Published in Genome Biol on April 06, 2010
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miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res (2011) 5.83
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miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res (2012) 1.37
Stars and symbiosis: microRNA- and microRNA*-mediated transcript cleavage involved in arbuscular mycorrhizal symbiosis. Plant Physiol (2011) 1.32
High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis. Genome Res (2011) 1.27
Transcriptome microRNA profiling of bovine mammary epithelial cells challenged with Escherichia coli or Staphylococcus aureus bacteria reveals pathogen directed microRNA expression profiles. BMC Genomics (2014) 1.09
Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis. Nucleic Acids Res (2012) 1.08
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mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing. RNA Biol (2013) 1.01
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NK4 antagonizes Tbx1/10 to promote cardiac versus pharyngeal muscle fate in the ascidian second heart field. PLoS Biol (2013) 0.92
Automatically clustering large-scale miRNA sequences: methods and experiments. BMC Genomics (2012) 0.86
miRFam: an effective automatic miRNA classification method based on n-grams and a multiclass SVM. BMC Bioinformatics (2011) 0.86
Discovery of novel microRNAs in rat kidney using next generation sequencing and microarray validation. PLoS One (2012) 0.86
Prediction of conserved precursors of miRNAs and their mature forms by integrating position-specific structural features. PLoS One (2012) 0.85
A Comprehensive Prescription for Plant miRNA Identification. Front Plant Sci (2017) 0.83
The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum. BMC Genomics (2014) 0.78
Effective classification of microRNA precursors using feature mining and AdaBoost algorithms. OMICS (2013) 0.78
isomiR-SEA: an RNA-Seq analysis tool for miRNAs/isomiRs expression level profiling and miRNA-mRNA interaction sites evaluation. BMC Bioinformatics (2016) 0.78
Fibroblast growth factor signalling controls nervous system patterning and pigment cell formation in Ciona intestinalis. Nat Commun (2014) 0.77
Impact of the genetic background on the composition of the chicken plasma MiRNome in response to a stress. PLoS One (2014) 0.76
Role of bioinformatics in establishing microRNAs as modulators of abiotic stress responses: the new revolution. Front Physiol (2015) 0.76
miRNA Digger: a comprehensive pipeline for genome-wide novel miRNA mining. Sci Rep (2016) 0.75
Automated detection of ncRNAs in the draft genome sequence of a colonial tunicate: the carpet sea squirt Didemnum vexillum. BMC Genomics (2016) 0.75
Rapid Evolutionary Rates and Unique Genomic Signatures Discovered in the First Reference Genome for the Southern Ocean Salp, Salpa thompsoni (Urochordata, Thaliacea). Genome Biol Evol (2016) 0.75
Genome-wide survey of miRNAs and their evolutionary history in the ascidian, Halocynthia roretzi. BMC Genomics (2017) 0.75
A microRNA-mRNA expression network during oral siphon regeneration in Ciona. Development (2017) 0.75
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Antisense transcription in the mammalian transcriptome. Science (2005) 15.69
Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell (2006) 15.12
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
Small non-coding RNAs in animal development. Nat Rev Mol Cell Biol (2008) 12.35
A slicer-mediated mechanism for repeat-associated siRNA 5' end formation in Drosophila. Science (2007) 10.73
Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol (2008) 10.17
Computational identification of Drosophila microRNA genes. Genome Biol (2003) 9.86
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
Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature (2006) 7.96
Genomics of microRNA. Trends Genet (2006) 7.75
The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell (2007) 7.70
Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes Dev (2008) 7.07
Computational and experimental identification of C. elegans microRNAs. Mol Cell (2003) 5.22
