Published in RNA on June 01, 2005
New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA. RNA (2007) 1.98
The splicing factor Prp43p, a DEAH box ATPase, functions in ribosome biogenesis. Mol Cell Biol (2006) 1.70
The 3D rRNA modification maps database: with interactive tools for ribosome analysis. Nucleic Acids Res (2007) 1.65
A computational screen for mammalian pseudouridylation guide H/ACA RNAs. RNA (2006) 1.52
H/ACA small nucleolar RNA pseudouridylation pockets bind substrate RNA to form three-way junctions that position the target U for modification. Proc Natl Acad Sci U S A (2007) 1.19
Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs. Nucleic Acids Res (2006) 1.11
An interaction between two RNA binding proteins, Nab2 and Pub1, links mRNA processing/export and mRNA stability. Mol Cell Biol (2007) 0.99
A novel experimental approach for systematic identification of box H/ACA snoRNAs from eukaryotes. Nucleic Acids Res (2005) 0.96
SnoRNAs from the filamentous fungus Neurospora crassa: structural, functional and evolutionary insights. BMC Genomics (2009) 0.96
Functionality and substrate specificity of human box H/ACA guide RNAs. RNA (2008) 0.94
RNA-based 5-fluorouracil toxicity requires the pseudouridylation activity of Cbf5p. Genetics (2008) 0.93
Genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in Leishmania major indicates conservation among trypanosomatids in the repertoire and in their rRNA targets. Eukaryot Cell (2006) 0.88
Different mechanisms for pseudouridine formation in yeast 5S and 5.8S rRNAs. Mol Cell Biol (2008) 0.84
Psiscan: a computational approach to identify H/ACA-like and AGA-like non-coding RNA in trypanosomatid genomes. BMC Bioinformatics (2008) 0.84
The spatial-functional coupling of box C/D and C'/D' RNPs is an evolutionarily conserved feature of the eukaryotic box C/D snoRNP nucleotide modification complex. Mol Cell Biol (2010) 0.80
Cell cycle-dependent transcription factors control the expression of yeast telomerase RNA. RNA (2013) 0.79
Fisher: a program for the detection of H/ACA snoRNAs using MFE secondary structure prediction and comparative genomics - assessment and update. BMC Res Notes (2008) 0.77
Identification and characterisation of non-coding small RNAs in the pathogenic filamentous fungus Trichophyton rubrum. BMC Genomics (2013) 0.77
Genetic interactions show the importance of rRNA modification machinery for the role of Rps15p during ribosome biogenesis in S. cerevisiae. PLoS One (2010) 0.77
Phylogenetic distribution of plant snoRNA families. BMC Genomics (2016) 0.75
Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast (1998) 48.29
Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature (2002) 45.19
The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods (2001) 15.37
Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs. Cell (1997) 10.71
Genome evolution in yeasts. Nature (2004) 10.50
'DNA Strider': a 'C' program for the fast analysis of DNA and protein sequences on the Apple Macintosh family of computers. Nucleic Acids Res (1988) 9.48
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Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions. Cell (2002) 6.62
A yeast small nuclear RNA is required for normal processing of pre-ribosomal RNA. EMBO J (1987) 6.26
The expanding snoRNA world. Biochimie (2002) 6.10
Small nucleolar RNAs direct site-specific synthesis of pseudouridine in ribosomal RNA. Cell (1997) 5.60
The RNA world of the nucleolus: two major families of small RNAs defined by different box elements with related functions. Cell (1996) 5.14
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The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation. Genes Dev (1997) 4.26
rRNA modifications and ribosome function. Trends Biochem Sci (2002) 4.01
Yeast snR30 is a small nucleolar RNA required for 18S rRNA synthesis. Mol Cell Biol (1993) 3.47
Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome. Nucleic Acids Res (2004) 2.94
Targeted mRNA degradation by deadenylation-independent decapping. Mol Cell (2004) 2.76
Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebacteria, mitochondria and chloroplasts. J Mol Biol (1997) 2.74
Nog2p, a putative GTPase associated with pre-60S subunits and required for late 60S maturation steps. EMBO J (2001) 2.44
Analysis of the yeast genome: identification of new non-coding and small ORF-containing RNAs. Nucleic Acids Res (1997) 2.40
Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics. Nucleic Acids Res (2003) 2.15
Genome-wide location of yeast RNA polymerase III transcription machinery. EMBO J (2003) 2.15
Clustering of pseudouridine residues around the peptidyltransferase center of yeast cytoplasmic and mitochondrial ribosomes. Biochemistry (1994) 1.99
Elements essential for accumulation and function of small nucleolar RNAs directing site-specific pseudouridylation of ribosomal RNAs. EMBO J (1999) 1.93
The ribosomal protein Rps15p is required for nuclear exit of the 40S subunit precursors in yeast. EMBO J (2004) 1.77
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The pseudouridine residues of ribosomal RNA. Biochem Cell Biol (1996) 1.58
Accumulation of H/ACA snoRNPs depends on the integrity of the conserved central domain of the RNA-binding protein Nhp2p. Nucleic Acids Res (2001) 1.37
Mapping of the 13 pseudouridine residues in Saccharomyces cerevisiae small subunit ribosomal RNA to nucleotide resolution. Nucleic Acids Res (1995) 1.27
A snoRNA that guides the two most conserved pseudouridine modifications within rRNA confers a growth advantage in yeast. RNA (2003) 1.22
Gar1p binds to the small nucleolar RNAs snR10 and snR30 in vitro through a nontypical RNA binding element. J Biol Chem (1998) 1.21
Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell (2005) 8.55
RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell (2005) 7.37
Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature (2009) 4.96
Human L1 element target-primed reverse transcription in vitro. EMBO J (2002) 3.54
Nuclear architecture and spatial positioning help establish transcriptional states of telomeres in yeast. Nat Cell Biol (2002) 3.16
Nuclear retention of unspliced mRNAs in yeast is mediated by perinuclear Mlp1. Cell (2004) 2.96
Staphylococcus aureus RNAIII and the endoribonuclease III coordinately regulate spa gene expression. EMBO J (2005) 2.95
Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism. Genes Dev (2007) 2.86
Targeted mRNA degradation by deadenylation-independent decapping. Mol Cell (2004) 2.76
THO/Sub2p functions to coordinate 3'-end processing with gene-nuclear pore association. Cell (2008) 2.58
Growth-regulated recruitment of the essential yeast ribosomal protein gene activator Ifh1. Nature (2004) 2.51
Tandem bromodomains in the chromatin remodeler RSC recognize acetylated histone H3 Lys14. EMBO J (2004) 2.46
Sequential protein association with nascent 60S ribosomal particles. Mol Cell Biol (2003) 2.40
GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. Bioinformatics (2006) 2.37
Sulfur sparing in the yeast proteome in response to sulfur demand. Mol Cell (2002) 2.27
Genome-wide location of the coactivator mediator: Binding without activation and transient Cdk8 interaction on DNA. Mol Cell (2006) 2.16
Genome-wide location of yeast RNA polymerase III transcription machinery. EMBO J (2003) 2.15
A high resolution protein interaction map of the yeast Mediator complex. Nucleic Acids Res (2004) 2.15
Mediator-dependent recruitment of TFIIH modules in preinitiation complex. Mol Cell (2008) 1.88
Linking functionally related genes by sensitive and quantitative characterization of genetic interaction profiles. Proc Natl Acad Sci U S A (2008) 1.74
Extensive degradation of RNA precursors by the exosome in wild-type cells. Mol Cell (2012) 1.67
A functional network involved in the recycling of nucleocytoplasmic pre-60S factors. J Cell Biol (2006) 1.64
Futile cycle of transcription initiation and termination modulates the response to nucleotide shortage in S. cerevisiae. Mol Cell (2008) 1.63
