Published in Genome Biol on October 13, 2006
Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide. Cell (2008) 9.02
Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell (2012) 1.99
Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis. BMC Mol Biol (2008) 1.73
Identification of microRNAs involved in pathogen-associated molecular pattern-triggered plant innate immunity. Plant Physiol (2010) 1.54
Distinct expression patterns of natural antisense transcripts in Arabidopsis. Plant Physiol (2007) 1.52
Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. Genome Res (2008) 1.51
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Global identification and characterization of transcriptionally active regions in the rice genome. PLoS One (2007) 1.41
Miniature inverted-repeat transposable elements (MITEs) have been accumulated through amplification bursts and play important roles in gene expression and species diversity in Oryza sativa. Mol Biol Evol (2011) 1.39
Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions. Plant J (2011) 1.33
Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa. Genome Res (2008) 1.28
A rice cis-natural antisense RNA acts as a translational enhancer for its cognate mRNA and contributes to phosphate homeostasis and plant fitness. Plant Cell (2013) 1.08
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Sugarcane functional genomics: gene discovery for agronomic trait development. Int J Plant Genomics (2008) 1.04
Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation. Nucleic Acids Res (2008) 1.03
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Evidence for common short natural trans sense-antisense pairing between transcripts from protein coding genes. Genome Biol (2008) 0.94
Extending the sRNAome of apple by next-generation sequencing. PLoS One (2014) 0.90
Regulatory mechanisms of long noncoding RNAs in vertebrate central nervous system development and function. Neuroscience (2013) 0.89
Analysis of wheat SAGE tags reveals evidence for widespread antisense transcription. BMC Genomics (2008) 0.88
Pseudogenes as an alternative source of natural antisense transcripts. BMC Evol Biol (2010) 0.87
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Bioinformatics in China: a personal perspective. PLoS Comput Biol (2008) 0.83
Transcriptional analysis of the Arabidopsis ovule by massively parallel signature sequencing. J Exp Bot (2012) 0.83
Prediction and identification of natural antisense transcripts and their small RNAs in soybean (Glycine max). BMC Genomics (2013) 0.78
Natural antisense transcripts of Trifolium repens dehydrins. Plant Signal Behav (2013) 0.77
Natural antisense transcripts in plants: a review and identification in soybean infected with Phakopsora pachyrhizi SuperSAGE library. ScientificWorldJournal (2013) 0.76
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The hunt for hypoxia responsive natural antisense short interfering RNAs. Plant Signal Behav (2010) 0.75
In Silico identification and annotation of non-coding RNAs by RNA-seq and De Novo assembly of the transcriptome of Tomato Fruits. PLoS One (2017) 0.75
Upregulation of LINC-AP2 is negatively correlated with AP2 gene expression with Turnip crinkle virus infection in Arabidopsis thaliana. Plant Cell Rep (2016) 0.75
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Characterizing gene sets with FuncAssociate. Bioinformatics (2003) 14.10
Elucidation of the small RNA component of the transcriptome. Science (2005) 8.66
Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell (2005) 7.58
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Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease. Nat Genet (2003) 5.38
Widespread RNA editing of embedded alu elements in the human transcriptome. Genome Res (2004) 5.14
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Specific interference with gene expression induced by long, double-stranded RNA in mouse embryonal teratocarcinoma cell lines. Proc Natl Acad Sci U S A (2001) 4.79
Dicing and slicing: the core machinery of the RNA interference pathway. FEBS Lett (2005) 4.63
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MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. Genome Res (2006) 4.08
In search of antisense. Trends Biochem Sci (2004) 3.93
MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for arabidopsis lateral root development. Plant Cell (2005) 3.88
