Published in Hortic Res on July 05, 2017
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol (2010) 75.21
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc (2012) 35.75
Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature (2010) 22.04
Origins and Mechanisms of miRNAs and siRNAs. Cell (2009) 20.77
Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science (2009) 20.75
RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell (2000) 20.32
MicroRNAs in plants. Genes Dev (2002) 20.12
Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science (2002) 18.37
Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet (2010) 15.70
microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell (2005) 14.81
Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell (2003) 11.69
RNA sequencing: advances, challenges and opportunities. Nat Rev Genet (2010) 8.96
Natural RNA circles function as efficient microRNA sponges. Nature (2013) 8.93
A new generation of homology search tools based on probabilistic inference. Genome Inform (2009) 8.93
Circular RNAs are a large class of animal RNAs with regulatory potency. Nature (2013) 8.54
The genome of the cucumber, Cucumis sativus L. Nat Genet (2009) 8.19
Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell (2005) 7.58
STRUCTURE OF A RIBONUCLEIC ACID. Science (1965) 7.11
lincRNAs: genomics, evolution, and mechanisms. Cell (2013) 6.50
CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res (2007) 5.88
Long non-coding RNAs: new players in cell differentiation and development. Nat Rev Genet (2013) 5.48
Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science (2012) 4.61
Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum. Genes Dev (2007) 4.34
The molecular basis of vernalization: the central role of FLOWERING LOCUS C (FLC). Proc Natl Acad Sci U S A (2000) 4.34
Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science (2010) 4.23
A pathogen-inducible endogenous siRNA in plant immunity. Proc Natl Acad Sci U S A (2006) 3.48
Evolution and functional diversification of MIRNA genes. Plant Cell (2011) 3.07
Dual effects of miR156-targeted SPL genes and CYP78A5/KLUH on plastochron length and organ size in Arabidopsis thaliana. Plant Cell (2008) 2.87
pho2, a phosphate overaccumulator, is caused by a nonsense mutation in a microRNA399 target gene. Plant Physiol (2006) 2.77
DNA methylation mediated by a microRNA pathway. Mol Cell (2010) 2.74
Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish. Nucleic Acids Res (2013) 2.73
MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis. Plant J (2007) 2.65
Functions of microRNAs in plant stress responses. Trends Plant Sci (2012) 2.63
Circular intronic long noncoding RNAs. Mol Cell (2013) 2.62
Classification and comparison of small RNAs from plants. Annu Rev Plant Biol (2013) 2.60
Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. EMBO J (2014) 2.47
Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display. Nat Methods (2015) 2.42
Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet (2005) 2.39
Expanded identification and characterization of mammalian circular RNAs. Genome Biol (2014) 2.39
High-throughput functional genomics using CRISPR-Cas9. Nat Rev Genet (2015) 2.35
AGO1-miR173 complex initiates phased siRNA formation in plants. Proc Natl Acad Sci U S A (2008) 2.34
A microRNA superfamily regulates nucleotide binding site-leucine-rich repeats and other mRNAs. Plant Cell (2012) 2.32
Repression of AUXIN RESPONSE FACTOR10 by microRNA160 is critical for seed germination and post-germination stages. Plant J (2007) 2.15
miRDeepFinder: a miRNA analysis tool for deep sequencing of plant small RNAs. Plant Mol Biol (2012) 2.14
Complementary sequence-mediated exon circularization. Cell (2014) 2.10
MicroRNA regulation of plant innate immune receptors. Proc Natl Acad Sci U S A (2012) 2.04
Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays. BMC Genomics (2010) 2.03
Sulphur starvation induces the expression of microRNA-395 and one of its target genes but in different cell types. Plant J (2008) 2.01
Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell (2012) 1.99
Circular RNA is expressed across the eukaryotic tree of life. PLoS One (2014) 1.84
Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). BMC Plant Biol (2010) 1.81
Characterization of GmENOD40, a gene showing novel patterns of cell-specific expression during soybean nodule development. Plant J (1993) 1.81
miR319a targeting of TCP4 is critical for petal growth and development in Arabidopsis. Proc Natl Acad Sci U S A (2009) 1.73
Central cell-derived peptides regulate early embryo patterning in flowering plants. Science (2014) 1.66
Toddler: an embryonic signal that promotes cell movement via Apelin receptors. Science (2014) 1.66
Long noncoding RNA modulates alternative splicing regulators in Arabidopsis. Dev Cell (2014) 1.65
miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants. Bioinformatics (2011) 1.65
A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice. Proc Natl Acad Sci U S A (2012) 1.59
