism of RNA repair by RtcB via sequential 2',3'-cyclic phosphodiesterase and 3'-Phosphate/5'-hydroxyl ligation reactions. J Biol Chem (2011) 1.60
RtcB, a novel RNA ligase, can catalyze tRNA splicing and HAC1 mRNA splicing in vivo. J Biol Chem (2011) 1.53
A widespread self-cleaving ribozyme class is revealed by bioinformatics. Nat Chem Biol (2013) 1.42
CLP1 links tRNA metabolism to progressive motor-neuron loss. Nature (2013) 1.41
Human CLP1 mutations alter tRNA biogenesis, affecting both peripheral and central nervous system function. Cell (2014) 1.40
T2 Family ribonucleases: ancient enzymes with diverse roles. Trends Biochem Sci (2010) 1.33
CLP1 founder mutation links tRNA splicing and maturation to cerebellar development and neurodegeneration. Cell (2014) 1.33
Two distinct recognition signals define the site of endonucleolytic cleavage at the 5'-end of yeast 18S rRNA. EMBO J (1995) 1.32
Getting RIDD of RNA: IRE1 in cell fate regulation. Trends Biochem Sci (2014) 1.30
The unfolded protein response in fission yeast modulates stability of select mRNAs to maintain protein homeostasis. Elife (2012) 1.29
Genome-scale approaches for discovering novel nonconventional splicing substrates of the Ire1 nuclease. Genome Biol (2004) 1.28
5'-exoribonuclease 1: Xrn1. Methods Enzymol (2001) 1.23
Yeast unfolded protein response pathway regulates expression of genes for anti-oxidative stress and for cell surface proteins. Genes Cells (2006) 1.13
Release of U18 snoRNA from its host intron requires interaction of Nop1p with the Rnt1p endonuclease. EMBO J (2001) 1.11
Global analysis of mRNA decay intermediates in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2012) 1.10
Linear ubiquitin fusion to Rps31 and its subsequent cleavage are required for the efficient production and functional integrity of 40S ribosomal subunits. Mol Microbiol (2009) 1.07
An RNA-seq method for defining endoribonuclease cleavage specificity identifies dual rRNA substrates for toxin MazF-mt3. Nat Commun (2014) 1.05
Rewriting the rules for end joining via enzymatic splicing of DNA 3'-PO4 and 5'-OH ends. Proc Natl Acad Sci U S A (2013) 1.02
Capture and sequence analysis of RNAs with terminal 2',3'-cyclic phosphates. RNA (2010) 1.01
Ribosomal readthrough at a short UGA stop codon context triggers dual localization of metabolic enzymes in Fungi and animals. PLoS Genet (2014) 0.98
Ire1 has distinct catalytic mechanisms for XBP1/HAC1 splicing and RIDD. Cell Rep (2014) 0.95
Analysis of stranded information using an automated procedure for strand specific RNA sequencing. BMC Genomics (2014) 0.94
Ribonuclease L and metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs. Nucleic Acids Res (2014) 0.92
Distinctive kinetics and substrate specificities of plant and fungal tRNA ligases. RNA (2014) 0.90
tRNA ligase catalyzes the GTP-dependent ligation of RNA with 3'-phosphate and 5'-hydroxyl termini. Biochemistry (2012) 0.88
RNase L targets distinct sites in influenza A virus RNAs. J Virol (2014) 0.85
Healing for destruction: tRNA intron degradation in yeast is a two-step cytoplasmic process catalyzed by tRNA ligase Rlg1 and 5'-to-3' exonuclease Xrn1. Genes Dev (2014) 0.82
Cellular mRNAs access second ORFs using a novel amino acid sequence-dependent coupled translation termination-reinitiation mechanism. RNA (2014) 0.80
Bacteriophage T4 polynucleotide kinase triggers degradation of mRNAs. Proc Natl Acad Sci U S A (2012) 0.79