Published in Nat Struct Mol Biol on January 10, 2010
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell (2010) 17.87
Circular RNAs are a large class of animal RNAs with regulatory potency. Nature (2013) 8.54
FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism. Cell (2011) 8.46
Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43. Nat Neurosci (2011) 6.01
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MicroRNA functions in stress responses. Mol Cell (2010) 4.46
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PAR-CliP--a method to identify transcriptome-wide the binding sites of RNA binding proteins. J Vis Exp (2010) 2.23
Capture of microRNA-bound mRNAs identifies the tumor suppressor miR-34a as a regulator of growth factor signaling. PLoS Genet (2011) 2.00
LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance. Mol Cell (2012) 1.93
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Human platelet microRNA-mRNA networks associated with age and gender revealed by integrated plateletomics. Blood (2014) 1.81
DGCR8 HITS-CLIP reveals novel functions for the Microprocessor. Nat Struct Mol Biol (2012) 1.81
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Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs. Genome Res (2011) 1.53
Ago HITS-CLIP expands understanding of Kaposi's sarcoma-associated herpesvirus miRNA function in primary effusion lymphomas. PLoS Pathog (2012) 1.53
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Functional analysis of three Arabidopsis ARGONAUTES using slicer-defective mutants. Plant Cell (2012) 1.49
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Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition. Mol Cell (2014) 1.46
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Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae. Genome Biol (2013) 1.20
microRNAs play critical roles in the survival and recovery of Caenorhabditis elegans from starvation-induced L1 diapause. Proc Natl Acad Sci U S A (2011) 1.19
Transcriptome-wide discovery of microRNA binding sites in human brain. Neuron (2014) 1.13
CLIP-based prediction of mammalian microRNA binding sites. Nucleic Acids Res (2013) 1.13
Two new and distinct roles for Drosophila Argonaute-2 in the nucleus: alternative pre-mRNA splicing and transcriptional repression. Genes Dev (2013) 1.10
MicroRNA in Aging: From Discovery to Biology. Curr Genomics (2012) 1.08
Use of target protector morpholinos to analyze the physiological roles of specific miRNA-mRNA pairs in vivo. Nat Protoc (2011) 1.07
The Microprocessor controls the activity of mammalian retrotransposons. Nat Struct Mol Biol (2013) 1.07
Improved annotation of C. elegans microRNAs by deep sequencing reveals structures associated with processing by Drosha and Dicer. RNA (2011) 1.05
Viral microRNA target allows insight into the role of translation in governing microRNA target accessibility. Proc Natl Acad Sci U S A (2011) 1.05
The nuclear export receptor XPO-1 supports primary miRNA processing in C. elegans and Drosophila. EMBO J (2010) 1.02
Analysis of microRNA expression and function. Methods Cell Biol (2011) 1.00
Small non-coding RNAs mount a silent revolution in gene expression. Curr Opin Cell Biol (2012) 1.00
Allogeneic T cell responses are regulated by a specific miRNA-mRNA network. J Clin Invest (2013) 0.98
The physiological impact of microRNA gene regulation in the retina. Cell Mol Life Sci (2012) 0.98
Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible 'seed-less' targets. Sci Rep (2012) 0.97
Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel. BMC Genomics (2012) 0.97
STarMir: a web server for prediction of microRNA binding sites. Nucleic Acids Res (2014) 0.96
Systematic analysis of tissue-restricted miRISCs reveals a broad role for microRNAs in suppressing basal activity of the C. elegans pathogen response. Mol Cell (2012) 0.96
miRNA-mediated risk for schizophrenia in 22q11.2 deletion syndrome. Front Genet (2012) 0.96
Genome and transcriptome of the porcine whipworm Trichuris suis. Nat Genet (2014) 0.96
A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing. BMC Genomics (2013) 0.96
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High-throughput characterization of protein-RNA interactions. Brief Funct Genomics (2014) 0.95
A tale of two sequences: microRNA-target chimeric reads. Genet Sel Evol (2016) 0.94
Argonaute CLIP-Seq reveals miRNA targetome diversity across tissue types. Sci Rep (2014) 0.94
MicroRNA-target interactions: new insights from genome-wide approaches. Ann N Y Acad Sci (2012) 0.93
Progress and challenge of microRNA research in immunity. Front Genet (2014) 0.93
Developing microRNA screening as a functional genomics tool for disease research. Front Physiol (2013) 0.92