Imprinting on distal chromosome 7 in the placenta involves repressive histone methylation independent of DNA methylation. Nat Genet (2004) 3.47
Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. Genome Res (2003) 3.40
Antisense transcripts in the human genome. Trends Genet (2002) 3.33
Computational discovery of sense-antisense transcription in the human and mouse genomes. Genome Biol (2002) 3.28
Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana. Genome Biol (2005) 2.80
Naturally occurring antisense: transcriptional leakage or real overlap? Genome Res (2005) 2.39
Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences. Nucleic Acids Res (2004) 2.19
Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation. Genome Biol (2005) 1.98
Inhibition of c-erbA mRNA splicing by a naturally occurring antisense RNA. J Biol Chem (1991) 1.98
Higher plant glycosyltransferases. Genome Biol (2001) 1.73
RNA editing and regulation of Drosophila 4f-rnp expression by sas-10 antisense readthrough mRNA transcripts. RNA (2003) 1.70
Antisense transcripts with rice full-length cDNAs. Genome Biol (2003) 1.69
Systematic identification of sense-antisense transcripts in mammalian cells. Nat Biotechnol (2003) 1.62
Naturally occurring antisense transcripts are present in chick embryo chondrocytes simultaneously with the down-regulation of the alpha 1 (I) collagen gene. J Biol Chem (1995) 1.12
Characterization of multiple alternative RNAs resulting from antisense transcription of the PR264/SC35 splicing factor gene. Nucleic Acids Res (1997) 1.08
Role of sequences within the first intron in the regulation of expression of eukaryotic initiation factor 2 alpha. J Biol Chem (1992) 1.07
Expression and regulation of the Msx1 natural antisense transcript during development. Nucleic Acids Res (2005) 0.95
Open reading frames provide a rich pool of potential natural antisense transcripts in fungal genomes. Nucleic Acids Res (2005) 0.91
GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res (2008) 6.91
A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii. Genes Dev (2007) 4.95
Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature (2006) 4.68
Expression dynamics of the pea rbcS multigene family and organ distribution of the transcripts. EMBO J (1986) 4.57
Agrobacterium-mediated transformation of Arabidopsis thaliana using the floral dip method. Nat Protoc (2006) 4.41
ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol Cell (2012) 4.18
MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for arabidopsis lateral root development. Plant Cell (2005) 3.88
Cucumber mosaic virus-encoded 2b suppressor inhibits Arabidopsis Argonaute1 cleavage activity to counter plant defense. Genes Dev (2006) 3.77
Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol (2004) 3.66
LAF1 ubiquitination by COP1 controls photomorphogenesis and is stimulated by SPA1. Nature (2003) 3.47
ABI5 acts downstream of ABI3 to execute an ABA-dependent growth arrest during germination. Plant J (2002) 3.28
SINAT5 promotes ubiquitin-related degradation of NAC1 to attenuate auxin signals. Nature (2002) 2.94
ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination. Plant J (2007) 2.84
The WUSCHEL gene promotes vegetative-to-embryonic transition in Arabidopsis. Plant J (2002) 2.83
Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana. Genome Biol (2005) 2.80
Prediction and identification of herpes simplex virus 1-encoded microRNAs. J Virol (2006) 2.67
Expression of artificial microRNAs in transgenic Arabidopsis thaliana confers virus resistance. Nat Biotechnol (2006) 2.64
Activation of the imprinted Dlk1-Dio3 region correlates with pluripotency levels of mouse stem cells. J Biol Chem (2010) 2.59
PSEUDO-RESPONSE REGULATORS 9, 7, and 5 are transcriptional repressors in the Arabidopsis circadian clock. Plant Cell (2010) 2.57
The GIGANTEA-regulated microRNA172 mediates photoperiodic flowering independent of CONSTANS in Arabidopsis. Plant Cell (2007) 2.53
HFR1 is targeted by COP1 E3 ligase for post-translational proteolysis during phytochrome A signaling. Genes Dev (2005) 2.48
The AIP2 E3 ligase acts as a novel negative regulator of ABA signaling by promoting ABI3 degradation. Genes Dev (2005) 2.47
Genome-wide gene expression profiling in Arabidopsis thaliana reveals new targets of abscisic acid and largely impaired gene regulation in the abi1-1 mutant. J Cell Sci (2002) 2.32
