Published in EMBO J on December 17, 2010
Argonaute divides its RNA guide into domains with distinct functions and RNA-binding properties. Cell (2012) 2.07
In vivo and transcriptome-wide identification of RNA binding protein target sites. Mol Cell (2011) 1.47
GLD-4-mediated translational activation regulates the size of the proliferative germ cell pool in the adult C. elegans germ line. PLoS Genet (2014) 1.44
Stem cell proliferation versus meiotic fate decision in Caenorhabditis elegans. Adv Exp Med Biol (2013) 1.07
The "Observer Effect" in genome-wide surveys of protein-RNA interactions. Mol Cell (2013) 1.06
Post-transcriptional RNA regulons affecting cell cycle and proliferation. Semin Cell Dev Biol (2014) 0.99
Finding the target sites of RNA-binding proteins. Wiley Interdiscip Rev RNA (2013) 0.99
Independent recruitments of a translational regulator in the evolution of self-fertile nematodes. Proc Natl Acad Sci U S A (2011) 0.96
High-throughput characterization of protein-RNA interactions. Brief Funct Genomics (2014) 0.95
Structure-function studies of STAR family Quaking proteins bound to their in vivo RNA target sites. Genes Dev (2013) 0.93
Genome-wide analysis of GLD-1-mediated mRNA regulation suggests a role in mRNA storage. PLoS Genet (2012) 0.92
Asymmetric transcript discovery by RNA-seq in C. elegans blastomeres identifies neg-1, a gene important for anterior morphogenesis. PLoS Genet (2015) 0.86
Control of Caenorhabditis elegans germ-line stem-cell cycling speed meets requirements of design to minimize mutation accumulation. BMC Biol (2015) 0.86
A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels. G3 (Bethesda) (2013) 0.85
The cytoplasmic poly(A) polymerases GLD-2 and GLD-4 promote general gene expression via distinct mechanisms. Nucleic Acids Res (2014) 0.84
Translational control of the oogenic program by components of OMA ribonucleoprotein particles in Caenorhabditis elegans. Genetics (2014) 0.83
Two classes of gap junction channels mediate soma-germline interactions essential for germline proliferation and gametogenesis in Caenorhabditis elegans. Genetics (2014) 0.82
Context-dependent function of a conserved translational regulatory module. Development (2012) 0.82
The TRIM-NHL protein LIN-41 and the OMA RNA-binding proteins antagonistically control the prophase-to-metaphase transition and growth of Caenorhabditis elegans oocytes. Genetics (2014) 0.82
The Drosophila RNA-binding protein HOW controls the stability of dgrasp mRNA in the follicular epithelium. Nucleic Acids Res (2013) 0.81
C. elegans RNA-binding protein GLD-1 recognizes its multiple targets using sequence, context, and structural information to repress translation. Worm (2013) 0.80
RNA recognition by the Caenorhabditis elegans oocyte maturation determinant OMA-1. J Biol Chem (2013) 0.79
Translational activation maintains germline tissue homeostasis during adulthood. Worm (2015) 0.79
POS-1 and GLD-1 repress glp-1 translation through a conserved binding-site cluster. Mol Biol Cell (2012) 0.79
Modifiers of solid RNP granules control normal RNP dynamics and mRNA activity in early development. J Cell Biol (2015) 0.78
RNA-binding protein GLD-1/quaking genetically interacts with the mir-35 and the let-7 miRNA pathways in Caenorhabditis elegans. Open Biol (2013) 0.78
Solution structure of the QUA1 dimerization domain of pXqua, the Xenopus ortholog of Quaking. PLoS One (2013) 0.76
Autophagy and modular restructuring of metabolism control germline tumor differentiation and proliferation in C. elegans. Autophagy (2016) 0.76
Structural and functional implications of the QUA2 domain on RNA recognition by GLD-1. Nucleic Acids Res (2014) 0.76
Transdifferentiation mediated tumor suppression by the endoplasmic reticulum stress sensor IRE-1 in C. elegans. Elife (2015) 0.75
Evolutionary Dynamics of GLD-1-mRNA complexes in Caenorhabditis nematodes. Genome Biol Evol (2014) 0.75
Post-transcriptional control of executioner caspases by RNA-binding proteins. Genes Dev (2016) 0.75
Efficient generation of transgenic reporter strains and analysis of expression patterns in Caenorhabditis elegans using library MosSCI. Dev Dyn (2016) 0.75
PUF-8 Functions Redundantly with GLD-1 to Promote the Meiotic Progression of Spermatocytes in Caenorhabditis elegans. G3 (Bethesda) (2015) 0.75
The globalization of messenger RNA regulation. Natl Sci Rev (2014) 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
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell (2010) 17.87
Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution. Cell (2005) 15.38