Uncovering new functions for microRNAs in Caenorhabditis elegans. Curr Biol (2011) 0.92
Identification of microRNAs inhibiting TGF-β-induced IL-11 production in bone metastatic breast cancer cells. PLoS One (2012) 0.91
Genome-wide approaches to dissect the roles of RNA binding proteins in translational control: implications for neurological diseases. Front Neurosci (2012) 0.91
The microRNA pathway controls germ cell proliferation and differentiation in C. elegans. Cell Res (2012) 0.91
The long and short of microRNAs in the kidney. J Am Soc Nephrol (2012) 0.89
Transposable element dynamics and PIWI regulation impacts lncRNA and gene expression diversity in Drosophila ovarian cell cultures. Genome Res (2014) 0.89
H19 long noncoding RNA controls the mRNA decay promoting function of KSRP. Proc Natl Acad Sci U S A (2014) 0.89
The evolution of evolvability in microRNA target sites in vertebrates. Genome Res (2013) 0.88
Circular RNAs are long-lived and display only minimal early alterations in response to a growth factor. Nucleic Acids Res (2015) 0.88
Divergent MicroRNA targetomes of closely related circulating strains of a polyomavirus. J Virol (2013) 0.87
Pairing beyond the Seed Supports MicroRNA Targeting Specificity. Mol Cell (2016) 0.87
RFMirTarget: predicting human microRNA target genes with a random forest classifier. PLoS One (2013) 0.87
MicroRNA binding sites in C. elegans 3' UTRs. RNA Biol (2014) 0.86
Principles of miRNA-target regulation in metazoan models. Int J Mol Sci (2013) 0.86
Systems Biology Reveals MicroRNA-Mediated Gene Regulation. Front Genet (2011) 0.86
Computational inference of mRNA stability from histone modification and transcriptome profiles. Nucleic Acids Res (2012) 0.85
Noncoding RNAs and cancer. Silence (2011) 0.85
RIP-chip-SRM--a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans. Genome Res (2012) 0.85
A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels. G3 (Bethesda) (2013) 0.85
Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles. BMC Biol (2015) 0.85
MicroRNA Target Recognition: Insights from Transcriptome-Wide Non-Canonical Interactions. Mol Cells (2016) 0.84
Diversity and expression of microRNAs in the filarial parasite, Brugia malayi. PLoS One (2014) 0.84
Tertiary structure-based analysis of microRNA-target interactions. RNA (2013) 0.83
Functional genomic analysis of the let-7 regulatory network in Caenorhabditis elegans. PLoS Genet (2013) 0.83
MicroRNAs in renal development. Pediatr Nephrol (2012) 0.83
microRNAs of parasitic helminths - Identification, characterization and potential as drug targets. Int J Parasitol Drugs Drug Resist (2014) 0.82
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell (2005) 96.87
MicroRNAs: target recognition and regulatory functions. Cell (2009) 92.17
The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell (1993) 64.62
Prediction of mammalian microRNA targets. Cell (2003) 53.70
Combinatorial microRNA target predictions. Nat Genet (2005) 50.48
Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature (2005) 48.95
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res (2005) 44.08
The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature (2000) 39.31
MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell (2007) 38.42
Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell (1993) 33.79
The impact of microRNAs on protein output. Nature (2008) 32.39
RAS is regulated by the let-7 microRNA family. Cell (2005) 30.24
Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell (2001) 25.86
Principles of microRNA-target recognition. PLoS Biol (2005) 23.70
The role of site accessibility in microRNA target recognition. Nat Genet (2007) 18.52
Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature (2005) 17.17
Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell (2005) 15.26
Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell (2006) 15.12
A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell (2006) 14.70
HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature (2008) 14.17
Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature (2009) 14.07
A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature (2003) 12.93
The cold shock domain protein LIN-28 controls developmental timing in C. elegans and is regulated by the lin-4 RNA. Cell (1997) 12.87
The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor. Mol Cell (2000) 10.92
A genome-wide map of conserved microRNA targets in C. elegans. Curr Biol (2006) 10.14
MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature (2008) 9.83
A gene expression map for Caenorhabditis elegans. Science (2001) 9.74
Potent effect of target structure on microRNA function. Nat Struct Mol Biol (2007) 8.92
