Published in BMC Bioinformatics on November 07, 2005
Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. Genome Res (2006) 5.23
MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res (2007) 3.69
Integration of microRNA miR-122 in hepatic circadian gene expression. Genes Dev (2009) 3.64
The expansion of the metazoan microRNA repertoire. BMC Genomics (2006) 2.80
The miR-15/107 group of microRNA genes: evolutionary biology, cellular functions, and roles in human diseases. J Mol Biol (2010) 2.20
A novel monoclonal antibody against human Argonaute proteins reveals unexpected characteristics of miRNAs in human blood cells. RNA (2007) 2.13
Current tools for the identification of miRNA genes and their targets. Nucleic Acids Res (2009) 2.12
Exosomal cell-to-cell transmission of alpha synuclein oligomers. Mol Neurodegener (2012) 2.11
The evolution of the DLK1-DIO3 imprinted domain in mammals. PLoS Biol (2008) 2.05
Host-virus interaction: a new role for microRNAs. Retrovirology (2006) 1.88
Unique folding of precursor microRNAs: quantitative evidence and implications for de novo identification. RNA (2006) 1.85
The microRNAs of Epstein-Barr Virus are expressed at dramatically differing levels among cell lines. Virology (2009) 1.79
miROrtho: computational survey of microRNA genes. Nucleic Acids Res (2008) 1.60
Cellular versus viral microRNAs in host-virus interaction. Nucleic Acids Res (2008) 1.50
MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans. BMC Bioinformatics (2007) 1.42
Important aspects of Toll-like receptors, ligands and their signaling pathways. Inflamm Res (2010) 1.40
Computational approaches for microRNA studies: a review. Mamm Genome (2009) 1.39
Identification of real microRNA precursors with a pseudo structure status composition approach. PLoS One (2015) 1.36
Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans. Genome Res (2010) 1.31
MicroRNA transcriptome in the newborn mouse ovaries determined by massive parallel sequencing. Mol Hum Reprod (2010) 1.31
MicroRNA networks in mouse lung organogenesis. PLoS One (2010) 1.28
Ab initio identification of human microRNAs based on structure motifs. BMC Bioinformatics (2007) 1.27
Deep annotation of mouse iso-miR and iso-moR variation. Nucleic Acids Res (2012) 1.27
MaturePred: efficient identification of microRNAs within novel plant pre-miRNAs. PLoS One (2011) 1.25
Bioinformatic discovery of microRNA precursors from human ESTs and introns. BMC Genomics (2006) 1.23
The genomes of two key bumblebee species with primitive eusocial organization. Genome Biol (2015) 1.21
miRRim: a novel system to find conserved miRNAs with high sensitivity and specificity. RNA (2007) 1.21
Mammalian microRNA prediction through a support vector machine model of sequence and structure. PLoS One (2007) 1.20
HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models. BMC Bioinformatics (2009) 1.16
Structural conservation versus functional divergence of maternally expressed microRNAs in the Dlk1/Gtl2 imprinting region. BMC Genomics (2008) 1.16
Vir-Mir db: prediction of viral microRNA candidate hairpins. Nucleic Acids Res (2007) 1.14
Deep-sequencing of endothelial cells exposed to hypoxia reveals the complexity of known and novel microRNAs. RNA (2012) 1.13
Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing. BMC Med Genomics (2009) 1.10
Discovery and characterization of medaka miRNA genes by next generation sequencing platform. BMC Genomics (2010) 1.07
The small RNA repertoire of Dictyostelium discoideum and its regulation by components of the RNAi pathway. Nucleic Acids Res (2007) 1.07
An evolutionary perspective of animal microRNAs and their targets. J Biomed Biotechnol (2009) 1.06
Prediction of novel microRNA genes in cancer-associated genomic regions--a combined computational and experimental approach. Nucleic Acids Res (2009) 1.05
Learning from positive examples when the negative class is undetermined--microRNA gene identification. Algorithms Mol Biol (2008) 1.02
In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity. BMC Genomics (2009) 1.01
MicroRNA-encoding long non-coding RNAs. BMC Genomics (2008) 1.01
A fast ab-initio method for predicting miRNA precursors in genomes. Nucleic Acids Res (2012) 1.00
Alu-directed transcriptional regulation of some novel miRNAs. BMC Genomics (2009) 1.00
A Review of Computational Tools in microRNA Discovery. Front Genet (2013) 0.98
