Published in BMC Genomics on February 15, 2006
Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature (2008) 6.81
Initial sequence and comparative analysis of the cat genome. Genome Res (2007) 4.67
Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput Biol (2007) 4.28
Noncoding RNA in development. Mamm Genome (2008) 3.42
MicroRNAs and the advent of vertebrate morphological complexity. Proc Natl Acad Sci U S A (2008) 3.00
Origins, evolution, and phenotypic impact of new genes. Genome Res (2010) 2.98
Evolution of microRNA diversity and regulation in animals. Nat Rev Genet (2011) 2.92
MicroRNA-206: the skeletal muscle-specific myomiR. Biochim Biophys Acta (2008) 2.64
Origins and evolution of eukaryotic RNA interference. Trends Ecol Evol (2008) 2.15
Evidence for a microRNA expansion in the bilaterian ancestor. Dev Genes Evol (2006) 2.11
Human miRNA precursors with box H/ACA snoRNA features. PLoS Comput Biol (2009) 2.06
Characterization and comparative profiling of the small RNA transcriptomes in two phases of locust. Genome Biol (2009) 1.96
Identification and characterization of novel amphioxus microRNAs by Solexa sequencing. Genome Biol (2009) 1.82
The interplay between transcription factors and microRNAs in genome-scale regulatory networks. Bioessays (2009) 1.72
Ago2 immunoprecipitation identifies predicted microRNAs in human embryonic stem cells and neural precursors. PLoS One (2009) 1.70
Birth and expression evolution of mammalian microRNA genes. Genome Res (2012) 1.64
The fate of miRNA* strand through evolutionary analysis: implication for degradation as merely carrier strand or potential regulatory molecule? PLoS One (2010) 1.58
Identification and characterization of novel microRNAs from Schistosoma japonicum. PLoS One (2008) 1.52
The biological functions of miRNAs: lessons from in vivo studies. Trends Cell Biol (2014) 1.47
miRNA regulation of cytokine genes. Cytokine (2009) 1.39
Evidence for the rapid expansion of microRNA-mediated regulation in early land plant evolution. BMC Plant Biol (2007) 1.38
From snoRNA to miRNA: Dual function regulatory non-coding RNAs. Biochimie (2011) 1.35
Clustered microRNAs' coordination in regulating protein-protein interaction network. BMC Syst Biol (2009) 1.28
Identification of novel Drosophila melanogaster microRNAs. PLoS One (2007) 1.28
A feedforward regulatory loop between HuR and the long noncoding RNA linc-MD1 controls early phases of myogenesis. Mol Cell (2014) 1.24
miRNAminer: a tool for homologous microRNA gene search. BMC Bioinformatics (2008) 1.21
Pharmacological inhibition of a microRNA family in nonhuman primates by a seed-targeting 8-mer antimiR. Sci Transl Med (2013) 1.21
Origins and evolution of microRNA genes in plant species. Genome Biol Evol (2012) 1.20
Repertoire of bovine miRNA and miRNA-like small regulatory RNAs expressed upon viral infection. PLoS One (2009) 1.19
Non-coding RNA annotation of the genome of Trichoplax adhaerens. Nucleic Acids Res (2009) 1.18
Structural conservation versus functional divergence of maternally expressed microRNAs in the Dlk1/Gtl2 imprinting region. BMC Genomics (2008) 1.16
Identification and differential expression of microRNAs during metamorphosis of the Japanese flounder (Paralichthys olivaceus). PLoS One (2011) 1.16
The evolution of core proteins involved in microRNA biogenesis. BMC Evol Biol (2008) 1.14
Overexpression of microRNA-206 in the skeletal muscle from myotonic dystrophy type 1 patients. J Transl Med (2010) 1.13
An "in-depth" description of the small non-coding RNA population of Schistosoma japonicum schistosomulum. PLoS Negl Trop Dis (2010) 1.11
MicroRNA genes derived from repetitive elements and expanded by segmental duplication events in mammalian genomes. PLoS One (2011) 1.10
The expression of microRNA and microRNA clusters in the aging heart. PLoS One (2012) 1.09
MicroRNAs and micromanaging the skeleton in disease, development and evolution. J Cell Mol Med (2009) 1.08
Interspecies regulation of microRNAs and their targets. Biochim Biophys Acta (2008) 1.08
Evolution and function of the extended miR-2 microRNA family. RNA Biol (2012) 1.08
Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum. BMC Genomics (2009) 1.06
