Systems Biology Reveals MicroRNA-Mediated Gene Regulation.

The emerging paradigm of network medicine in the study of human disease. Circ Res (2012) 1.12

Identification of micro-RNA networks in end-stage heart failure because of dilated cardiomyopathy. J Cell Mol Med (2013) 0.84

Network of microRNAs-mRNAs interactions in pancreatic cancer. Biomed Res Int (2014) 0.83

Managing Pancreatic Adenocarcinoma: A Special Focus in MicroRNA Gene Therapy. Int J Mol Sci (2016) 0.82

Recent progress using systems biology approaches to better understand molecular mechanisms of immunity. Semin Immunol (2012) 0.80

Understanding microRNA-mediated gene regulatory networks through mathematical modelling. Nucleic Acids Res (2016) 0.78

Association between a variant in microRNA-646 and the susceptibility to hepatocellular carcinoma in a large-scale population. ScientificWorldJournal (2014) 0.75

MiR-299-5p regulates apoptosis through autophagy in neurons and ameliorates cognitive capacity in APPswe/PS1dE9 mice. Sci Rep (2016) 0.75

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52

MicroRNAs: genomics, biogenesis, mechanism, and function. Cell (2004) 198.59

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

MicroRNA expression profiles classify human cancers. Nature (2005) 69.12

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

Oncomirs - microRNAs with a role in cancer. Nat Rev Cancer (2006) 46.47

KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res (1999) 40.62

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

MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet (2004) 37.83

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

Human MicroRNA targets. PLoS Biol (2004) 34.51

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

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

Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10

MicroRNA targets in Drosophila. Genome Biol (2003) 23.59

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

A uniform system for microRNA annotation. RNA (2003) 20.28

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

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

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

The diverse functions of microRNAs in animal development and disease. Dev Cell (2006) 15.62

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

Endogenous human microRNAs that suppress breast cancer metastasis. Nature (2008) 14.37

Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature (2009) 14.07

Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat Rev Genet (2004) 12.97

The colorectal microRNAome. Proc Natl Acad Sci U S A (2006) 11.59

MicroRNAs regulate brain morphogenesis in zebrafish. Science (2005) 11.16

microRNAs as oncogenes and tumor suppressors. Dev Biol (2006) 10.68

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

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

Ribo-gnome: the big world of small RNAs. Science (2005) 10.10

DIP: the database of interacting proteins. Nucleic Acids Res (2000) 10.06

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

MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res (2004) 8.58

Specific activation of microRNA-127 with downregulation of the proto-oncogene BCL6 by chromatin-modifying drugs in human cancer cells. Cancer Cell (2006) 8.46

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

Cell-type-specific signatures of microRNAs on target mRNA expression. Proc Natl Acad Sci U S A (2006) 7.11

A guide through present computational approaches for the identification of mammalian microRNA targets. Nat Methods (2006) 7.00

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

Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature (2008) 6.81

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

The miR-15a-miR-16-1 cluster controls prostate cancer by targeting multiple oncogenic activities. Nat Med (2008) 5.74

Isolation of microRNA targets by miRNP immunopurification. RNA (2007) 5.50

Real-time expression profiling of microRNA precursors in human cancer cell lines. Nucleic Acids Res (2005) 5.44

How microRNAs control cell division, differentiation and death. Curr Opin Genet Dev (2005) 5.22

miR-24 Inhibits cell proliferation by targeting E2F2, MYC, and other cell-cycle genes via binding to "seedless" 3'UTR microRNA recognition elements. Mol Cell (2009) 5.22

A high-throughput method to monitor the expression of microRNA precursors. Nucleic Acids Res (2004) 5.21

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

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

Therapeutic silencing of miR-10b inhibits metastasis in a mouse mammary tumor model. Nat Biotechnol (2010) 4.80

Dynamic regulation of miRNA expression in ordered stages of cellular development. Genes Dev (2007) 4.79

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

Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS Biol (2009) 4.32

Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Comput Biol (2007) 4.31

MicroRNA-124 promotes microglia quiescence and suppresses EAE by deactivating macrophages via the C/EBP-α-PU.1 pathway. Nat Med (2010) 4.24

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

Hematopoietic-specific microRNA expression in human cells. Leuk Res (2005) 3.95

mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts. Nat Methods (2008) 3.88

Desperately seeking microRNA targets. Nat Struct Mol Biol (2010) 3.85

Differential patterns of microRNA expression in neuroblastoma are correlated with prognosis, differentiation, and apoptosis. Cancer Res (2007) 3.74

Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol (2009) 3.66

In-depth characterization of the microRNA transcriptome in a leukemia progression model. Genome Res (2008) 3.55

LNA-modified oligonucleotides mediate specific inhibition of microRNA function. Gene (2006) 3.49