The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3'UTR. Genes Dev (2004) 8.42
Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5' UTR as in the 3' UTR. Proc Natl Acad Sci U S A (2007) 7.93
Cell-type-specific signatures of microRNAs on target mRNA expression. Proc Natl Acad Sci U S A (2006) 7.11
The Caenorhabditis elegans hunchback-like gene lin-57/hbl-1 controls developmental time and is regulated by microRNAs. Dev Cell (2003) 6.86
The C elegans hunchback homolog, hbl-1, controls temporal patterning and is a probable microRNA target. Dev Cell (2003) 6.74
An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nat Struct Mol Biol (2009) 6.37
The let-7 MicroRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans. Dev Cell (2005) 5.90
Incorporating structure to predict microRNA targets. Proc Natl Acad Sci U S A (2005) 5.68
Isolation of microRNA targets by miRNP immunopurification. RNA (2007) 5.50
MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode. Nature (2004) 5.31
A biochemical approach to identifying microRNA targets. Proc Natl Acad Sci U S A (2007) 5.16
A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence. Proc Natl Acad Sci U S A (2008) 5.11
Identification of human microRNA targets from isolated argonaute protein complexes. RNA Biol (2007) 4.96
miR-148 targets human DNMT3b protein coding region. RNA (2008) 4.56
Mechanisms of miRNA-mediated post-transcriptional regulation in animal cells. Curr Opin Cell Biol (2009) 4.56
Concern Substrate requirements for let-7 function in the developing zebrafish embryo. Nucleic Acids Res (2004) 4.50
MicroRNA silencing through RISC recruitment of eIF6. Nature (2007) 4.37
LIN-12/Notch activation leads to microRNA-mediated down-regulation of Vav in C. elegans. Science (2005) 4.28
Systematic identification of C. elegans miRISC proteins, miRNAs, and mRNA targets by their interactions with GW182 proteins AIN-1 and AIN-2. Mol Cell (2007) 4.22
mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts. Nat Methods (2008) 3.88
Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res (2009) 3.83
Biological basis for restriction of microRNA targets to the 3' untranslated region in mammalian mRNAs. Nat Struct Mol Biol (2009) 3.70
Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance. PLoS One (2008) 3.38
Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Genome Res (2008) 3.33
The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans. Dev Cell (2005) 2.81
Alternative splicing events identified in human embryonic stem cells and neural progenitors. PLoS Comput Biol (2007) 2.71
Repression of C. elegans microRNA targets at the initiation level of translation requires GW182 proteins. EMBO J (2009) 2.32
Formation of the 3' end of histone mRNA: getting closer to the end. Gene (2007) 2.07
MicroRNA-126 regulates HOXA9 by binding to the homeobox. Mol Cell Biol (2008) 1.95
The mir-84 and let-7 paralogous microRNA genes of Caenorhabditis elegans direct the cessation of molting via the conserved nuclear hormone receptors NHR-23 and NHR-25. Development (2006) 1.86
A whole-genome RNAi Screen for C. elegans miRNA pathway genes. Curr Biol (2007) 1.77
Systematic analysis of dynamic miRNA-target interactions during C. elegans development. Development (2009) 1.14
Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell (2005) 15.26
Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model. Proc Natl Acad Sci U S A (2008) 11.86
Divergent transcription from active promoters. Science (2008) 11.03
Somatic coding mutations in human induced pluripotent stem cells. Nature (2011) 9.50
A model for neural development and treatment of Rett syndrome using human induced pluripotent stem cells. Cell (2010) 7.51
An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nat Struct Mol Biol (2009) 6.37
MicroRNA-responsive 'sensor' transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression. Nat Genet (2004) 6.11
Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43. Nat Neurosci (2011) 6.01
RNA sequence analysis defines Dicer's role in mouse embryonic stem cells. Proc Natl Acad Sci U S A (2007) 5.26
L1 retrotransposition in human neural progenitor cells. Nature (2009) 4.78
MicroRNA silencing through RISC recruitment of eIF6. Nature (2007) 4.37
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Targeted degradation of sense and antisense C9orf72 RNA foci as therapy for ALS and frontotemporal degeneration. Proc Natl Acad Sci U S A (2013) 2.95
Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs. Nat Neurosci (2012) 2.93
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep (2012) 2.76
The EJC factor eIF4AIII modulates synaptic strength and neuronal protein expression. Cell (2007) 2.72