Regulation of translation initiation in eukaryotes: mechanisms and biological targets. Cell (2009) 14.51
HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature (2008) 14.17
Creation of low-copy integrated transgenic lines in Caenorhabditis elegans. Genetics (2001) 10.29
RNA regulons: coordination of post-transcriptional events. Nat Rev Genet (2007) 10.12
CLIP identifies Nova-regulated RNA networks in the brain. Science (2003) 8.88
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol (2006) 8.38
RNA and disease. Cell (2009) 7.98
Single-copy insertion of transgenes in Caenorhabditis elegans. Nat Genet (2008) 7.58
Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol (2004) 6.38
RNA-binding proteins: modular design for efficient function. Nat Rev Mol Cell Biol (2007) 5.33
Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc Natl Acad Sci U S A (2000) 4.99
Receptor-mediated endocytosis in the Caenorhabditis elegans oocyte. Mol Biol Cell (1999) 4.79
Target RNA motif and target mRNAs of the Quaking STAR protein. Nat Struct Mol Biol (2005) 3.70
Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Nat Biotechnol (2009) 3.44
3' UTRs are the primary regulators of gene expression in the C. elegans germline. Curr Biol (2008) 3.39
RNA-binding proteins in human genetic disease. Trends Genet (2008) 3.14
gld-1, a tumor suppressor gene required for oocyte development in Caenorhabditis elegans. Genetics (1995) 2.94
MicroRNA function is globally suppressed in mouse oocytes and early embryos. Curr Biol (2010) 2.57
GLD-1, a cytoplasmic protein essential for oocyte differentiation, shows stage- and sex-specific expression during Caenorhabditis elegans germline development. Dev Biol (1996) 2.55
The STAR protein, GLD-1, is a translational regulator of sexual identity in Caenorhabditis elegans. EMBO J (1999) 2.54
Mutations in gld-1, a female germ cell-specific tumor suppressor gene in Caenorhabditis elegans, affect a conserved domain also found in Src-associated protein Sam68. Genes Dev (1995) 2.41
Structural basis for recognition of the intron branch site RNA by splicing factor 1. Science (2001) 2.35
RNA target specificity of the STAR/GSG domain post-transcriptional regulatory protein GLD-1. Nat Struct Mol Biol (2003) 2.34
Translational repression of C. elegans p53 by GLD-1 regulates DNA damage-induced apoptosis. Cell (2005) 2.21
Identification of in vivo mRNA targets of GLD-1, a maxi-KH motif containing protein required for C. elegans germ cell development. Genes Dev (2001) 2.19
Post-transcriptional gene regulation: from genome-wide studies to principles. Cell Mol Life Sci (2008) 2.18
MicroRNA activity is suppressed in mouse oocytes. Curr Biol (2010) 2.15
STAR, a gene family involved in signal transduction and activation of RNA. Trends Genet (1997) 2.14
Nuclear retention of fission yeast dicer is a prerequisite for RNAi-mediated heterochromatin assembly. Dev Cell (2010) 2.09
Analysis of the multiple roles of gld-1 in germline development: interactions with the sex determination cascade and the glp-1 signaling pathway. Genetics (1995) 2.04
Identification of genes expressed in the hermaphrodite germ line of C. elegans using SAGE. BMC Genomics (2009) 1.63
Translational regulators maintain totipotency in the Caenorhabditis elegans germline. Science (2006) 1.54
Translational repression of a C. elegans Notch mRNA by the STAR/KH domain protein GLD-1. Development (2003) 1.45
Emerging roles of RNA and RNA-binding protein network in cancer cells. BMB Rep (2009) 1.39
Translational repression of cyclin E prevents precocious mitosis and embryonic gene activation during C. elegans meiosis. Dev Cell (2009) 1.19
The STAR/Maxi-KH domain protein GLD-1 mediates a developmental switch in the translational control of C. elegans PAL-1. Development (2004) 1.17
Translation repression by GLD-1 protects its mRNA targets from nonsense-mediated mRNA decay in C. elegans. Genes Dev (2004) 1.17
The STAR RNA binding proteins GLD-1, QKI, SAM68 and SLM-2 bind bipartite RNA motifs. BMC Mol Biol (2009) 1.11
Ribonucleoprotein complexes in neurologic diseases. Curr Opin Neurobiol (2008) 1.10
The Quaking family of RNA-binding proteins: coordinators of the cell cycle and differentiation. Cell Cycle (2010) 1.06
Tissue development and RNA control: "HOW" is it coordinated? Trends Genet (2008) 1.05
Caenorhabditis elegans MES-3 is a target of GLD-1 and functions epigenetically in germline development. Genetics (2001) 1.04
Dissection of the target specificity of the RNA-binding protein HOW reveals dpp mRNA as a novel HOW target. Development (2007) 0.86
Genome evolution in yeasts. Nature (2004) 10.50