Rsc4 connects the chromatin remodeler RSC to RNA polymerases. Mol Cell Biol (2006) 1.63
Ssu72 is a phosphatase essential for transcription termination of snoRNAs and specific mRNAs in yeast. EMBO J (2003) 1.59
Genome-wide location analysis reveals a role of TFIIS in RNA polymerase III transcription. Genes Dev (2008) 1.53
Cytoplasmic recycling of 60S preribosomal factors depends on the AAA protein Drg1. Mol Cell Biol (2007) 1.46
Direct interaction of RNA polymerase II and mediator required for transcription in vivo. Science (2011) 1.46
Ammonia pulses and metabolic oscillations guide yeast colony development. Mol Biol Cell (2002) 1.44
Cdc48-associated complex bound to 60S particles is required for the clearance of aberrant translation products. Proc Natl Acad Sci U S A (2013) 1.42
Distinct roles for Mediator Cdk8 module subunits in Drosophila development. EMBO J (2007) 1.38
A gene-specific requirement of RNA polymerase II CTD phosphorylation for sexual differentiation in S. pombe. Curr Biol (2010) 1.37
Large-scale exploration of growth inhibition caused by overexpression of genomic fragments in Saccharomyces cerevisiae. Genome Biol (2004) 1.33
Microarray detection of novel nuclear RNA substrates for the exosome. Yeast (2006) 1.33
TFIIS elongation factor and Mediator act in conjunction during transcription initiation in vivo. Proc Natl Acad Sci U S A (2007) 1.30
Dealing with pervasive transcription. Mol Cell (2013) 1.29
Domestication of wild Saccharomyces cerevisiae is accompanied by changes in gene expression and colony morphology. Mol Microbiol (2003) 1.28
The yeast homolog of human PinX1 is involved in rRNA and small nucleolar RNA maturation, not in telomere elongation inhibition. J Biol Chem (2002) 1.28
The Ccr4-Not complex independently controls both Msn2-dependent transcriptional activation--via a newly identified Glc7/Bud14 type I protein phosphatase module--and TFIID promoter distribution. Mol Cell Biol (2005) 1.27
yMGV: a cross-species expression data mining tool. Nucleic Acids Res (2004) 1.27
Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells. Nucleic Acids Res (2011) 1.23
Recruitment of P-TEFb (Cdk9-Pch1) to chromatin by the cap-methyl transferase Pcm1 in fission yeast. EMBO J (2007) 1.23
A snoRNA that guides the two most conserved pseudouridine modifications within rRNA confers a growth advantage in yeast. RNA (2003) 1.22
Statistical inference of the time-varying structure of gene-regulation networks. BMC Syst Biol (2010) 1.22
The Hsp40 chaperone Jjj1 is required for the nucleo-cytoplasmic recycling of preribosomal factors in Saccharomyces cerevisiae. RNA (2007) 1.22
New insights into the pleiotropic drug resistance network from genome-wide characterization of the YRR1 transcription factor regulation system. Mol Cell Biol (2002) 1.20
Gcn4 misregulation reveals a direct role for the evolutionary conserved EKC/KEOPS in the t6A modification of tRNAs. Nucleic Acids Res (2011) 1.20
Nsa2 is an unstable, conserved factor required for the maturation of 27 SB pre-rRNAs. J Biol Chem (2006) 1.19
Hmo1 is required for TOR-dependent regulation of ribosomal protein gene transcription. Mol Cell Biol (2007) 1.18
Anc1 interacts with the catalytic subunits of the general transcription factors TFIID and TFIIF, the chromatin remodeling complexes RSC and INO80, and the histone acetyltransferase complex NuA3. Biochem Biophys Res Commun (2005) 1.17
An Rpb4/Rpb7-like complex in yeast RNA polymerase III contains the orthologue of mammalian CGRP-RCP. Mol Cell Biol (2003) 1.14
A yeast exosome cofactor, Mpp6, functions in RNA surveillance and in the degradation of noncoding RNA transcripts. Mol Cell Biol (2008) 1.12
Two RNA polymerase I subunits control the binding and release of Rrn3 during transcription. Mol Cell Biol (2007) 1.12
A general strategy to uncover transcription factor properties identifies a new regulator of drug resistance in yeast. J Biol Chem (2003) 1.11
The central role of PDR1 in the foundation of yeast drug resistance. J Biol Chem (2006) 1.10
