Published in PLoS One on March 26, 2010
A microRNA superfamily regulates nucleotide binding site-leucine-rich repeats and other mRNAs. Plant Cell (2012) 2.32
Sequencing of RDR6-dependent double-stranded RNAs reveals novel features of plant siRNA biogenesis. Nucleic Acids Res (2012) 1.03
High-throughput sequencing of RNA silencing-associated small RNAs in olive (Olea europaea L.). PLoS One (2011) 1.02
NPK macronutrients and microRNA homeostasis. Front Plant Sci (2015) 0.94
Identification of stable, high copy number, medium-sized RNA degradation intermediates that accumulate in plants under non-stress conditions. Plant Mol Biol (2013) 0.91
Gene regulatory network inference from multifactorial perturbation data using both regression and correlation analyses. PLoS One (2012) 0.84
HC-Pro silencing suppressor significantly alters the gene expression profile in tobacco leaves and flowers. BMC Plant Biol (2011) 0.84
Trans-acting small interfering RNA4: key to nutraceutical synthesis in grape development? Trends Plant Sci (2013) 0.79
Biogenesis and Biological Activity of Secondary siRNAs in Plants. Scientifica (Cairo) (2013) 0.78
Organ-specific alterations in tobacco transcriptome caused by the PVX-derived P25 silencing suppressor transgene. BMC Plant Biol (2013) 0.77
Cotton Leaf Curl Multan Virus-Derived Viral Small RNAs Can Target Cotton Genes to Promote Viral Infection. Front Plant Sci (2016) 0.76
Jacalin lectin At5g28520 is regulated by ABA and miR846. Plant Signal Behav (2013) 0.76
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
Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A (1988) 193.60
Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res (2003) 103.76
Collective dynamics of 'small-world' networks. Nature (1998) 98.45
Emergence of scaling in random networks Science (1999) 89.38
Whole-genome re-sequencing. Curr Opin Genet Dev (2006) 35.24
Exploring complex networks. Nature (2001) 21.06
Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet (2002) 19.57
microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell (2005) 14.81
A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev (2006) 11.71
Characterization of the piRNA complex from rat testes. Science (2006) 7.86
Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell (2005) 7.58
A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev (2005) 6.04
A two-hit trigger for siRNA biogenesis in plants. Cell (2006) 5.60
DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2005) 5.16
Pentatricopeptide repeat proteins: a socket set for organelle gene expression. Trends Plant Sci (2008) 4.70
DRB4-dependent TAS3 trans-acting siRNAs control leaf morphology through AGO7. Curr Biol (2006) 3.90
Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. Plant Cell (2007) 3.40
Trans-acting siRNA-mediated repression of ETTIN and ARF4 regulates heteroblasty in Arabidopsis. Development (2006) 2.93
Large-scale topological and dynamical properties of the Internet. Phys Rev E Stat Nonlin Soft Matter Phys (2002) 2.77
AGO1-miR173 complex initiates phased siRNA formation in plants. Proc Natl Acad Sci U S A (2008) 2.34
Bioinformatic prediction and experimental validation of a microRNA-directed tandem trans-acting siRNA cascade in Arabidopsis. Proc Natl Acad Sci U S A (2007) 2.28
On the expansion of the pentatricopeptide repeat gene family in plants. Mol Biol Evol (2008) 2.15
The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties. Genome Biol (2002) 1.59
RNA secondary structure analysis using the Vienna RNA package. Curr Protoc Bioinformatics (2004) 1.32
Transposon-mediated expansion and diversification of a family of ULP-like genes. Mol Biol Evol (2006) 1.15
Short silencing RNA: the dark matter of genetics? Cold Spring Harb Symp Quant Biol (2006) 1.09
Networks: teasing out the missing links. Nature (2008) 0.93
The Pfam protein families database. Nucleic Acids Res (2004) 56.46
InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53
Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature (2009) 6.44
miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature (2007) 4.72
Modulation of floral development by a gibberellin-regulated microRNA. Development (2004) 4.31
Spreading of RNA targeting and DNA methylation in RNA silencing requires transcription of the target gene and a putative RNA-dependent RNA polymerase. Plant Cell (2002) 3.73
Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells. Science (2010) 3.57
PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis. Proc Natl Acad Sci U S A (2008) 3.33
Application of 'next-generation' sequencing technologies to microbial genetics. Nat Rev Microbiol (2009) 3.30