The Arabidopsis miR472-RDR6 silencing pathway modulates PAMP- and effector-triggered immunity through the post-transcriptional control of disease resistance genes. PLoS Pathog (2014) 1.59
Circular RNA ITCH has inhibitory effect on ESCC by suppressing the Wnt/β-catenin pathway. Oncotarget (2015) 1.58
Efficient gene editing in tomato in the first generation using the clustered regularly interspaced short palindromic repeats/CRISPR-associated9 system. Plant Physiol (2014) 1.53
Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. Genome Res (2008) 1.51
MicroRNA-mediated regulation of stomatal development in Arabidopsis. Plant Cell (2007) 1.50
Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis. Proc Natl Acad Sci U S A (2013) 1.48
Proper regulation of a sperm-specific cis-nat-siRNA is essential for double fertilization in Arabidopsis. Genes Dev (2010) 1.44
Long noncoding RNAs in development and disease of the central nervous system. Trends Genet (2013) 1.42
AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling. Plant Physiol (2009) 1.33
Stress-induced alternative splicing provides a mechanism for the regulation of microRNA processing in Arabidopsis thaliana. Mol Cell (2012) 1.31
The microRNA159-regulated GAMYB-like genes inhibit growth and promote programmed cell death in Arabidopsis. Plant Physiol (2010) 1.30
Targeted genome modifications in soybean with CRISPR/Cas9. BMC Biotechnol (2015) 1.28
Functional specialization of the plant miR396 regulatory network through distinct microRNA-target interactions. PLoS Genet (2012) 1.27
Targeted genome editing of sweet orange using Cas9/sgRNA. PLoS One (2014) 1.26
Targeting non-coding RNAs with the CRISPR/Cas9 system in human cell lines. Nucleic Acids Res (2014) 1.26
RNA exosome-regulated long non-coding RNA transcription controls super-enhancer activity. Cell (2015) 1.25
CIRI: an efficient and unbiased algorithm for de novo circular RNA identification. Genome Biol (2015) 1.25
Establishing leaf polarity: the role of small RNAs and positional signals in the shoot apex. Development (2007) 1.24
Small open reading frames associated with morphogenesis are hidden in plant genomes. Proc Natl Acad Sci U S A (2013) 1.21
Function and evolution of a MicroRNA that regulates a Ca2+-ATPase and triggers the formation of phased small interfering RNAs in tomato reproductive growth. Plant Cell (2011) 1.20
Auxin regulation of the microRNA390-dependent transacting small interfering RNA pathway in Arabidopsis lateral root development. Nucleic Acids Res (2009) 1.19
Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice. Genome Biol (2014) 1.18
Visiting "noncodarnia". Biotechniques (2013) 1.18
cis- and trans-Regulation of miR163 and target genes confers natural variation of secondary metabolites in two Arabidopsis species and their allopolyploids. Plant Cell (2011) 1.15
Primary transcripts of microRNAs encode regulatory peptides. Nature (2015) 1.13
Enod40, a short open reading frame-containing mRNA, induces cytoplasmic localization of a nuclear RNA binding protein in Medicago truncatula. Plant Cell (2004) 1.12
An autoregulatory feedback loop involving PAP1 and TAS4 in response to sugars in Arabidopsis. Plant Mol Biol (2011) 1.11
Translation of CircRNAs. Mol Cell (2017) 1.11
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
Translational and structural requirements of the early nodulin gene enod40, a short-open reading frame-containing RNA, for elicitation of a cell-specific growth response in the alfalfa root cortex. Mol Cell Biol (2001) 1.07
Functional consequences of splicing of the antisense transcript COOLAIR on FLC transcription. Mol Cell (2014) 1.07
Discovery and annotation of small proteins using genomics, proteomics, and computational approaches. Genome Res (2011) 1.06
Identification of microRNAs from Amur grape (Vitis amurensis Rupr.) by deep sequencing and analysis of microRNA variations with bioinformatics. BMC Genomics (2012) 1.04
Small RNA and transcriptome deep sequencing proffers insight into floral gene regulation in Rosa cultivars. BMC Genomics (2012) 1.03
Deep RNA-Seq uncovers the peach transcriptome landscape. Plant Mol Biol (2013) 1.03
The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14. Nat Commun (2013) 1.03
Identification and characterization of miRNA transcriptome in potato by high-throughput sequencing. PLoS One (2013) 1.03
Technologies to probe functions and mechanisms of long noncoding RNAs. Nat Struct Mol Biol (2015) 1.03
Small-interfering RNAs from natural antisense transcripts derived from a cellulose synthase gene modulate cell wall biosynthesis in barley. Proc Natl Acad Sci U S A (2008) 0.99
Plant microRNAs and development. J Genet Genomics (2013) 0.99
Biogenesis and function of rice small RNAs from non-coding RNA precursors. Curr Opin Plant Biol (2013) 0.99
PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme. BMC Bioinformatics (2014) 0.98
Advances and perspectives on the use of CRISPR/Cas9 systems in plant genomics research. Curr Opin Plant Biol (2016) 0.95