AFP is a novel negative regulator of ABA signaling that promotes ABI5 protein degradation. Genes Dev (2003) 2.22
Arabidopsis DCP2, DCP1, and VARICOSE form a decapping complex required for postembryonic development. Plant Cell (2006) 2.13
Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids. Proc Natl Acad Sci U S A (2009) 2.08
Photoreceptor ubiquitination by COP1 E3 ligase desensitizes phytochrome A signaling. Genes Dev (2004) 2.08
The Arabidopsis auxin-inducible gene ARGOS controls lateral organ size. Plant Cell (2003) 2.06
Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell (2012) 1.99
microRNA-directed cleavage of ATHB15 mRNA regulates vascular development in Arabidopsis inflorescence stems. Plant J (2005) 1.92
Phytochrome signalling modulates the SA-perceptive pathway in Arabidopsis. Plant J (2002) 1.85
A membrane-bound NAC transcription factor regulates cell division in Arabidopsis. Plant Cell (2006) 1.80
LEAFY COTYLEDON1 is a key regulator of fatty acid biosynthesis in Arabidopsis. Plant Physiol (2008) 1.79
The Arabidopsis E3 SUMO ligase SIZ1 regulates plant growth and drought responses. Plant Cell (2007) 1.79
Small ubiquitin-like modifier modulates abscisic acid signaling in Arabidopsis. Plant Cell (2003) 1.70
Direct reprogramming of Sertoli cells into multipotent neural stem cells by defined factors. Cell Res (2011) 1.67
Insights into salt tolerance from the genome of Thellungiella salsuginea. Proc Natl Acad Sci U S A (2012) 1.62
Arabidopsis PHYTOCHROME INTERACTING FACTOR proteins promote phytochrome B polyubiquitination by COP1 E3 ligase in the nucleus. Plant Cell (2010) 1.59
betaC1, the pathogenicity factor of TYLCCNV, interacts with AS1 to alter leaf development and suppress selective jasmonic acid responses. Genes Dev (2008) 1.55
Targeted degradation of PSEUDO-RESPONSE REGULATOR5 by an SCFZTL complex regulates clock function and photomorphogenesis in Arabidopsis thaliana. Plant Cell (2007) 1.52
Androgenetic haploid embryonic stem cells produce live transgenic mice. Nature (2012) 1.51
A chemical-regulated inducible RNAi system in plants. Plant J (2003) 1.49
F-box proteins FKF1 and LKP2 act in concert with ZEITLUPE to control Arabidopsis clock progression. Plant Cell (2010) 1.48
PsRobot: a web-based plant small RNA meta-analysis toolbox. Nucleic Acids Res (2012) 1.43
Roles of DCL4 and DCL3b in rice phased small RNA biogenesis. Plant J (2011) 1.42
Cell type-specific role of the retinoblastoma/E2F pathway during Arabidopsis leaf development. Plant Physiol (2005) 1.42
Structure of Arabidopsis HYPONASTIC LEAVES1 and its molecular implications for miRNA processing. Structure (2010) 1.41
N6-methyl-adenosine (m6A) in RNA: an old modification with a novel epigenetic function. Genomics Proteomics Bioinformatics (2012) 1.41
Visualization of peroxisomes in living plant cells reveals acto-myosin-dependent cytoplasmic streaming and peroxisome budding. Plant Cell Physiol (2002) 1.38
Widespread long noncoding RNAs as endogenous target mimics for microRNAs in plants. Plant Physiol (2013) 1.38
The novel MYB protein EARLY-PHYTOCHROME-RESPONSIVE1 is a component of a slave circadian oscillator in Arabidopsis. Plant Cell (2003) 1.35
Comparative analysis of JmjC domain-containing proteins reveals the potential histone demethylases in Arabidopsis and rice. J Integr Plant Biol (2008) 1.35
Two cap-binding proteins CBP20 and CBP80 are involved in processing primary MicroRNAs. Plant Cell Physiol (2008) 1.35
Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions. Plant J (2011) 1.33
The Arabidopsis ARGOS-LIKE gene regulates cell expansion during organ growth. Plant J (2006) 1.31
Structure and biochemical function of a prototypical Arabidopsis U-box domain. J Biol Chem (2004) 1.27
Regulated proteolysis in light-related signaling pathways. Curr Opin Plant Biol (2008) 1.27
The Arabidopsis AtIPT8/PGA22 gene encodes an isopentenyl transferase that is involved in de novo cytokinin biosynthesis. Plant Physiol (2003) 1.25
ASYMMETRIC LEAVES2-LIKE19/LATERAL ORGAN BOUNDARIES DOMAIN30 and ASL20/LBD18 regulate tracheary element differentiation in Arabidopsis. Plant Cell (2008) 1.25
Arabidopsis decapping 5 is required for mRNA decapping, P-body formation, and translational repression during postembryonic development. Plant Cell (2009) 1.24
Small RNA profiling in two Brassica napus cultivars identifies microRNAs with oil production- and development-correlated expression and new small RNA classes. Plant Physiol (2011) 1.23
