Genome-wide approaches in the study of microRNA biology.

MicroRNA-125b induces metastasis by targeting STARD13 in MCF-7 and MDA-MB-231 breast cancer cells. PLoS One (2012) 1.19

Mechanistic Roles of Noncoding RNAs in Lung Cancer Biology and Their Clinical Implications. Genet Res Int (2012) 1.03

A genome-wide miRNA screen revealed miR-603 as a MGMT-regulating miRNA in glioblastomas. Oncotarget (2014) 0.99

MicroRNA 218 acts as a tumor suppressor by targeting multiple cancer phenotype-associated genes in medulloblastoma. J Biol Chem (2012) 0.96

Cis-acting polymorphisms affect complex traits through modifications of microRNA regulation pathways. 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

mirMark: a site-level and UTR-level classifier for miRNA target prediction. Genome Biol (2014) 0.88

Accuracy of microRNA discovery pipelines in non-model organisms using closely related species genomes. PLoS One (2014) 0.80

Tiny giants of gene regulation: experimental strategies for microRNA functional studies. Wiley Interdiscip Rev Dev Biol (2016) 0.80

Bioinformatic challenges of big data in non-coding RNA research. Front Genet (2012) 0.79

miR-148a and miR-17-5p synergistically regulate milk TAG synthesis via PPARGC1A and PPARA in goat mammary epithelial cells. RNA Biol (2017) 0.75

Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81

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

Identification of novel genes coding for small expressed RNAs. Science (2001) 44.44

An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science (2001) 44.16

The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature (2000) 39.31

miRBase: tools for microRNA genomics. Nucleic Acids Res (2007) 38.61

MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell (2007) 38.42

Most mammalian mRNAs are conserved targets of microRNAs. Genome Res (2008) 37.16

Human MicroRNA targets. PLoS Biol (2004) 34.51

An extensive class of small RNAs in Caenorhabditis elegans. Science (2001) 34.17

A mammalian microRNA expression atlas based on small RNA library sequencing. Cell (2007) 34.03

Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell (1993) 33.79

Silencing of microRNAs in vivo with 'antagomirs'. Nature (2005) 32.56

The impact of microRNAs on protein output. Nature (2008) 32.39

Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature (2005) 31.60

Widespread changes in protein synthesis induced by microRNAs. Nature (2008) 31.44

A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science (2001) 31.33

Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics (2002) 30.58

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

MicroRNA targets in Drosophila. Genome Biol (2003) 23.59

bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell (2003) 22.14

Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature (2010) 22.04

Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev (2001) 21.82

Specificity of microRNA target selection in translational repression. Genes Dev (2004) 21.14

The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science (2005) 20.51

Vienna RNA secondary structure server. Nucleic Acids Res (2003) 19.69

miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev (2002) 19.24

Prediction of plant microRNA targets. Cell (2002) 19.20

Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature (2000) 19.15

The role of site accessibility in microRNA target recognition. Nat Genet (2007) 18.52

MicroRNA-directed cleavage of HOXB8 mRNA. Science (2004) 18.33

Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science (2006) 18.14

Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell (2010) 17.87

The microRNAs of Caenorhabditis elegans. Genes Dev (2003) 17.70

Vertebrate microRNA genes. Science (2003) 17.42

Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature (2005) 17.17

Switching from repression to activation: microRNAs can up-regulate translation. Science (2007) 17.00

Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell (2008) 16.38

Requirement of bic/microRNA-155 for normal immune function. Science (2007) 16.24

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

MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nat Methods (2007) 13.94

Phylogenetic shadowing and computational identification of human microRNA genes. Cell (2005) 13.24

Embryonic stem cell-specific MicroRNAs. Dev Cell (2003) 13.05

Identification of microRNAs of the herpesvirus family. Nat Methods (2005) 12.98

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

Identification of Drosophila MicroRNA targets. PLoS Biol (2003) 12.72

Disrupting the pairing between let-7 and Hmga2 enhances oncogenic transformation. Science (2007) 12.42

A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science (2001) 11.86

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature (2007) 11.66

The small RNA profile during Drosophila melanogaster development. Dev Cell (2003) 11.46

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

Therapeutic silencing of microRNA-122 in primates with chronic hepatitis C virus infection. Science (2009) 10.30

Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res (2008) 10.18

Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol (2008) 10.17

A genome-wide map of conserved microRNA targets in C. elegans. Curr Biol (2006) 10.14

MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr Biol (2003) 9.90

Computational identification of Drosophila microRNA genes. Genome Biol (2003) 9.86

MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature (2008) 9.83

Potent effect of target structure on microRNA function. Nat Struct Mol Biol (2007) 8.92