High throughput virus-induced gene silencing implicates heat shock protein 90 in plant disease resistance. EMBO J (2003) 3.25
An RNA-dependent RNA polymerase prevents meristem invasion by potato virus X and is required for the activity but not the production of a systemic silencing signal. Plant Physiol (2005) 3.14
Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature (2009) 3.01
Interaction between domains of a plant NBS-LRR protein in disease resistance-related cell death. EMBO J (2002) 2.90
A toolkit for analysing large-scale plant small RNA datasets. Bioinformatics (2008) 2.80
Ubiquitin ligase-associated protein SGT1 is required for host and nonhost disease resistance in plants. Proc Natl Acad Sci U S A (2002) 2.76
22-Nucleotide RNAs trigger secondary siRNA biogenesis in plants. Proc Natl Acad Sci U S A (2010) 2.74
Genome evolution following host jumps in the Irish potato famine pathogen lineage. Science (2010) 2.62
An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. Plant Cell (2007) 2.55
The Arabidopsis RNA-directed DNA methylation argonautes functionally diverge based on their expression and interaction with target loci. Plant Cell (2010) 2.51
De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads. FEMS Microbiol Lett (2008) 2.50
The Polerovirus silencing suppressor P0 targets ARGONAUTE proteins for degradation. Curr Biol (2007) 2.48
Constitutive gain-of-function mutants in a nucleotide binding site-leucine rich repeat protein encoded at the Rx locus of potato. Plant J (2002) 2.43
Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana. PLoS Biol (2011) 2.38
A microRNA superfamily regulates nucleotide binding site-leucine-rich repeats and other mRNAs. Plant Cell (2012) 2.32
Virus-induced gene silencing in plants. Methods (2003) 2.29
De novo assembly of short sequence reads. Brief Bioinform (2010) 2.29
Cloning and characterization of micro-RNAs from moss. Plant J (2005) 2.19
Defective RNA processing enhances RNA silencing and influences flowering of Arabidopsis. Proc Natl Acad Sci U S A (2006) 2.05
Extraordinary transgressive phenotypes of hybrid tomato are influenced by epigenetics and small silencing RNAs. EMBO J (2011) 1.98
Multimegabase silencing in nucleolar dominance involves siRNA-directed DNA methylation and specific methylcytosine-binding proteins. Mol Cell (2008) 1.94
Identification and characterization of small RNAs from the phloem of Brassica napus. Plant J (2007) 1.92
An atypical RNA polymerase involved in RNA silencing shares small subunits with RNA polymerase II. Nat Struct Mol Biol (2008) 1.90
An antiviral defense role of AGO2 in plants. PLoS One (2011) 1.88
Elicitor-mediated oligomerization of the tobacco N disease resistance protein. Plant Cell (2005) 1.84
Comparative genome analysis provides insights into the evolution and adaptation of Pseudomonas syringae pv. aesculi on Aesculus hippocastanum. PLoS One (2010) 1.80
Pseudomonas syringae pv. actinidiae (PSA) isolates from recent bacterial canker of kiwifruit outbreaks belong to the same genetic lineage. PLoS One (2012) 1.75
G8: a novel domain associated with polycystic kidney disease and non-syndromic hearing loss. Bioinformatics (2006) 1.71
An EDS1 orthologue is required for N-mediated resistance against tobacco mosaic virus. Plant J (2002) 1.69
Genome sequence of Azotobacter vinelandii, an obligate aerobe specialized to support diverse anaerobic metabolic processes. J Bacteriol (2009) 1.64
Widespread role for the flowering-time regulators FCA and FPA in RNA-mediated chromatin silencing. Science (2007) 1.63
Multidimensional protein identification technology (MudPIT) analysis of ubiquitinated proteins in plants. Mol Cell Proteomics (2007) 1.57
A draft genome sequence of Pseudomonas syringae pv. tomato T1 reveals a type III effector repertoire significantly divergent from that of Pseudomonas syringae pv. tomato DC3000. Mol Plant Microbe Interact (2009) 1.52
The plant pathogen Pseudomonas syringae pv. tomato is genetically monomorphic and under strong selection to evade tomato immunity. PLoS Pathog (2011) 1.52
Intercellular and systemic movement of RNA silencing signals. EMBO J (2011) 1.52
Nonagricultural reservoirs contribute to emergence and evolution of Pseudomonas syringae crop pathogens. New Phytol (2013) 1.51
Virus-induced gene silencing in Solanum species. Plant J (2004) 1.45
NRG1, a CC-NB-LRR protein, together with N, a TIR-NB-LRR protein, mediates resistance against tobacco mosaic virus. Curr Biol (2005) 1.36
Identification of trans-acting siRNAs in moss and an RNA-dependent RNA polymerase required for their biogenesis. Plant J (2006) 1.33