Dynamic regulation of miRNA expression in ordered stages of cellular development. Genes Dev (2007) 4.79
A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res (2008) 3.74
The deep evolution of metazoan microRNAs. Evol Dev (2009) 3.56
Posttranscriptional crossregulation between Drosha and DGCR8. Cell (2009) 3.54
Characterization of endogenous human Argonautes and their miRNA partners in RNA silencing. Proc Natl Acad Sci U S A (2008) 3.03
MicroRNA biogenesis and function in plants. FEBS Lett (2005) 3.02
MicroRNAs and the advent of vertebrate morphological complexity. Proc Natl Acad Sci U S A (2008) 3.00
Endogenous small interfering RNAs in animals. Nat Rev Mol Cell Biol (2008) 3.00
The phylogenetic distribution of metazoan microRNAs: insights into evolutionary complexity and constraint. J Exp Zool B Mol Dev Evol (2006) 2.63
A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes Dev (2008) 2.45
Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci. Genes Dev (2008) 2.35
MicroRNAs and metazoan macroevolution: insights into canalization, complexity, and the Cambrian explosion. Bioessays (2009) 2.31
Evidence for a microRNA expansion in the bilaterian ancestor. Dev Genes Evol (2006) 2.11
Control of protein synthesis and mRNA degradation by microRNAs. Curr Opin Cell Biol (2008) 2.00
MicroRNAs in the Drosophila bithorax complex. Genes Dev (2008) 1.99
A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate. Nat Struct Mol Biol (2009) 1.90
Identification and characterization of novel amphioxus microRNAs by Solexa sequencing. Genome Biol (2009) 1.82
What do natural antisense transcripts regulate? RNA Biol (2009) 1.66
Evidence for human microRNA-offset RNAs in small RNA sequencing data. Bioinformatics (2009) 1.55
Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance. Genome Res (2004) 1.47
Endo-siRNAs: yet another layer of complexity in RNA silencing. Nat Struct Mol Biol (2008) 1.10
A study of microRNAs in silico and in vivo: bioinformatics approaches to microRNA discovery and target identification. FEBS J (2009) 1.07
In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity. BMC Genomics (2009) 1.01
Evolutionary origin and genomic organization of micro-RNA genes in immunoglobulin lambda variable region gene family. Mol Biol Evol (2009) 0.99
Developmental timing: let-7 function conserved through evolution. Curr Biol (2008) 0.97
Computational prediction and experimental validation of Ciona intestinalis microRNA genes. BMC Genomics (2007) 0.90
The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution. Genome Res (2008) 0.89
The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science (2002) 11.11
RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat Genet (2007) 9.56
Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci U S A (2002) 8.56
Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo. Genes Dev (2007) 4.59
Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo. Cell (2002) 4.00
Synchronous and stochastic patterns of gene activation in the Drosophila embryo. Science (2009) 3.58
Genomic regulatory networks and animal development. Dev Cell (2005) 3.01
Characterization of the intergenic RNA profile at abdominal-A and Abdominal-B in the Drosophila bithorax complex. Proc Natl Acad Sci U S A (2002) 2.94
Regulatory blueprint for a chordate embryo. Science (2006) 2.67
Shadow enhancers foster robustness of Drosophila gastrulation. Curr Biol (2010) 2.63
Immunity regulatory DNAs share common organizational features in Drosophila. Mol Cell (2004) 2.58
A regulatory code for neurogenic gene expression in the Drosophila embryo. Development (2004) 2.41
FGF signaling delineates the cardiac progenitor field in the simple chordate, Ciona intestinalis. Genes Dev (2006) 2.22
Dorsal gradient networks in the Drosophila embryo. Dev Biol (2002) 2.18
Coordinate enhancers share common organizational features in the Drosophila genome. Proc Natl Acad Sci U S A (2004) 1.90
Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo. Proc Natl Acad Sci U S A (2011) 1.80
Promoter-proximal tethering elements regulate enhancer-promoter specificity in the Drosophila Antennapedia complex. Proc Natl Acad Sci U S A (2002) 1.74
pyramus and thisbe: FGF genes that pattern the mesoderm of Drosophila embryos. Genes Dev (2004) 1.73