An evolutionary perspective of animal microRNAs and their targets. J Biomed Biotechnol (2009) 1.06
Evolution of microRNAs and the diversification of species. Genome Biol Evol (2010) 1.02
A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome. Annu Rev Genet (2015) 1.02
In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity. BMC Genomics (2009) 1.01
Identification of Schistosoma mansoni microRNAs. BMC Genomics (2011) 1.00
Clusters of microRNAs emerge by new hairpins in existing transcripts. Nucleic Acids Res (2013) 1.00
Genome-wide analysis of mir-548 gene family reveals evolutionary and functional implications. J Biomed Biotechnol (2012) 0.99
Evolution of the let-7 microRNA family. RNA Biol (2012) 0.97
MicroRNA expression in lymphoid malignancies: new hope for diagnosis and therapy? J Cell Mol Med (2008) 0.97
Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors. Genome Biol (2013) 0.97
Genome-wide comparative analysis of microRNAs in three non-human primates. BMC Res Notes (2010) 0.96
A bootstrap based analysis pipeline for efficient classification of phylogenetically related animal miRNAs. BMC Genomics (2007) 0.96
A deep analysis of the small non-coding RNA population in Schistosoma japonicum eggs. PLoS One (2013) 0.95
On the Nature and Evolutionary Impact of Phenotypic Robustness Mechanisms. Annu Rev Ecol Evol Syst (2014) 0.94
MicroRNA in teleost fish. Genome Biol Evol (2014) 0.93
Transcription factors are targeted by differentially expressed miRNAs in primates. Genome Biol Evol (2012) 0.93
Haplotype distribution and evolutionary pattern of miR-17 and miR-124 families based on population analysis. PLoS One (2009) 0.92
Evolution of MIR159/319 microRNA genes and their post-transcriptional regulatory link to siRNA pathways. BMC Evol Biol (2011) 0.92
Evolution of the miR199-214 cluster and vertebrate skeletal development. RNA Biol (2014) 0.92
Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs. Nucleic Acids Res (2012) 0.92
Control by a hair's breadth: the role of microRNAs in the skin. Cell Mol Life Sci (2012) 0.90
Expression of microRNAs during embryonic development of Xenopus tropicalis. Gene Expr Patterns (2008) 0.89
Evolutionary changes of the target sites of two microRNAs encoded in the Hox gene cluster of Drosophila and other insect species. Genome Biol Evol (2010) 0.88
Characterization and evolution of microRNA genes derived from repetitive elements and duplication events in plants. PLoS One (2012) 0.88
The evolution of evolvability in microRNA target sites in vertebrates. Genome Res (2013) 0.88
The microRNA-183 cluster: the family that plays together stays together. Nucleic Acids Res (2015) 0.88
An exploration of evolution, maturation, expression and function relationships in mir-23 ∼ 27 ∼ 24 cluster. PLoS One (2014) 0.87
Evolutionary relationships between miRNA genes and their activity. BMC Genomics (2012) 0.87
Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved. RNA (2015) 0.85
A cross-species analysis of microRNAs in the developing avian face. PLoS One (2012) 0.84
Filtering of false positive microRNA candidates by a clustering-based approach. BMC Bioinformatics (2008) 0.83
mESAdb: microRNA expression and sequence analysis database. Nucleic Acids Res (2011) 0.83
Progressive multiple sequence alignments from triplets. BMC Bioinformatics (2007) 0.82
Conservation and losses of non-coding RNAs in avian genomes. PLoS One (2015) 0.82
Large-scale analysis of microRNA evolution. BMC Genomics (2012) 0.81
General hallmarks of microRNAs in brain evolution and development. RNA Biol (2015) 0.81
Novel microRNAs (miRNAs) encoded by herpesvirus of Turkeys: evidence of miRNA evolution by duplication. J Virol (2009) 0.81
In-silico and in-vivo analyses of EST databases unveil conserved miRNAs from Carthamus tinctorius and Cynara cardunculus. BMC Bioinformatics (2012) 0.81
The Expansion of Animal MicroRNA Families Revisited. Life (Basel) (2015) 0.81
The Three Paralogous MicroRNA Clusters in Development and Disease, miR-17-92, miR-106a-363, and miR-106b-25. Scientifica (Cairo) (2016) 0.80
Global analysis of miRNA gene clusters and gene families reveals dynamic and coordinated expression. Biomed Res Int (2014) 0.80