Integrated sequence-structure motifs suffice to identify microRNA precursors. PLoS One (2012) 0.96
Genome-wide approaches in the study of microRNA biology. Wiley Interdiscip Rev Syst Biol Med (2010) 0.95
Using a kernel density estimation based classifier to predict species-specific microRNA precursors. BMC Bioinformatics (2008) 0.94
Computational prediction of the localization of microRNAs within their pre-miRNA. Nucleic Acids Res (2013) 0.94
Self containment, a property of modular RNA structures, distinguishes microRNAs. PLoS Comput Biol (2008) 0.94
Transcriptome sequencing and annotation for the Jamaican fruit bat (Artibeus jamaicensis). PLoS One (2012) 0.94
Identification of microRNA precursors with support vector machine and string kernel. Genomics Proteomics Bioinformatics (2008) 0.93
Identifications of conserved 7-mers in 3'-UTRs and microRNAs in Drosophila. BMC Bioinformatics (2007) 0.91
MicroRNA expressions associated with progression of prostate cancer cells to antiandrogen therapy resistance. Mol Cancer (2014) 0.90
SAGE detects microRNA precursors. BMC Genomics (2006) 0.90
Prediction of viral microRNA precursors based on human microRNA precursor sequence and structural features. Virol J (2009) 0.89
Macronuclear genome structure of the ciliate Nyctotherus ovalis: single-gene chromosomes and tiny introns. BMC Genomics (2008) 0.87
ncRNAclassifier: a tool for detection and classification of transposable element sequences in RNA hairpins. BMC Bioinformatics (2012) 0.86
Large scale chromosomal mapping of human microRNA structural clusters. Nucleic Acids Res (2013) 0.85
A new microRNA target prediction tool identifies a novel interaction of a putative miRNA with CCND2. RNA Biol (2012) 0.84
New genetic regulators question relevance of abundant yolk protein production in C. elegans. Sci Rep (2015) 0.84
Genome-Wide Association Study with Targeted and Non-targeted NMR Metabolomics Identifies 15 Novel Loci of Urinary Human Metabolic Individuality. PLoS Genet (2015) 0.84
Identification of microRNA precursors based on random forest with network-level representation method of stem-loop structure. BMC Bioinformatics (2011) 0.83
Predicting microRNA precursors with a generalized Gaussian components based density estimation algorithm. BMC Bioinformatics (2010) 0.83
Experimental verification of a predicted intronic microRNA in human NGFR gene with a potential pro-apoptotic function. PLoS One (2012) 0.83
Filtering of false positive microRNA candidates by a clustering-based approach. BMC Bioinformatics (2008) 0.83
Identification and characterization of FGF2-dependent mRNA: microRNA networks during lens fiber cell differentiation. G3 (Bethesda) (2013) 0.82
miRdentify: high stringency miRNA predictor identifies several novel animal miRNAs. Nucleic Acids Res (2014) 0.82
Re-inspection of small RNA sequence datasets reveals several novel human miRNA genes. PLoS One (2010) 0.81
miRBoost: boosting support vector machines for microRNA precursor classification. RNA (2015) 0.80
MicroRNA from tuberculosis RNA: A bioinformatics study. J Thorac Dis (2012) 0.80
The miR-367-3p Increases Sorafenib Chemotherapy Efficacy to Suppress Hepatocellular Carcinoma Metastasis through Altering the Androgen Receptor Signals. EBioMedicine (2016) 0.78
Effective classification of microRNA precursors using feature mining and AdaBoost algorithms. OMICS (2013) 0.78
Number variation of high stability regions is correlated with gene functions. Genome Biol Evol (2013) 0.78
A framework for improving microRNA prediction in non-human genomes. Nucleic Acids Res (2015) 0.77
Integration of expressed sequence tag data flanking predicted RNA secondary structures facilitates novel non-coding RNA discovery. PLoS One (2011) 0.77
Contribution of bioinformatics prediction in microRNA-based cancer therapeutics. Adv Drug Deliv Rev (2014) 0.76
miR-Explore: Predicting MicroRNA Precursors by Class Grouping and Secondary Structure Positional Alignment. Bioinform Biol Insights (2013) 0.76
Functional Annotation of Small Noncoding RNAs Target Genes Provides Evidence for a Deregulated Ubiquitin-Proteasome Pathway in Spinocerebellar Ataxia Type 1. J Nucleic Acids (2012) 0.76
Ensemble-based classification approach for micro-RNA mining applied on diverse metagenomic sequences. BMC Res Notes (2014) 0.76