A novel class of small RNAs bind to MILI protein in mouse testes. Nature (2006) 8.80
DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature (2011) 8.75
Single processing center models for human Dicer and bacterial RNase III. Cell (2004) 8.19
Halogen bonds in biological molecules. Proc Natl Acad Sci U S A (2004) 7.19
The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res (2002) 5.35
RNAML: a standard syntax for exchanging RNA information. RNA (2002) 5.34
Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat Struct Biol (2003) 4.64
Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs. RNA (2008) 4.53
Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res (2003) 4.12
MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells. Nat Struct Mol Biol (2008) 3.98
The RNA Ontology Consortium: an open invitation to the RNA community. RNA (2006) 3.60
Topology of three-way junctions in folded RNAs. RNA (2006) 3.14
Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome. Science (2009) 3.00
Analysis of RNA motifs. Curr Opin Struct Biol (2003) 2.97
The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev (2005) 2.94
The building blocks and motifs of RNA architecture. Curr Opin Struct Biol (2006) 2.94
Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments. Nucleic Acids Res (2005) 2.88
Step-wise methylation of histone H3K9 positions heterochromatin at the nuclear periphery. Cell (2012) 2.67
Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding. Nucleic Acids Res (2005) 2.51
Structure of the ribosome-bound cricket paralysis virus IRES RNA. Nat Struct Mol Biol (2006) 2.32
Nuclear retention of fission yeast dicer is a prerequisite for RNAi-mediated heterochromatin assembly. Dev Cell (2010) 2.09
The dynamic landscapes of RNA architecture. Cell (2009) 2.09
Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution. Proc Natl Acad Sci U S A (2010) 1.99
Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C-miRNA complexes and the degradation of miRNA targets. Genome Res (2009) 1.98
Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure. Bioinformatics (2005) 1.97
Crystal structure of a complex between the aminoglycoside tobramycin and an oligonucleotide containing the ribosomal decoding a site. Chem Biol (2002) 1.97
Genomic prevalence of heterochromatic H3K9me2 and transcription do not discriminate pluripotent from terminally differentiated cells. PLoS Genet (2011) 1.97
Computational analysis of small RNA cloning data. Methods (2008) 1.96
Comparative genomics of protoploid Saccharomycetaceae. Genome Res (2009) 1.96
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. RNA (2012) 1.88
A new understanding of the decoding principle on the ribosome. Nature (2012) 1.88
Frequency and isostericity of RNA base pairs. Nucleic Acids Res (2009) 1.88
Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science (2010) 1.86
An mRNA is capped by a 2', 5' lariat catalyzed by a group I-like ribozyme. Science (2005) 1.82
Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels. Bioinformatics (2010) 1.80
New metrics for comparing and assessing discrepancies between RNA 3D structures and models. RNA (2009) 1.78
Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme. Proc Natl Acad Sci U S A (2003) 1.75
Transcriptional code and disease map for adult retinal cell types. Nat Neurosci (2012) 1.71
Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome. Proc Natl Acad Sci U S A (2010) 1.68
High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome. Nature (2013) 1.66
Strand-specific 5'-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity. RNA (2007) 1.61
Molecular basis of RNA recognition by the embryonic polarity determinant MEX-5. J Biol Chem (2007) 1.61
The molecular basis for A-site mutations conferring aminoglycoside resistance: relationship between ribosomal susceptibility and X-ray crystal structures. Chembiochem (2003) 1.60
Anion binding to nucleic acids. Structure (2004) 1.59
Argonaute protein identity and pairing geometry determine cooperativity in mammalian RNA silencing. RNA (2011) 1.59
Effects of magnesium ions on the stabilization of RNA oligomers of defined structures. RNA (2002) 1.49
Crystal structure of geneticin bound to a bacterial 16S ribosomal RNA A site oligonucleotide. J Mol Biol (2003) 1.47
Beta1-integrins are critical for cerebellar granule cell precursor proliferation. J Neurosci (2004) 1.44
Quantitative approaches to monitor protein-nucleic acid interactions using fluorescent probes. RNA (2010) 1.40
Molecular modeling of the three-dimensional structure of the bacterial RNase P holoenzyme. J Mol Biol (2003) 1.40
