Published in Cell on December 15, 2006
MicroRNAs: target recognition and regulatory functions. Cell (2009) 92.17
Most mammalian mRNAs are conserved targets of microRNAs. Genome Res (2008) 37.16
The impact of microRNAs on protein output. Nature (2008) 32.39
A microRNA component of the p53 tumour suppressor network. Nature (2007) 19.25
Small silencing RNAs: an expanding universe. Nat Rev Genet (2009) 13.88
Unlocking the secrets of the genome. Nature (2009) 11.80
A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev (2006) 11.71
Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res (2008) 10.18
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
Intronic microRNA precursors that bypass Drosha processing. Nature (2007) 9.65
Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res (2007) 9.61
Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide. Cell (2008) 9.02
RNA sequencing: advances, challenges and opportunities. Nat Rev Genet (2010) 8.96
Small RNAs as guardians of the genome. Cell (2009) 8.88
An endogenous small interfering RNA pathway in Drosophila. Nature (2008) 7.88
Genetic variation in microRNA networks: the implications for cancer research. Nat Rev Cancer (2010) 7.39
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
Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature (2008) 6.81
Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods (2008) 6.22
miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res (2011) 5.83
Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat Struct Mol Biol (2011) 5.57
miRNA profiling of naïve, effector and memory CD8 T cells. PLoS One (2007) 5.43
Systematic analysis of microRNA expression of RNA extracted from fresh frozen and formalin-fixed paraffin-embedded samples. RNA (2007) 5.35
A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res (2007) 5.33
Most Caenorhabditis elegans microRNAs are individually not essential for development or viability. PLoS Genet (2007) 5.33
RNA sequence analysis defines Dicer's role in mouse embryonic stem cells. Proc Natl Acad Sci U S A (2007) 5.26
Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet (2008) 5.23
The regulatory activity of microRNA* species has substantial influence on microRNA and 3' UTR evolution. Nat Struct Mol Biol (2008) 4.88
PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans. Mol Cell (2008) 4.48
Limitations and possibilities of small RNA digital gene expression profiling. Nat Methods (2009) 4.34
On the road to reading the RNA-interference code. Nature (2009) 4.33
Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. Genome Res (2007) 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
Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans. Nat Struct Mol Biol (2010) 4.22
Argonaute loading improves the 5' precision of both MicroRNAs and their miRNA* strands in flies. Curr Biol (2008) 4.07
mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts. Nat Methods (2008) 3.88
Diversifying microRNA sequence and function. Nat Rev Mol Cell Biol (2013) 3.80
A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res (2008) 3.74
WormBase 2007. Nucleic Acids Res (2007) 3.69
Selective stabilization of mammalian microRNAs by 3' adenylation mediated by the cytoplasmic poly(A) polymerase GLD-2. Genes Dev (2009) 3.62
In-depth characterization of the microRNA transcriptome in a leukemia progression model. Genome Res (2008) 3.55
The monarch butterfly genome yields insights into long-distance migration. Cell (2011) 3.51
piRNAs can trigger a multigenerational epigenetic memory in the germline of C. elegans. Cell (2012) 3.49
Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline. Mol Cell (2009) 3.43
Noncoding RNA in development. Mamm Genome (2008) 3.42
Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. Plant Cell (2007) 3.40
Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline. Mol Cell (2008) 3.37
Hidden layers of human small RNAs. BMC Genomics (2008) 3.31
Common functions for diverse small RNAs of land plants. Plant Cell (2007) 3.30
A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. Genes Dev (2008) 3.19
RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond. Nat Rev Genet (2013) 3.17
The Argonaute CSR-1 and its 22G-RNA cofactors are required for holocentric chromosome segregation. Cell (2009) 3.14
MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries. Stem Cells (2008) 3.14
Function, targets, and evolution of Caenorhabditis elegans piRNAs. Science (2012) 3.11
Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets. Genome Res (2008) 3.09
The rise of regulatory RNA. Nat Rev Genet (2014) 3.02
Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature (2009) 3.01
Endogenous small interfering RNAs in animals. Nat Rev Mol Cell Biol (2008) 3.00
TRAMP-mediated RNA surveillance prevents spurious entry of RNAs into the Schizosaccharomyces pombe siRNA pathway. Nat Struct Mol Biol (2008) 2.98
Evolution of microRNA diversity and regulation in animals. Nat Rev Genet (2011) 2.92
Many families of C. elegans microRNAs are not essential for development or viability. Curr Biol (2010) 2.90
Dynamic expression of small non-coding RNAs, including novel microRNAs and piRNAs/21U-RNAs, during Caenorhabditis elegans development. Genome Biol (2009) 2.81
Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs. Proc Natl Acad Sci U S A (2015) 2.72
Expression profiling of microRNAs by deep sequencing. Brief Bioinform (2009) 2.71
Reprogramming of miRNA networks in cancer and leukemia. Genome Res (2010) 2.65
C. elegans piRNAs mediate the genome-wide surveillance of germline transcripts. Cell (2012) 2.65
Zcchc11-dependent uridylation of microRNA directs cytokine expression. Nat Cell Biol (2009) 2.63
Distinct phases of siRNA synthesis in an endogenous RNAi pathway in C. elegans soma. Mol Cell (2010) 2.57
An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. Plant Cell (2007) 2.55
Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity. Genome Res (2008) 2.52
MicroRNA assassins: factors that regulate the disappearance of miRNAs. Nat Struct Mol Biol (2010) 2.42
Repertoire of microRNAs in epithelial ovarian cancer as determined by next generation sequencing of small RNA cDNA libraries. PLoS One (2009) 2.37
The evolution of RNAi as a defence against viruses and transposable elements. Philos Trans R Soc Lond B Biol Sci (2009) 2.35
Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity. Genome Res (2011) 2.34
High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genomics (2008) 2.31
Regulation of MicroRNA Biogenesis: A miRiad of mechanisms. Cell Commun Signal (2009) 2.27
A C. elegans Piwi, PRG-1, regulates 21U-RNAs during spermatogenesis. Curr Biol (2008) 2.25
Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing. Nucleic Acids Res (2009) 2.25
Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi. Mol Cell (2010) 2.23
miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data. Genome Biol (2010) 2.18
A spatial and temporal map of C. elegans gene expression. Genome Res (2010) 2.16
MicroRNAs and their isomiRs function cooperatively to target common biological pathways. Genome Biol (2011) 2.15
Deep sequencing of human nuclear and cytoplasmic small RNAs reveals an unexpectedly complex subcellular distribution of miRNAs and tRNA 3' trailers. PLoS One (2010) 2.12
Loss of individual microRNAs causes mutant phenotypes in sensitized genetic backgrounds in C. elegans. Curr Biol (2010) 2.02
Structural determinants of miRNAs for RISC loading and slicer-independent unwinding. Nat Struct Mol Biol (2009) 2.01
An elegant miRror: microRNAs in stem cells, developmental timing and cancer. Chromosoma (2009) 1.99
MicroRNAs both promote and antagonize longevity in C. elegans. Curr Biol (2010) 1.99
Computational and analytical framework for small RNA profiling by high-throughput sequencing. RNA (2009) 1.97
Characterization and comparative profiling of the small RNA transcriptomes in two phases of locust. Genome Biol (2009) 1.96
PIWI-interacting RNAs: from generation to transgenerational epigenetics. Nat Rev Genet (2013) 1.92
The piRNA pathway: a fly's perspective on the guardian of the genome. Trends Genet (2010) 1.91
In-depth analysis of Kaposi's sarcoma-associated herpesvirus microRNA expression provides insights into the mammalian microRNA-processing machinery. J Virol (2009) 1.90
Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression. Nat Methods (2009) 1.82
A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans. Nat Methods (2010) 1.82
Argonautes ALG-3 and ALG-4 are required for spermatogenesis-specific 26G-RNAs and thermotolerant sperm in Caenorhabditis elegans. Proc Natl Acad Sci U S A (2010) 1.81
Structural bias in T4 RNA ligase-mediated 3'-adapter ligation. Nucleic Acids Res (2012) 1.81
deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res (2009) 1.78
The mouse homolog of HEN1 is a potential methylase for Piwi-interacting RNAs. RNA (2007) 1.77
Biology of PIWI-interacting RNAs: new insights into biogenesis and function inside and outside of germlines. Genes Dev (2012) 1.75
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell (2005) 96.87
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature (2007) 65.18
Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol (2011) 53.86
Prediction of mammalian microRNA targets. Cell (2003) 53.70
Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63
Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature (2005) 48.95
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
The impact of microRNAs on protein output. Nature (2008) 32.39
Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature (2008) 30.29
MicroRNAs modulate hematopoietic lineage differentiation. Science (2003) 30.05
Control of developmental regulators by Polycomb in human embryonic stem cells. Cell (2006) 28.21
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol (2009) 27.17
Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature (2005) 23.04
High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A (2010) 22.97
Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature (2010) 22.04
ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res (2008) 20.61
The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science (2005) 20.51
The worldwide leaf economics spectrum. Nature (2004) 20.42
A uniform system for microRNA annotation. RNA (2003) 20.28
MicroRNAs in plants. Genes Dev (2002) 20.12
Prediction of plant microRNA targets. Cell (2002) 19.20
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol (2010) 18.44