Evolutionary and expression analysis of miR-#-5p and miR-#-3p at the miRNAs/isomiRs levels. Biomed Res Int (2015) 0.80
Accuracy of microRNA discovery pipelines in non-model organisms using closely related species genomes. PLoS One (2014) 0.80
Modeling the asymmetric evolution of a mouse and rat-specific microRNA gene cluster intron 10 of the Sfmbt2 gene. BMC Genomics (2011) 0.79
Genomic features and computational identification of human microRNAs under long-range developmental regulation. BMC Genomics (2011) 0.78
Exploring the miRNA regulatory network using evolutionary correlations. PLoS Comput Biol (2014) 0.78
Genome-Wide Identification and Classification of MicroRNAs Derived from Repetitive Elements. Genomics Inform (2014) 0.78
microRNAs and the evolution of complex multicellularity: identification of a large, diverse complement of microRNAs in the brown alga Ectocarpus. Nucleic Acids Res (2015) 0.78
Concise review: custodians of the transcriptome: how microRNAs guard stemness in squamous epithelia. Stem Cells (2015) 0.78
Differences in molecular evolutionary rates among microRNAs in the human and chimpanzee genomes. BMC Genomics (2016) 0.77
RNA relics and origin of life. Int J Mol Sci (2009) 0.77
Controlled ovarian hyperstimulation induced changes in the expression of circulatory miRNA in bovine follicular fluid and blood plasma. J Ovarian Res (2015) 0.77
A study of the evolution of human microRNAs by their apparent repression effectiveness on target genes. PLoS One (2011) 0.76
microRNA expression patterns across seven cancers are highly correlated and dominated by evolutionarily ancient families. Biomed Rep (2014) 0.76
Genetic analysis of loop sequences in the let-7 gene family reveal a relationship between loop evolution and multiple isomiRs. PLoS One (2014) 0.76
Functional Implications of Human-Specific Changes in Great Ape microRNAs. PLoS One (2016) 0.76
Clustering rfam 10.1: clans, families, and classes. Genes (Basel) (2012) 0.76
Biological function in the twilight zone of sequence conservation. BMC Biol (2017) 0.76
Phylogenetic distribution of plant snoRNA families. BMC Genomics (2016) 0.75
Basic local alignment search tool. J Mol Biol (1990) 659.07
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res (1994) 392.47
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res (1997) 175.36
The functions of animal microRNAs. Nature (2004) 64.85
Rapid similarity searches of nucleic acid and protein data banks. Proc Natl Acad Sci U S A (1983) 53.12
The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature (2000) 39.31
Identification of tissue-specific microRNAs from mouse. Curr Biol (2002) 34.55
The microRNA Registry. Nucleic Acids Res (2004) 29.45
Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res (2005) 25.49
A uniform system for microRNA annotation. RNA (2003) 20.28
Vienna RNA secondary structure server. Nucleic Acids Res (2003) 19.69
MicroRNA maturation: stepwise processing and subcellular localization. EMBO J (2002) 19.47
miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev (2002) 19.24
Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature (2000) 19.15
MicroRNA-directed cleavage of HOXB8 mRNA. Science (2004) 18.33
Vertebrate microRNA genes. Science (2003) 17.42
Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet (2005) 15.96
MicroRNA expression in zebrafish embryonic development. Science (2005) 15.52
Phylogenetic shadowing and computational identification of human microRNA genes. Cell (2005) 13.24
Embryonic stem cell-specific MicroRNAs. Dev Cell (2003) 13.05
New microRNAs from mouse and human. RNA (2003) 10.35
SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics (1998) 9.87
Computational identification of Drosophila microRNA genes. Genome Biol (2003) 9.86
Secondary structure prediction for aligned RNA sequences. J Mol Biol (2002) 8.80
Two classes of short interfering RNA in RNA silencing. EMBO J (2002) 8.54
Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol (2003) 8.51
Zebrafish hox clusters and vertebrate genome evolution. Science (1998) 8.50
Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc Natl Acad Sci U S A (2003) 7.95