A Review of Computational Methods for Finding Non-Coding RNA Genes. Genes (Basel) (2016) 0.76
Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential. BMC Syst Biol (2015) 0.75
Integrated Strategy Improves the Prediction Accuracy of miRNA in Large Dataset. PLoS One (2016) 0.75
The impact of small RNAs. Microsymposium on small RNAs. EMBO Rep (2006) 0.75
Small RNAs in Plant Responses to Abiotic Stresses: Regulatory Roles and Study Methods. Int J Mol Sci (2015) 0.75
Mi-DISCOVERER: A bioinformatics tool for the detection of mi-RNA in human genome. Bioinformation (2010) 0.75
RAmiRNA: Software suite for generation of SVMbased prediction models of mature miRNAs. Bioinformation (2012) 0.75
MicroRNAs: genomics, biogenesis, mechanism, and function. Cell (2004) 198.59
Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res (2003) 77.89
The functions of animal microRNAs. Nature (2004) 64.85
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res (1981) 61.59
MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet (2004) 37.83
The nuclear RNase III Drosha initiates microRNA processing. Nature (2003) 35.49
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature (2005) 31.60
A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science (2001) 31.33
The microRNA Registry. Nucleic Acids Res (2004) 29.45
MicroRNA genes are transcribed by RNA polymerase II. EMBO J (2004) 20.65
The microRNAs of Caenorhabditis elegans. Genes Dev (2003) 17.70
Vertebrate microRNA genes. Science (2003) 17.42
Nuclear export of microRNA precursors. Science (2003) 16.59
Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation. Genome Biol (2004) 15.15
Identification of mammalian microRNA host genes and transcription units. Genome Res (2004) 14.63
Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA (2005) 14.14
Phylogenetic shadowing and computational identification of human microRNA genes. Cell (2005) 13.24
Identification of microRNAs of the herpesvirus family. Nat Methods (2005) 12.98
Identification of virus-encoded microRNAs. Science (2004) 12.56
Computational identification of Drosophila microRNA genes. Genome Biol (2003) 9.86
Molecular evolution of a microRNA cluster. J Mol Biol (2004) 5.94
A large imprinted microRNA gene cluster at the mouse Dlk1-Gtl2 domain. Genome Res (2004) 5.77
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics (2004) 4.95
Clustering and conservation patterns of human microRNAs. Nucleic Acids Res (2005) 4.79
Structural features of microRNA (miRNA) precursors and their relevance to miRNA biogenesis and small interfering RNA/short hairpin RNA design. J Biol Chem (2004) 2.01
Prediction of locally stable RNA secondary structures for genome-wide surveys. Bioinformatics (2004) 1.93
Profile-based detection of microRNA precursors in animal genomes. Bioinformatics (2004) 1.79
Viral RNA and evolved mutational robustness. J Exp Zool (1999) 1.38
Identification of tissue-specific microRNAs from mouse. Curr Biol (2002) 34.55
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
MicroRNA targets in Drosophila. Genome Biol (2003) 23.59
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A (2002) 20.48
International network of cancer genome projects. Nature (2010) 20.35
A uniform system for microRNA annotation. RNA (2003) 20.28
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell (2010) 17.87
Mechanisms of gene silencing by double-stranded RNA. Nature (2004) 16.82
Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol Cell (2004) 16.10
A pancreatic islet-specific microRNA regulates insulin secretion. Nature (2004) 15.02
Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell (2002) 14.37
Identification of microRNAs of the herpesvirus family. Nat Methods (2005) 12.98
Identification of virus-encoded microRNAs. Science (2004) 12.56
The small RNA profile during Drosophila melanogaster development. Dev Cell (2003) 11.46
MicroRNA-21 contributes to myocardial disease by stimulating MAP kinase signalling in fibroblasts. Nature (2008) 10.73
New microRNAs from mouse and human. RNA (2003) 10.35
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
The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (2009) 8.23
Sequence-specific inhibition of microRNA- and siRNA-induced RNA silencing. RNA (2004) 7.71
Structural basis for 5'-end-specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature (2005) 7.12