Visualization of macromolecular structures. Nat Methods (2010) 1.34
A pH-responsive riboregulator. Genes Dev (2009) 1.33
Structure of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding. J Mol Biol (2005) 1.31
Dicer associates with chromatin to repress genome activity in Schizosaccharomyces pombe. Nat Struct Mol Biol (2010) 1.30
The ribozyme core of group II introns: a structure in want of partners. Trends Biochem Sci (2009) 1.28
The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications. Nucleic Acids Res (2006) 1.28
Identification of active regulatory regions from DNA methylation data. Nucleic Acids Res (2013) 1.26
The RNA structure alignment ontology. RNA (2009) 1.26
Functional hammerhead ribozymes naturally encoded in the genome of Arabidopsis thaliana. Plant Cell (2005) 1.26
RNA as a drug target: the case of aminoglycosides. Chembiochem (2003) 1.25
Molecular recognition of aminoglycoside antibiotics by ribosomal RNA and resistance enzymes: an analysis of x-ray crystal structures. Biopolymers (2003) 1.24
The T-box transcription factors TBX-37 and TBX-38 link GLP-1/Notch signaling to mesoderm induction in C. elegans embryos. Development (2004) 1.24
Pronounced instability of tandem IU base pairs in RNA. Nucleic Acids Res (2004) 1.23
Determination of thermodynamic parameters for HIV DIS type loop-loop kissing complexes. Nucleic Acids Res (2004) 1.21
Symmetric K+ and Mg2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations. J Mol Biol (2004) 1.20
Translational repression of cyclin E prevents precocious mitosis and embryonic gene activation during C. elegans meiosis. Dev Cell (2009) 1.19
Searching genomes for ribozymes and riboswitches. Genome Biol (2007) 1.19
Proximity of conserved U6 and U2 snRNA elements to the 5' splice site region in activated spliceosomes. EMBO J (2006) 1.18
Molecular contacts between antibiotics and the 30S ribosomal particle. Methods Enzymol (2006) 1.18
The three-dimensional architecture of the class I ligase ribozyme. RNA (2004) 1.17
Binding of neomycin-class aminoglycoside antibiotics to mutant ribosomes with alterations in the A site of 16S rRNA. Antimicrob Agents Chemother (2006) 1.15
Analysis of the contribution of individual substituents in 4,6-aminoglycoside-ribosome interaction. Antimicrob Agents Chemother (2005) 1.15
The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations. Chem Biol (2003) 1.15
Sequence-based identification of 3D structural modules in RNA with RMDetect. Nat Methods (2011) 1.15
Pichia sorbitophila, an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization. G3 (Bethesda) (2012) 1.12
The N-terminal peptide of the syntaxin Tlg2p modulates binding of its closed conformation to Vps45p. Proc Natl Acad Sci U S A (2009) 1.12
RNA target specificity of the embryonic cell fate determinant POS-1. RNA (2008) 1.12
Quaking regulates Hnrnpa1 expression through its 3' UTR in oligodendrocyte precursor cells. PLoS Genet (2011) 1.11
RNA recognition by the embryonic cell fate determinant and germline totipotency factor MEX-3. Proc Natl Acad Sci U S A (2009) 1.11
RNAi keeps Atf1-bound stress response genes in check at nuclear pores. Genes Dev (2012) 1.10
Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels. Mol Syst Biol (2012) 1.10
RNA structure analysis of human spliceosomes reveals a compact 3D arrangement of snRNAs at the catalytic core. EMBO J (2013) 1.08
Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide-protein complexes. Nucleic Acids Res (2011) 1.06
The mammalian TRIM-NHL protein TRIM71/LIN-41 is a repressor of mRNA function. Nucleic Acids Res (2012) 1.06
The Quaking family of RNA-binding proteins: coordinators of the cell cycle and differentiation. Cell Cycle (2010) 1.06
New structural insights into the decoding mechanism: translation infidelity via a G·U pair with Watson-Crick geometry. FEBS Lett (2013) 1.05
Binding of manganese(II) to a tertiary stabilized hammerhead ribozyme as studied by electron paramagnetic resonance spectroscopy. RNA (2005) 1.04
Antibacterial aminoglycosides with a modified mode of binding to the ribosomal-RNA decoding site. Angew Chem Int Ed Engl (2004) 1.04
Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site. Nucleic Acids Res (2006) 1.03
Metal ion binding to RNA. Met Ions Life Sci (2011) 1.03
Monitoring intermediate folding states of the td group I intron in vivo. EMBO J (2002) 1.03
Architecture of a Diels-Alderase ribozyme with a preformed catalytic pocket. Chem Biol (2004) 1.02
The RNA structurome: high-throughput probing. Nat Methods (2010) 1.02
Docking of aminoglycosides to hydrated and flexible RNA. J Med Chem (2006) 1.01