ABA activates ADPR cyclase and cADPR induces a subset of ABA-responsive genes in Arabidopsis. Plant J (2004) 1.23
A HEX-1 crystal lattice required for Woronin body function in Neurospora crassa. Nat Struct Biol (2003) 1.23
Monitoring genome-wide changes in gene expression in response to endogenous cytokinin reveals targets in Arabidopsis thaliana. FEBS Lett (2003) 1.22
Growth inhibition and apoptosis induction of tanshinone II-A on human hepatocellular carcinoma cells. World J Gastroenterol (2004) 1.21
Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis. Genome Res (2014) 1.20
Bidirectional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1. Nat Struct Mol Biol (2013) 1.20
Modulation of sensitivity and selectivity in plant signaling by proteasomal destabilization. Curr Opin Plant Biol (2003) 1.20
Conserved miRNA analysis in Gossypium hirsutum through small RNA sequencing. Genomics (2009) 1.18
FHL is required for full phytochrome A signaling and shares overlapping functions with FHY1. Plant J (2005) 1.18
The ENHANCER OF SHOOT REGENERATION 2 gene in Arabidopsis regulates CUP-SHAPED COTYLEDON 1 at the transcriptional level and controls cotyledon development. Plant Cell Physiol (2006) 1.17
The ethylene receptor ETR2 delays floral transition and affects starch accumulation in rice. Plant Cell (2009) 1.16
FAR-RED ELONGATED HYPOCOTYL1 and FHY1-LIKE associate with the Arabidopsis transcription factors LAF1 and HFR1 to transmit phytochrome A signals for inhibition of hypocotyl elongation. Plant Cell (2009) 1.15
NITROGEN LIMITATION ADAPTATION recruits PHOSPHATE2 to target the phosphate transporter PT2 for degradation during the regulation of Arabidopsis phosphate homeostasis. Plant Cell (2014) 1.13
Genomic resources for songbird research and their use in characterizing gene expression during brain development. Proc Natl Acad Sci U S A (2007) 1.13
Excision of selectable marker genes from transgenic plants. Nat Biotechnol (2002) 1.13
PP7 is a positive regulator of blue light signaling in Arabidopsis. Plant Cell (2003) 1.11
Rapid analysis of Jatropha curcas gene functions by virus-induced gene silencing. Plant Biotechnol J (2009) 1.11
Independent and interdependent functions of LAF1 and HFR1 in phytochrome A signaling. Genes Dev (2007) 1.10
The nuclear localization signal and the C-terminal region of FHY1 are required for transmission of phytochrome A signals. Plant J (2004) 1.09
The topological specificity factor AtMinE1 is essential for correct plastid division site placement in Arabidopsis. Plant J (2002) 1.08
The plant cytoskeleton: vacuoles and cell walls make the difference. Cell (2002) 1.08
Mir-24 regulates junctophilin-2 expression in cardiomyocytes. Circ Res (2012) 1.07
In vivo suppression of microRNA-24 prevents the transition toward decompensated hypertrophy in aortic-constricted mice. Circ Res (2013) 1.07
Molecular evolution of a viral non-coding sequence under the selective pressure of amiRNA-mediated silencing. PLoS Pathog (2009) 1.06
De novo centromere formation on a chromosome fragment in maize. Proc Natl Acad Sci U S A (2013) 1.05
PLncDB: plant long non-coding RNA database. Bioinformatics (2013) 1.05
Autologous platelet-rich fibrin matrix as cell therapy in the healing of chronic lower-extremity ulcers. Wound Repair Regen (2009) 1.05
AtNAP1 represents an atypical SufB protein in Arabidopsis plastids. J Biol Chem (2004) 1.05
Overexpression of PGA37/MYB118 and MYB115 promotes vegetative-to-embryonic transition in Arabidopsis. Cell Res (2009) 1.04
MicroRNAs in the shoot apical meristem of soybean. J Exp Bot (2011) 1.03
RING1 E3 ligase localizes to plasma membrane lipid rafts to trigger FB1-induced programmed cell death in Arabidopsis. Plant J (2008) 1.03
Processing bodies and plant development. Curr Opin Plant Biol (2010) 1.03
The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation. BMC Plant Biol (2012) 1.03
The Arabidopsis STICHEL gene is a regulator of trichome branch number and encodes a novel protein. Plant Physiol (2003) 1.02
Rapid and reversible light-mediated chromatin modifications of Arabidopsis phytochrome A locus. Plant Cell (2011) 1.02
The abi1-1 mutation blocks ABA signaling downstream of cADPR action. Plant J (2003) 1.01
The Arabidopsis SPA1 gene is required for circadian clock function and photoperiodic flowering. Plant J (2006) 1.01