Patterns of known and novel small RNAs in human cervical cancer. Cancer Res (2007) 3.46

MicroRNAs and the regulation of cell death. Trends Genet (2004) 3.42

Detecting microRNA binding and siRNA off-target effects from expression data. Nat Methods (2008) 3.41

Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance. PLoS One (2008) 3.38

Using expression profiling data to identify human microRNA targets. Nat Methods (2007) 3.37

Lost in translation: an assessment and perspective for computational microRNA target identification. Bioinformatics (2009) 3.34

Expression profiling of microRNAs by deep sequencing. Brief Bioinform (2009) 2.71

Epigenetic regulation of microRNA expression in colorectal cancer. Int J Cancer (2009) 2.62

miR-24-mediated downregulation of H2AX suppresses DNA repair in terminally differentiated blood cells. Nat Struct Mol Biol (2009) 2.54

MicroRNA-target pairs in the rat kidney identified by microRNA microarray, proteomic, and bioinformatic analysis. Genome Res (2008) 2.51

MicroRNAs and gene regulatory networks: managing the impact of noise in biological systems. Genes Dev (2010) 2.51

Tandem array-based expression screens identify host mRNA targets of virus-encoded microRNAs. Nat Genet (2008) 2.42

Reproducibility of quantitative RT-PCR array in miRNA expression profiling and comparison with microarray analysis. BMC Genomics (2009) 2.39

Ancient animal microRNAs and the evolution of tissue identity. Nature (2010) 2.35

miR-132 regulates antiviral innate immunity through suppression of the p300 transcriptional co-activator. Nat Cell Biol (2010) 2.29

MicroRNAs: key participants in gene regulatory networks. Curr Opin Chem Biol (2003) 2.28

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

Identification of miRNA targets with stable isotope labeling by amino acids in cell culture. Nucleic Acids Res (2006) 1.97

In-depth analysis of Kaposi's sarcoma-associated herpesvirus microRNA expression provides insights into the mammalian microRNA-processing machinery. J Virol (2009) 1.90

The role of incoherent microRNA-mediated feedforward loops in noise buffering. PLoS Comput Biol (2011) 1.84

MicroRNA regulation of human protein protein interaction network. RNA (2007) 1.82

The microRNA network and tumor metastasis. Oncogene (2009) 1.71

The cardiac transcription network modulated by Gata4, Mef2a, Nkx2.5, Srf, histone modifications, and microRNAs. PLoS Genet (2011) 1.69

Analyzing micro-RNA expression using microarrays. Methods Enzymol (2006) 1.68

Comprehensive survey of human brain microRNA by deep sequencing. BMC Genomics (2010) 1.59

Profiling microRNA expression with microarrays. Trends Biotechnol (2008) 1.48

Strategies for profiling microRNA expression. J Cell Physiol (2009) 1.41

Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science (2007) 5.87

Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. Genome Res (2003) 2.63

Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res (2010) 2.00

Permuted tRNA genes expressed via a circular RNA intermediate in Cyanidioschyzon merolae. Science (2007) 1.98

Identification and expression analysis of putative mRNA-like non-coding RNA in Drosophila. Genes Cells (2005) 1.36

Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order thermoproteales. Mol Biol Evol (2008) 1.36

SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level. In Silico Biol (2006) 1.33

Computational methods for microRNA target prediction. Methods Enzymol (2007) 1.32

Comparative expression analysis uncovers novel features of endogenous antisense transcription. Hum Mol Genet (2008) 1.18

Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli. BMC Genomics (2011) 1.16

Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea. Proc Natl Acad Sci U S A (2009) 1.07

Prediction of non-coding and antisense RNA genes in Escherichia coli with Gapped Markov Model. Gene (2006) 1.05

A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity. Nucleic Acids Res (2011) 1.04

tRNADB-CE 2011: tRNA gene database curated manually by experts. Nucleic Acids Res (2010) 1.04

Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes. BMC Evol Biol (2007) 1.01

Computational analysis of microRNA-mediated antiviral defense in humans. FEBS Lett (2007) 1.01

Computational analysis of microRNA targets in Caenorhabditis elegans. Gene (2005) 1.00

Cooperative regulation for Okazaki fragment processing by RNase HII and FEN-1 purified from a hyperthermophilic archaeon, Pyrococcus furiosus. Biochem Biophys Res Commun (2003) 0.99

Comparative analysis of cis-encoded antisense RNAs in eukaryotes. Gene (2006) 0.98

Sequence evidence in the archaeal genomes that tRNAs emerged through the combination of ancestral genes as 5' and 3' tRNA halves. PLoS One (2008) 0.95

Large-scale tRNA intron transposition in the archaeal order Thermoproteales represents a novel mechanism of intron gain. Mol Biol Evol (2010) 0.95