CLIP identifies Nova-regulated RNA networks in the brain. Science (2003) 8.88

Human embryonic stem cells express a unique set of microRNAs. Dev Biol (2004) 8.87

Elucidation of the small RNA component of the transcriptome. Science (2005) 8.66

The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3'UTR. Genes Dev (2004) 8.42

Sequence variants in SLITRK1 are associated with Tourette's syndrome. Science (2005) 8.20

MicroRNA-145 regulates OCT4, SOX2, and KLF4 and represses pluripotency in human embryonic stem cells. Cell (2009) 8.14

Microarray identification of FMRP-associated brain mRNAs and altered mRNA translational profiles in fragile X syndrome. Cell (2001) 8.04

Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc Natl Acad Sci U S A (2003) 7.95

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

Redirection of silencing targets by adenosine-to-inosine editing of miRNAs. Science (2007) 7.15

Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev (2010) 7.14

Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes Dev (2008) 7.07

Differential regulation of microRNAs by p53 revealed by massively parallel sequencing: miR-34a is a p53 target that induces apoptosis and G1-arrest. Cell Cycle (2007) 7.00

Diversity of microRNAs in human and chimpanzee brain. Nat Genet (2006) 6.57

Determinants of targeting by endogenous and exogenous microRNAs and siRNAs. RNA (2007) 6.44

Transcripts targeted by the microRNA-16 family cooperatively regulate cell cycle progression. Mol Cell Biol (2007) 6.43

MicroRNA-373 induces expression of genes with complementary promoter sequences. Proc Natl Acad Sci U S A (2008) 6.38

An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nat Struct Mol Biol (2009) 6.37

CLIP: a method for identifying protein-RNA interaction sites in living cells. Methods (2005) 6.26

Pervasive regulation of Drosophila Notch target genes by GY-box-, Brd-box-, and K-box-class microRNAs. Genes Dev (2005) 5.78

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

SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies. Nucleic Acids Res (2009) 5.40

RNA sequence analysis defines Dicer's role in mouse embryonic stem cells. Proc Natl Acad Sci U S A (2007) 5.26

Computational and experimental identification of C. elegans microRNAs. Mol Cell (2003) 5.22

A biochemical approach to identifying microRNA targets. Proc Natl Acad Sci U S A (2007) 5.16

Embryonic stem cell-specific microRNAs promote induced pluripotency. Nat Biotechnol (2009) 5.14

Opposing microRNA families regulate self-renewal in mouse embryonic stem cells. Nature (2010) 5.10

Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc Natl Acad Sci U S A (2000) 4.99

Identification of human microRNA targets from isolated argonaute protein complexes. RNA Biol (2007) 4.96

Human polymorphism at microRNAs and microRNA target sites. Proc Natl Acad Sci U S A (2007) 4.87

Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs. RNA (2008) 4.53

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

A model for neural development and treatment of Rett syndrome using human induced pluripotent stem cells. Cell (2010) 7.51

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

Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans. Nat Struct Mol Biol (2010) 4.22

RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons. Nucleic Acids Res (2004) 3.70

Transcriptional signature and memory retention of human-induced pluripotent stem cells. PLoS One (2009) 3.07

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

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

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

Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing. Mol Cell (2013) 1.56

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

A regulator of Dscam mutually exclusive splicing fidelity. Nat Struct Mol Biol (2007) 1.35

High-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection. J Virol (2011) 1.28

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

The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion. Annu Rev Biochem (2015) 1.04

Coordinate Nodal and BMP inhibition directs Baf60c-dependent cardiomyocyte commitment. Genes Dev (2013) 0.96

Evidence for premature aging due to oxidative stress in iPSCs from Cockayne syndrome. Hum Mol Genet (2012) 0.94

Alternative splicing in stem cell self-renewal and diferentiation. Adv Exp Med Biol (2010) 0.92

Reactivation of fetal splicing programs in diabetic hearts is mediated by protein kinase C signaling. J Biol Chem (2013) 0.92

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

Genome-wide approaches to dissect the roles of RNA binding proteins in translational control: implications for neurological diseases. Front Neurosci (2012) 0.91

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

Intracellular mRNA regulation with self-assembled locked nucleic acid polymer nanoparticles. J Am Chem Soc (2014) 0.82

Comprehensive identification of miRNA target sites in live animals. Methods Mol Biol (2011) 0.81

RNA-seq analysis of gene expression and alternative splicing by double-random priming strategy. Methods Mol Biol (2011) 0.79

Preface. Adv Exp Med Biol (2014) 0.75

Preface. Adv Exp Med Biol (2014) 0.75