Identification of TINO: a new evolutionarily conserved BCL-2 AU-rich element RNA-binding protein. J Biol Chem (2004) 1.08
yMGV: helping biologists with yeast microarray data mining. Nucleic Acids Res (2002) 1.07
Structure and properties of transcriptional networks driving selenite stress response in yeasts. BMC Genomics (2008) 1.07
60S ribosomal subunit assembly dynamics defined by semi-quantitative mass spectrometry of purified complexes. Nucleic Acids Res (2008) 1.04
Competitive promoter occupancy by two yeast paralogous transcription factors controlling the multidrug resistance phenomenon. J Biol Chem (2003) 1.03
The Rpb9 subunit of RNA polymerase II binds transcription factor TFIIE and interferes with the SAGA and elongator histone acetyltransferases. J Biol Chem (2002) 1.02
Genome adaptation to chemical stress: clues from comparative transcriptomics in Saccharomyces cerevisiae and Candida glabrata. Genome Biol (2008) 1.02
Transcriptional regulation by Lge1p requires a function independent of its role in histone H2B ubiquitination. J Biol Chem (2004) 1.01
Physical and genetic interactions of yeast Cwc21p, an ortholog of human SRm300/SRRM2, suggest a role at the catalytic center of the spliceosome. RNA (2009) 0.98
Nucleosome depletion activates poised RNA polymerase III at unconventional transcription sites in Saccharomyces cerevisiae. J Biol Chem (2006) 0.98
RNA sequencing revealed novel actors of the acquisition of drug resistance in Candida albicans. BMC Genomics (2012) 0.96
The p21-activated protein kinase inhibitor Skb15 and its budding yeast homologue are 60S ribosome assembly factors. Mol Cell Biol (2007) 0.92
Mediator links transcription and DNA repair by facilitating Rad2/XPG recruitment. Genes Dev (2013) 0.92
Ecm1 is a new pre-ribosomal factor involved in pre-60S particle export. RNA (2010) 0.92
Sodium selenide toxicity is mediated by O2-dependent DNA breaks. PLoS One (2012) 0.90
Spc24 interacts with Mps2 and is required for chromosome segregation, but is not implicated in spindle pole body duplication. Mol Microbiol (2002) 0.90
Global analysis of DNA methylation and transcription of human repetitive sequences. Epigenetics (2009) 0.89
The yeast RPL9B gene is regulated by modulation between two modes of transcription termination. EMBO J (2012) 0.87
Sumoylation of the THO complex regulates the biogenesis of a subset of mRNPs. Nucleic Acids Res (2014) 0.87
Yeast ribosomal protein L7 and its homologue Rlp7 are simultaneously present at distinct sites on pre-60S ribosomal particles. Nucleic Acids Res (2013) 0.84
Interaction of yeast eIF4G with spliceosome components: implications in pre-mRNA processing events. RNA Biol (2009) 0.82
Cordycepin interferes with 3' end formation in yeast independently of its potential to terminate RNA chain elongation. RNA (2009) 0.82
High-frequency promoter firing links THO complex function to heavy chromatin formation. Cell Rep (2013) 0.80
The conserved foot domain of RNA pol II associates with proteins involved in transcriptional initiation and/or early elongation. Genetics (2011) 0.79
The reconstruction of condition-specific transcriptional modules provides new insights in the evolution of yeast AP-1 proteins. PLoS One (2011) 0.78
Comparative functional genomics of stress responses in yeasts. OMICS (2010) 0.77
The evolution of gene expression regulatory networks in yeasts. C R Biol (2011) 0.77
TMEM126A is a mitochondrial located mRNA (MLR) protein of the mitochondrial inner membrane. Biochim Biophys Acta (2013) 0.76
Response of pathogenic and non-pathogenic yeasts to steroids. J Steroid Biochem Mol Biol (2010) 0.76
bPeaks: a bioinformatics tool to detect transcription factor binding sites from ChIPseq data in yeasts and other organisms with small genomes. Yeast (2014) 0.75
Role of Hog1 and Yaf9 in the transcriptional response of Saccharomyces cerevisiae to cesium chloride. Physiol Genomics (2008) 0.75
Enrichment of unstable non-coding RNAs and their genome-wide identification. Methods Mol Biol (2011) 0.75