Cell-type-specific signatures of microRNAs on target mRNA expression. Proc Natl Acad Sci U S A (2006) 7.11
Cellular cofactors affecting hepatitis C virus infection and replication. Proc Natl Acad Sci U S A (2007) 6.79
Analysis of gene function in somatic mammalian cells using small interfering RNAs. Methods (2002) 6.67
The human DiGeorge syndrome critical region gene 8 and Its D. melanogaster homolog are required for miRNA biogenesis. Curr Biol (2004) 6.56
A promoter-level mammalian expression atlas. Nature (2014) 6.25
An atlas of combinatorial transcriptional regulation in mouse and man. Cell (2010) 6.24
Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods (2008) 6.22
Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinformatics (2007) 6.21
Identification of novel argonaute-associated proteins. Curr Biol (2005) 6.13
miRNAs in human cancer. J Pathol (2010) 6.02
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet (2009) 6.02
A human snoRNA with microRNA-like functions. Mol Cell (2008) 5.84
Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex. Nature (2008) 5.78
Recognition of 5' triphosphate by RIG-I helicase requires short blunt double-stranded RNA as contained in panhandle of negative-strand virus. Immunity (2009) 5.70
Structure of the guide-strand-containing argonaute silencing complex. Nature (2008) 5.36
Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes. Nature (2009) 5.24
Endogenous MHC class II processing of a viral nuclear antigen after autophagy. Science (2004) 5.10
Clustering and conservation patterns of human microRNAs. Nucleic Acids Res (2005) 4.79
siRNAs: applications in functional genomics and potential as therapeutics. Nat Rev Drug Discov (2004) 4.73
RISC is a 5' phosphomonoester-producing RNA endonuclease. Genes Dev (2004) 4.73
MicroRNA-155 is a negative regulator of activation-induced cytidine deaminase. Immunity (2008) 4.59
Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs. RNA (2008) 4.53
The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members. Development (2008) 4.40
Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability. Mol Cell (2011) 4.29
The PTEN-regulating microRNA miR-26a is amplified in high-grade glioma and facilitates gliomagenesis in vivo. Genes Dev (2009) 4.15
Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage. Mol Cell (2005) 4.11
Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes. Genome Res (2003) 4.07
A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins. Nat Methods (2011) 4.06
MicroRNAs 103 and 107 regulate insulin sensitivity. Nature (2011) 3.98
MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells. Nat Struct Mol Biol (2008) 3.98
Antisense-mediated depletion reveals essential and specific functions of microRNAs in Drosophila development. Cell (2005) 3.95
Cyclic [G(2',5')pA(3',5')p] is the metazoan second messenger produced by DNA-activated cyclic GMP-AMP synthase. Cell (2013) 3.92
Specificity, duplex degradation and subcellular localization of antagomirs. Nucleic Acids Res (2007) 3.89
miR-375 maintains normal pancreatic alpha- and beta-cell mass. Proc Natl Acad Sci U S A (2009) 3.89
Cucumber mosaic virus-encoded 2b suppressor inhibits Arabidopsis Argonaute1 cleavage activity to counter plant defense. Genes Dev (2006) 3.77
Quantitative technologies establish a novel microRNA profile of chronic lymphocytic leukemia. Blood (2007) 3.64
Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing. Antisense Nucleic Acid Drug Dev (2003) 3.46
Expanding small RNA interference. Nat Biotechnol (2002) 3.41
Identification and characterization of small RNAs involved in RNA silencing. FEBS Lett (2005) 3.39
PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. PLoS Comput Biol (2005) 3.35
Characterization of small RNAs in Aplysia reveals a role for miR-124 in constraining synaptic plasticity through CREB. Neuron (2009) 3.27
A probabilistic method to detect regulatory modules. Bioinformatics (2003) 3.24
MicroRNAs in human cancer. Adv Exp Med Biol (2013) 3.19
Abnormal microRNA-16 locus with synteny to human 13q14 linked to CLL in NZB mice. Blood (2007) 3.11
Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system. PLoS One (2008) 3.09
miRNA in situ hybridization in formaldehyde and EDC-fixed tissues. Nat Methods (2009) 3.03
MicroRNA sequence and expression analysis in breast tumors by deep sequencing. Cancer Res (2011) 3.02