Ciona intestinalis: an emerging model for whole-genome analyses. Trends Genet (2003) 1.69
Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo. Proc Natl Acad Sci U S A (2005) 1.67
Clusters of temporal discordances reveal distinct embryonic patterning mechanisms in Drosophila and anopheles. PLoS Biol (2011) 1.65
The snail repressor inhibits release, not elongation, of paused Pol II in the Drosophila embryo. Curr Biol (2011) 1.63
Regulation of Hox gene activity by transcriptional elongation in Drosophila. Curr Biol (2009) 1.55
Stalled Hox promoters as chromosomal boundaries. Genes Dev (2009) 1.55
A simplified miRNA-based gene silencing method for Drosophila melanogaster. Dev Biol (2008) 1.54
Neural-specific elongation of 3' UTRs during Drosophila development. Proc Natl Acad Sci U S A (2011) 1.40
Mechanisms of transcriptional precision in animal development. Trends Genet (2012) 1.38
Genome-wide identification of tissue-specific enhancers in the Ciona tadpole. Proc Natl Acad Sci U S A (2002) 1.36
Evolutionary origins of the vertebrate heart: Specification of the cardiac lineage in Ciona intestinalis. Proc Natl Acad Sci U S A (2003) 1.34
The transcription/migration interface in heart precursors of Ciona intestinalis. Science (2008) 1.32
Early chordate origins of the vertebrate second heart field. Science (2010) 1.31
Identification of a rudimentary neural crest in a non-vertebrate chordate. Nature (2012) 1.30
Long-range enhancer-promoter interactions in the Scr-Antp interval of the Drosophila Antennapedia complex. Proc Natl Acad Sci U S A (2003) 1.30
pannier and pointedP2 act sequentially to regulate Drosophila heart development. Development (2003) 1.29
Uncoupling heart cell specification and migration in the simple chordate Ciona intestinalis. Development (2005) 1.27
Coordinated regulation of cholinergic motor neuron traits through a conserved terminal selector gene. Nat Neurosci (2011) 1.26
Decoding cis-regulatory DNAs in the Drosophila genome. Curr Opin Genet Dev (2002) 1.26
Developmental and evolutionary basis for drought tolerance of the Anopheles gambiae embryo. Dev Biol (2009) 1.26
Localized repressors delineate the neurogenic ectoderm in the early Drosophila embryo. Dev Biol (2005) 1.23
Ventral dominance governs sequential patterns of gene expression across the dorsal-ventral axis of the neuroectoderm in the Drosophila embryo. Dev Biol (2003) 1.19
Whole-genome analysis of Drosophila gastrulation. Curr Opin Genet Dev (2004) 1.18
A genomewide survey of developmentally relevant genes in Ciona intestinalis. I. Genes for bHLH transcription factors. Dev Genes Evol (2003) 1.18
ELAV mediates 3' UTR extension in the Drosophila nervous system. Genes Dev (2012) 1.16
Linear signaling in the Toll-Dorsal pathway of Drosophila: activated Pelle kinase specifies all threshold outputs of gene expression while the bHLH protein Twist specifies a subset. Development (2002) 1.16
FoxF is essential for FGF-induced migration of heart progenitor cells in the ascidian Ciona intestinalis. Development (2007) 1.15
International EMS systems: The United States: past, present, and future. Resuscitation (2004) 1.14
Precision of hunchback expression in the Drosophila embryo. Curr Biol (2012) 1.14
Gene regulatory networks underlying the compartmentalization of the Ciona central nervous system. Development (2008) 1.12
A genomewide survey of developmentally relevant genes in Ciona intestinalis. II. Genes for homeobox transcription factors. Dev Genes Evol (2003) 1.11
Rapid transcription fosters coordinate snail expression in the Drosophila embryo. Cell Rep (2013) 1.10
Analysis of the Tribolium homeotic complex: insights into mechanisms constraining insect Hox clusters. Dev Genes Evol (2008) 1.09
The cardiovascular effects of cocaine. J Emerg Med (2005) 1.08
Electroporation of transgenic DNAs in the sea squirt Ciona. Cold Spring Harb Protoc (2009) 1.07
The Snail repressor positions Notch signaling in the Drosophila embryo. Development (2002) 1.06
Organization of developmental enhancers in the Drosophila embryo. Nucleic Acids Res (2009) 1.06
Acute Methylenedioxypyrovalerone Toxicity. J Med Toxicol (2015) 1.04