Does cerebral small vessel disease predict future decline of cognitive function in elderly people with type 2 diabetes? Diabetes Res Clin Pract (2011) 0.93

Permuted tRNA genes in the nuclear and nucleomorph genomes of photosynthetic eukaryotes. Mol Biol Evol (2009) 0.93

Disrupted tRNA gene diversity and possible evolutionary scenarios. J Mol Evol (2009) 0.93

Factors associated with cognitive decline in elderly diabetics. Dement Geriatr Cogn Dis Extra (2011) 0.92

Toward large-scale modeling of the microbial cell for computer simulation. J Biotechnol (2004) 0.92

Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals. BMC Genomics (2010) 0.89

Effect of codon adaptation on codon-level and gene-level translation efficiency in vivo. BMC Genomics (2014) 0.89

Computational analysis of stop codon readthrough in D.melanogaster. Bioinformatics (2003) 0.88

Soluble adhesion molecules and C-reactive protein in the progression of silent cerebral infarction in patients with type 2 diabetes mellitus. Metabolism (2006) 0.88

Comprehensive computational analysis of bacterial CRP/FNR superfamily and its target motifs reveals stepwise evolution of transcriptional networks. Genome Biol Evol (2013) 0.87

Stage-specific expression of Caenorhabditis elegans ribonuclease H1 enzymes with different substrate specificities and bivalent cation requirements. FEBS J (2006) 0.86

Glucose control levels, ischaemic brain lesions, and hyperinsulinaemia were associated with cognitive dysfunction in diabetic elderly. Age Ageing (2008) 0.86

Proteome-wide prediction of novel DNA/RNA-binding proteins using amino acid composition and periodicity in the hyperthermophilic archaeon Pyrococcus furiosus. DNA Res (2007) 0.85

Nematode-specific tRNAs that decode an alternative genetic code for leucine. Nucleic Acids Res (2011) 0.82

Identification of novel endogenous antisense transcripts by DNA microarray analysis targeting complementary strand of annotated genes. BMC Genomics (2009) 0.82

Metatranscriptomic analysis of microbes in an Oceanfront deep-subsurface hot spring reveals novel small RNAs and type-specific tRNA degradation. Appl Environ Microbiol (2011) 0.81

Identification of highly-disrupted tRNA genes in nuclear genome of the red alga, Cyanidioschyzon merolae 10D. Sci Rep (2013) 0.81

Transcription-associated mutagenesis increases protein sequence diversity more effectively than does random mutagenesis in Escherichia coli. PLoS One (2010) 0.81

Genomic heterogeneity in a natural archaeal population suggests a model of tRNA gene disruption. PLoS One (2012) 0.80

Alternative genetic code for amino acids and transfer RNA revisited. Biomol Concepts (2013) 0.79

Vertebrate virus-encoded microRNAs and their sequence conservation. Jpn J Infect Dis (2011) 0.79

Characterization of RNase HII substrate recognition using RNase HII-argonaute chimaeric enzymes from Pyrococcus furiosus. Biochem J (2010) 0.78

X-ray structure of the fourth type of archaeal tRNA splicing endonuclease: insights into the evolution of a novel three-unit composition and a unique loop involved in broad substrate specificity. Nucleic Acids Res (2012) 0.78

GTP-dependent RNA 3'-terminal phosphate cyclase from the hyperthermophilic archaeon Pyrococcus furiosus. Genes Cells (2011) 0.77

1H, 13C and 15N resonance assignments of the 2'-5' RNA ligase-like protein from Pyrococcus furiosus. J Biomol NMR (2006) 0.77

Association of soluble adhesion molecule and C-reactive protein levels with silent brain infarction in patients with and without type 2 diabetes. Curr Neurovasc Res (2008) 0.76

A screening system for artificial small RNAs that inhibit the growth of Escherichia coli. J Biochem (2011) 0.76

Solution structure of a GAAG tetraloop in helix 6 of SRP RNA from Pyrococcus furiosus. Nucleosides Nucleotides Nucleic Acids (2006) 0.75

Comprehensive expressional analyses of antisense transcripts in colon cancer tissues using artificial antisense probes. BMC Med Genomics (2011) 0.75

Characterization of RNA aptamers against SRP19 protein having sequences different from SRP RNA. Nucleic Acids Symp Ser (Oxf) (2009) 0.75

[Unexpected tRNAs that do not consistently obey the universal genetic code]. Seikagaku (2014) 0.75

[Bioinformatics analyses of non-coding RNA]. Tanpakushitsu Kakusan Koso (2006) 0.75

[Tri-split tRNA: a transfer RNA encoded on three separate genes found in hyperthermoacidophilic archaeon Caldivirga maquilingensis]. Seikagaku (2010) 0.75