RNA regulation: a new genetics? Nat Rev Genet (2004) 5.97
Small RNAs correspond to centromere heterochromatic repeats. Science (2002) 5.96
Molecular evolution of a microRNA cluster. J Mol Biol (2004) 5.94
Pervasive regulation of Drosophila Notch target genes by GY-box-, Brd-box-, and K-box-class microRNAs. Genes Dev (2005) 5.78
A large imprinted microRNA gene cluster at the mouse Dlk1-Gtl2 domain. Genome Res (2004) 5.77
Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBO J (2000) 5.41
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
The sequences of an expressed rat alpha-tubulin gene and a pseudogene with an inserted repetitive element. Nature (1982) 4.42
Evolutionary history of a multigene family: an expressed human beta-tubulin gene and three processed pseudogenes. Cell (1983) 4.26
Genome duplication, a trait shared by 22000 species of ray-finned fish. Genome Res (2003) 4.19
Retracted Hairpin RNAs and retrotransposon LTRs effect RNAi and chromatin-based gene silencing. Science (2003) 3.98
Gene duplications and the origins of vertebrate development. Dev Suppl (1994) 3.98
In search of antisense. Trends Biochem Sci (2004) 3.93
Extensive gene traffic on the mammalian X chromosome. Science (2004) 3.89
Antiquity of microRNAs and their targets in land plants. Plant Cell (2005) 3.88
The developmental role of microRNA in plants. Curr Opin Plant Biol (2005) 3.81
Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol Biol Evol (2005) 3.74
Mammalian microRNAs derived from genomic repeats. Trends Genet (2005) 3.60
Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. Bioessays (2003) 3.59
Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles. J Mol Biol (2001) 3.59
Evidence that a human beta-tubulin pseudogene is derived from its corresponding mRNA. Nature (1982) 3.08
The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev (2005) 2.94
Identification of clustered microRNAs using an ab initio prediction method. BMC Bioinformatics (2005) 2.76
Characterization of a highly variable eutherian microRNA gene. RNA (2005) 2.72
Identification and characterization of new plant microRNAs using EST analysis. Cell Res (2005) 2.35
Alpha-tubulin from early-diverging eukaryotic lineages and the evolution of the tubulin family. Mol Biol Evol (1996) 1.83
Profile-based detection of microRNA precursors in animal genomes. Bioinformatics (2004) 1.79
Evolution of microRNAs located within Hox gene clusters. J Exp Zool B Mol Dev Evol (2005) 1.77
Evolutionary patterns of non-coding RNAs. Theory Biosci (2005) 1.49
Wide genome comparisons reveal the origins of the human X chromosome. Trends Genet (2004) 1.39
Expression of the 22 nucleotide let-7 heterochronic RNA throughout the Metazoa: a role in life history evolution? Evol Dev (2003) 1.23
Non-coding RNAs in Ciona intestinalis. Bioinformatics (2005) 1.21
An abundance of tubulins. Trends Cell Biol (2000) 1.07
Genome duplication strikes back. Nat Genet (2002) 0.98
Phylogenetic relationships of Drosophila melanogaster species group deduced from spacer regions of histone gene H2A-H2B. Mol Phylogenet Evol (2004) 0.87
Tubulin pseudogenes as markers for hominoid divergence. J Mol Biol (1986) 0.80
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Paired-end mapping reveals extensive structural variation in the human genome. Science (2007) 30.46
Landscape of transcription in human cells. Nature (2012) 20.18
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science (2007) 18.59
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res (2012) 15.41
ViennaRNA Package 2.0. Algorithms Mol Biol (2011) 9.43
The Vienna RNA websuite. Nucleic Acids Res (2008) 9.02
Secondary structure prediction for aligned RNA sequences. J Mol Biol (2002) 8.80
Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci U S A (2005) 8.15
The primary transcriptome of the major human pathogen Helicobacter pylori. Nature (2010) 7.70
Molecular evolution of a microRNA cluster. J Mol Biol (2004) 5.94
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol (2010) 5.39
Interleukin-6 dependent survival of multiple myeloma cells involves the Stat3-mediated induction of microRNA-21 through a highly conserved enhancer. Blood (2007) 5.14