Alternative splicing events identified in human embryonic stem cells and neural progenitors. PLoS Comput Biol (2007) 2.71
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MicroRNA assassins: factors that regulate the disappearance of miRNAs. Nat Struct Mol Biol (2010) 2.42
Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters. Proc Natl Acad Sci U S A (2007) 2.17
LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance. Mol Cell (2012) 1.93
The PIWI proteins SMEDWI-2 and SMEDWI-3 are required for stem cell function and piRNA expression in planarians. RNA (2008) 1.87
Autoregulation of microRNA biogenesis by let-7 and Argonaute. Nature (2012) 1.85
Coordinate regulation of small temporal RNAs at the onset of Drosophila metamorphosis. Dev Biol (2003) 1.79
Inference of splicing regulatory activities by sequence neighborhood analysis. PLoS Genet (2006) 1.71
Plant-derived flavanol (-)epicatechin enhances angiogenesis and retention of spatial memory in mice. J Neurosci (2007) 1.63
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LIN-28 co-transcriptionally binds primary let-7 to regulate miRNA maturation in Caenorhabditis elegans. Nat Struct Mol Biol (2011) 1.51
Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. Nat Struct Mol Biol (2013) 1.49
ALS-linked TDP-43 mutations produce aberrant RNA splicing and adult-onset motor neuron disease without aggregation or loss of nuclear TDP-43. Proc Natl Acad Sci U S A (2013) 1.48
Misregulated RNA processing in amyotrophic lateral sclerosis. Brain Res (2012) 1.42
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Hippocampus-dependent learning is associated with adult neurogenesis in MRL/MpJ mice. Hippocampus (2009) 1.13
Deep sequencing identifies new and regulated microRNAs in Schmidtea mediterranea. RNA (2009) 1.13
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Uncoupling of lin-14 mRNA and protein repression by nutrient deprivation in Caenorhabditis elegans. RNA (2009) 0.94
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Regulation of lin-4 miRNA expression, organismal growth and development by a conserved RNA binding protein in C. elegans. Dev Biol (2010) 0.94
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Alternative splicing in stem cell self-renewal and diferentiation. Adv Exp Med Biol (2010) 0.92
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The evolving role of microRNAs in animal gene expression. Bioessays (2006) 0.91
Retrotransposon long interspersed nucleotide element-1 (LINE-1) is activated during salamander limb regeneration. Dev Growth Differ (2012) 0.91
Human cytomegalovirus infection of human embryonic stem cell-derived primitive neural stem cells is restricted at several steps but leads to the persistence of viral DNA. J Virol (2014) 0.91
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Computational prediction and experimental validation of Ciona intestinalis microRNA genes. BMC Genomics (2007) 0.90
The miR-35-41 family of microRNAs regulates RNAi sensitivity in Caenorhabditis elegans. PLoS Genet (2012) 0.88
A distinct microRNA signature for definitive endoderm derived from human embryonic stem cells. Stem Cells Dev (2010) 0.85
Functional genomic analysis of the let-7 regulatory network in Caenorhabditis elegans. PLoS Genet (2013) 0.83
Multiple cis-elements and trans-acting factors regulate dynamic spatio-temporal transcription of let-7 in Caenorhabditis elegans. Dev Biol (2012) 0.83
Intracellular mRNA regulation with self-assembled locked nucleic acid polymer nanoparticles. J Am Chem Soc (2014) 0.82
MicroRNAs and cancer: a meeting summary of the eponymous Keystone Conference. Epigenetics (2010) 0.81
Identifying Argonaute binding sites in Caenorhabditis elegans using iCLIP. Methods (2013) 0.81
Comprehensive identification of miRNA target sites in live animals. Methods Mol Biol (2011) 0.81
Decoding a signature-based model of transcription cofactor recruitment dictated by cardinal cis-regulatory elements in proximal promoter regions. PLoS Genet (2013) 0.81
Nuclear receptor-enhanced transcription requires motor- and LSD1-dependent gene networking in interchromatin granules. Cell (2008) 0.80
RNA-seq analysis of gene expression and alternative splicing by double-random priming strategy. Methods Mol Biol (2011) 0.79
Mass spectrometry-based shotgun proteomic analysis of C. elegans protein complexes. WormBook (2014) 0.77
Identification of miRNAs and their targets in C. elegans. Adv Exp Med Biol (2014) 0.76
A team effort blocks the ribosome in its tracks. Nat Struct Mol Biol (2012) 0.76
MicroRNAs that interfere with RNAi. Worm (2013) 0.75
A genome wide view of hunchback-like-1 targets. Cell Cycle (2010) 0.75
Preface. Adv Exp Med Biol (2014) 0.75
Preface. Adv Exp Med Biol (2014) 0.75