The polycomb group mutant esc leads to augmented levels of paused Pol II in the Drosophila embryo. Mol Cell (2011) 1.02
Neural tube patterning by Ephrin, FGF and Notch signaling relays. Development (2011) 1.02
FGF signaling establishes the anterior border of the Ciona neural tube. Development (2012) 1.00
The Drosophila gap gene network is composed of two parallel toggle switches. PLoS One (2011) 1.00
Evolving enhancer-promoter interactions within the tinman complex of the flour beetle, Tribolium castaneum. Development (2009) 0.99
Analyzing gene regulation in ascidian embryos: new tools for new perspectives. Differentiation (2002) 0.99
A genomewide survey of developmentally relevant genes in Ciona intestinalis. III. Genes for Fox, ETS, nuclear receptors and NFkappaB. Dev Genes Evol (2003) 0.98
Conservation patterns in different functional sequence categories of divergent Drosophila species. Genomics (2006) 0.97
Ethanol ingestion in two infants under 2 months old: a previously unreported cause of ALTE. Pediatrics (2013) 0.93
Vectors and parameters that enhance the efficacy of RNAi-mediated gene disruption in transgenic Drosophila. Proc Natl Acad Sci U S A (2010) 0.93
Spatio-temporal intersection of Lhx3 and Tbx6 defines the cardiac field through synergistic activation of Mesp. Dev Biol (2009) 0.92
FGF3 in the floor plate directs notochord convergent extension in the Ciona tadpole. Development (2008) 0.91
Neuronal subtype specification in the spinal cord of a protovertebrate. Development (2011) 0.91
Transcriptional repression via antilooping in the Drosophila embryo. Proc Natl Acad Sci U S A (2012) 0.89
Tail morphogenesis in the ascidian, Ciona intestinalis, requires cooperation between notochord and muscle. Dev Biol (2002) 0.89
Isolation of sea squirt (Ciona) gametes, fertilization, dechorionation, and development. Cold Spring Harb Protoc (2009) 0.89
Whole-mount in situ hybridization on sea squirt (Ciona intestinalis) embryos. Cold Spring Harb Protoc (2009) 0.89
CtBP-independent repression in the Drosophila embryo. Mol Cell Biol (2003) 0.89
Media effects of experimental presentation of the ideal physique on eating disorder symptoms: a meta-analysis of laboratory studies. Clin Psychol Rev (2012) 0.89
BMP signaling coordinates gene expression and cell migration during precardiac mesoderm development. Dev Biol (2009) 0.88
Mosaic and regulative development: two faces of one coin. Curr Biol (2006) 0.88
Unraveling genomic regulatory networks in the simple chordate, Ciona intestinalis. Genome Res (2005) 0.88
Time series analysis of human and bovine brucellosis in South Korea from 2005 to 2010. Prev Vet Med (2012) 0.88
Control of intercalation is cell-autonomous in the notochord of Ciona intestinalis. Dev Biol (2002) 0.86
Modified reperfusion and ischemia-reperfusion injury in human lung transplantation. J Thorac Cardiovasc Surg (2003) 0.86
Liberalization of donor criteria in lung transplantation. Am Surg (2003) 0.84
p120RasGAP mediates ephrin/Eph-dependent attenuation of FGF/ERK signals during cell fate specification in ascidian embryos. Development (2013) 0.84
Whole-genome expression profiles identify gene batteries in Drosophila. Dev Cell (2002) 0.84
The sea squirt Ciona intestinalis. Cold Spring Harb Protoc (2009) 0.84
Morphogen gradients: limits to signaling or limits to measurement? Curr Biol (2010) 0.82
Case files of the medical toxicology fellowship at Banner Good Samaritan Medical Center in Phoenix, AZ: methemoglobinemia following dapsone exposure. J Med Toxicol (2011) 0.82
Meteorological influence on the occurrence of gastric dilatation-volvulus in military working dogs in Texas. Int J Biometeorol (2007) 0.81
Microinjection of morpholino oligos and RNAs in sea squirt (Ciona) embryos. Cold Spring Harb Protoc (2009) 0.81
Isolation of individual cells and tissues from electroporated sea squirt (Ciona) embryos by fluorescence-activated cell sorting (FACS). Cold Spring Harb Protoc (2009) 0.80
Computational identification of regulatory DNAs underlying animal development. Nat Methods (2005) 0.80
Toxicology in the ICU: Part 2: specific toxins. Chest (2011) 0.80
Diphenhydramine-induced Brugada pattern. Resuscitation (2010) 0.80