MicroRNA-directed cleavage of HOXB8 mRNA. Science (2004) 18.33
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
The microRNAs of Caenorhabditis elegans. Genes Dev (2003) 17.70
Vertebrate microRNA genes. Science (2003) 17.42
Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell (2008) 16.38
A map of the interactome network of the metazoan C. elegans. Science (2004) 15.60
MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol (2006) 14.44
Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA (2005) 14.14
Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res (2006) 13.32
Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell (2004) 12.97
High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods (2008) 12.56
Disrupting the pairing between let-7 and Hmga2 enhances oncogenic transformation. Science (2007) 12.42
A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev (2006) 11.71
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature (2007) 11.66
The genome sequence of the filamentous fungus Neurospora crassa. Nature (2003) 11.39
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet (2008) 11.17
MicroRNAs regulate brain morphogenesis in zebrafish. Science (2005) 11.16
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature (2004) 11.03
Widespread shortening of 3'UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell (2009) 10.50
Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res (2008) 10.49
A biochemical framework for RNA silencing in plants. Genes Dev (2003) 9.95
Intronic microRNA precursors that bypass Drosha processing. Nature (2007) 9.65
Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res (2007) 9.61
Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes. Cell (2005) 9.35
Genome sequence of Aedes aegypti, a major arbovirus vector. Science (2007) 9.19
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol (2011) 9.18
Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods (2010) 9.09
A high-resolution map of human evolutionary constraint using 29 mammals. Nature (2011) 8.67
The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science (2008) 8.52
Integrative analysis of the melanoma transcriptome. Genome Res (2010) 8.46
A catalog of reference genomes from the human microbiome. Science (2010) 8.10
Characterization of the piRNA complex from rat testes. Science (2006) 7.86
Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell (2004) 7.68
Criteria for annotation of plant MicroRNAs. Plant Cell (2008) 7.49
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
The genome sequence of the rice blast fungus Magnaporthe grisea. Nature (2005) 6.95
Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature (2008) 6.81
ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Genome Biol (2009) 6.76
The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev (2004) 6.69
lincRNAs: genomics, evolution, and mechanisms. Cell (2013) 6.50
Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature (2009) 6.44
MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5' region. EMBO J (2004) 6.27
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A (2009) 6.01
Comparative functional genomics of the fission yeasts. Science (2011) 6.00
Small RNAs correspond to centromere heterochromatic repeats. Science (2002) 5.96
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
Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71
Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell (2011) 5.65
A two-hit trigger for siRNA biogenesis in plants. Cell (2006) 5.60
Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat Struct Mol Biol (2011) 5.57
Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature (2006) 5.52
Most Caenorhabditis elegans microRNAs are individually not essential for development or viability. PLoS Genet (2007) 5.33
A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol (2011) 5.11
The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs. Nature (2008) 5.05
Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr Biol (2008) 5.00
Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs. Curr Biol (2005) 4.98
The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res (2002) 4.58
PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans. Mol Cell (2008) 4.48
Characterizing and measuring bias in sequence data. Genome Biol (2013) 4.39
Expanding the microRNA targeting code: functional sites with centered pairing. Mol Cell (2010) 4.20
miR-150, a microRNA expressed in mature B and T cells, blocks early B cell development when expressed prematurely. Proc Natl Acad Sci U S A (2007) 4.15
MicroRNAs: at the root of plant development? Plant Physiol (2003) 4.12
Improved automatic detection and segmentation of cell nuclei in histopathology images. IEEE Trans Biomed Eng (2009) 4.01
Antiquity of microRNAs and their targets in land plants. Plant Cell (2005) 3.88
Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs. Nature (2010) 3.87
Finished bacterial genomes from shotgun sequence data. Genome Res (2012) 3.86
Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nat Biotechnol (2011) 3.81
The microRNA miR-196 acts upstream of Hoxb8 and Shh in limb development. Nature (2005) 3.78
MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs. Curr Biol (2004) 3.63