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nat Biotechnol (2009) 5.13
tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res (2008) 4.88
Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat Biotechnol (2005) 4.68
Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput Biol (2007) 4.28
Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput Biol (2009) 4.24
The GENCODE pseudogene resource. Genome Biol (2012) 4.18
Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinformatics (2011) 4.15
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. Nucleic Acids Res (2006) 3.59
The reality of pervasive transcription. PLoS Biol (2011) 3.41
MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol (2012) 3.41
RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics (2008) 3.29
Thermodynamics of RNA-RNA binding. Bioinformatics (2006) 3.10
The African coelacanth genome provides insights into tetrapod evolution. Nature (2013) 2.78
Memory efficient folding algorithms for circular RNA secondary structures. Bioinformatics (2006) 2.77
Partition function and base pairing probabilities of RNA heterodimers. Algorithms Mol Biol (2006) 2.74
Structured RNAs in the ENCODE selected regions of the human genome. Genome Res (2007) 2.69
The impact of target site accessibility on the design of effective siRNAs. Nat Biotechnol (2008) 2.51
Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. J Mol Biol (2004) 2.49
Alignment of RNA base pairing probability matrices. Bioinformatics (2004) 2.42
Evolution. Transitions from nonliving to living matter. Science (2004) 2.26
Local RNA base pairing probabilities in large sequences. Bioinformatics (2005) 2.17
Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data. Bioinformatics (2006) 2.13
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. Genome Res (2012) 2.13
Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis. Nucleic Acids Res (2008) 2.10
Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing. Nat Genet (2012) 2.07
Variations on RNA folding and alignment: lessons from Benasque. J Math Biol (2007) 1.91
The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures. Nucleic Acids Res (2007) 1.88
RNAz 2.0: improved noncoding RNA detection. Pac Symp Biocomput (2010) 1.87
A survey of nematode SmY RNAs. RNA Biol (2009) 1.85
Conserved RNA secondary structures in Flaviviridae genomes. J Gen Virol (2004) 1.81
RNAplex: a fast tool for RNA-RNA interaction search. Bioinformatics (2008) 1.80
Evolution of microRNAs located within Hox gene clusters. J Exp Zool B Mol Dev Evol (2005) 1.77
Centers of complex networks. J Theor Biol (2003) 1.74
RNAcentral: A vision for an international database of RNA sequences. RNA (2011) 1.73
The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks. Bioinformatics (2006) 1.61
A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection. Genome Biol (2014) 1.60
AREsite: a database for the comprehensive investigation of AU-rich elements. Nucleic Acids Res (2010) 1.58
Evidence for human microRNA-offset RNAs in small RNA sequencing data. Bioinformatics (2009) 1.55
The "fish-specific" Hox cluster duplication is coincident with the origin of teleosts. Mol Biol Evol (2005) 1.54
SnoReport: computational identification of snoRNAs with unknown targets. Bioinformatics (2007) 1.51
LocARNA-P: accurate boundary prediction and improved detection of structural RNAs. RNA (2012) 1.51
Evolutionary patterns of non-coding RNAs. Theory Biosci (2005) 1.49
Alu elements in ANRIL non-coding RNA at chromosome 9p21 modulate atherogenic cell functions through trans-regulation of gene networks. PLoS Genet (2013) 1.48
Independent Hox-cluster duplications in lampreys. J Exp Zool B Mol Dev Evol (2003) 1.48
Visualization of barrier tree sequences. IEEE Trans Vis Comput Graph (2006) 1.45
RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. RNA (2011) 1.42
Genomic and morphological evidence converge to resolve the enigma of Strepsiptera. Curr Biol (2012) 1.40
Structure and function of the smallest vertebrate telomerase RNA from teleost fish. J Biol Chem (2007) 1.38
RNAs everywhere: genome-wide annotation of structured RNAs. J Exp Zool B Mol Dev Evol (2007) 1.38