Stepwise artificial evolution of a plant disease resistance gene. Proc Natl Acad Sci U S A (2013) 1.33
Cell-to-cell movement of potato potexvirus X is dependent on suppression of RNA silencing. Plant J (2005) 1.30
Genome-wide survey of Arabidopsis natural variation in downy mildew resistance using combined association and linkage mapping. Proc Natl Acad Sci U S A (2010) 1.29
Multiple candidate effectors from the oomycete pathogen Hyaloperonospora arabidopsidis suppress host plant immunity. PLoS Pathog (2011) 1.29
Physical association of the NB-LRR resistance protein Rx with a Ran GTPase-activating protein is required for extreme resistance to Potato virus X. Plant Cell (2007) 1.29
Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis thaliana. J Proteomics (2009) 1.25
The silencing suppressor P25 of Potato virus X interacts with Argonaute1 and mediates its degradation through the proteasome pathway. Mol Plant Pathol (2010) 1.24
Putative Arabidopsis THO/TREX mRNA export complex is involved in transgene and endogenous siRNA biosynthesis. Proc Natl Acad Sci U S A (2010) 1.21
SDE5, the putative homologue of a human mRNA export factor, is required for transgene silencing and accumulation of trans-acting endogenous siRNA. Plant J (2007) 1.19
Maternal siRNAs as regulators of parental genome imbalance and gene expression in endosperm of Arabidopsis seeds. Proc Natl Acad Sci U S A (2012) 1.16
Silencing signals in plants: a long journey for small RNAs. Genome Biol (2011) 1.15
JMJ14, a JmjC domain protein, is required for RNA silencing and cell-to-cell movement of an RNA silencing signal in Arabidopsis. Genes Dev (2010) 1.15
Analysis of small RNA in fission yeast; centromeric siRNAs are potentially generated through a structured RNA. EMBO J (2009) 1.14
Artificial evolution extends the spectrum of viruses that are targeted by a disease-resistance gene from potato. Proc Natl Acad Sci U S A (2006) 1.13
Profiling the secretomes of plant pathogenic Proteobacteria. FEMS Microbiol Rev (2005) 1.12
Translational recoding signals between gag and pol in diverse LTR retrotransposons. RNA (2003) 1.10
AGO6 functions in RNA-mediated transcriptional gene silencing in shoot and root meristems in Arabidopsis thaliana. PLoS One (2011) 1.09
Pseudomonas syringae strains naturally lacking the classical P. syringae hrp/hrc Locus are common leaf colonizers equipped with an atypical type III secretion system. Mol Plant Microbe Interact (2010) 1.08
Mobile 24 nt small RNAs direct transcriptional gene silencing in the root meristems of Arabidopsis thaliana. Curr Biol (2011) 1.07
SIRE1, an endogenous retrovirus family from Glycine max, is highly homogeneous and evolutionarily young. Mol Biol Evol (2003) 1.06
DNA binding activity of the Escherichia coli nitric oxide sensor NorR suggests a conserved target sequence in diverse proteobacteria. J Bacteriol (2004) 1.04
Tobacco rattle virus 16-kilodalton protein encodes a suppressor of RNA silencing that allows transient viral entry in meristems. J Virol (2008) 1.04
PhosCalc: a tool for evaluating the sites of peptide phosphorylation from mass spectrometer data. BMC Res Notes (2008) 1.04
Silencing of a gene encoding a protein component of the oxygen-evolving complex of photosystem II enhances virus replication in plants. Virology (2002) 1.00
Deletion of a previously uncharacterized flagellar-hook-length control gene fliK modulates the sigma54-dependent regulon in Campylobacter jejuni. Microbiology (2007) 0.96
Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects. Sci Rep (2013) 0.95
Genome-wide sequencing of Phytophthora lateralis reveals genetic variation among isolates from Lawson cypress (Chamaecyparis lawsoniana) in Northern Ireland. FEMS Microbiol Lett (2013) 0.93
Integrated bioinformatic and phenotypic analysis of RpoN-dependent traits in the plant growth-promoting bacterium Pseudomonas fluorescens SBW25. Environ Microbiol (2007) 0.91
Draft genome sequence of Pseudomonas fuscovaginae, a broad-host-range pathogen of plants. J Bacteriol (2012) 0.90
Identifying small interfering RNA loci from high-throughput sequencing data. Bioinformatics (2011) 0.89
RNA silencing of hydrogenase(-like) genes and investigation of their physiological roles in the green alga Chlamydomonas reinhardtii. Biochem J (2010) 0.87
An atypical epigenetic mechanism affects uniparental expression of Pol IV-dependent siRNAs. PLoS One (2011) 0.86
Recently published Streptomyces genome sequences. Microb Biotechnol (2014) 0.86
Draft genome sequence of Pseudomonas syringae pathovar syringae strain FF5, causal agent of stem tip dieback disease on ornamental pear. J Bacteriol (2012) 0.86
Metastable differentially methylated regions within Arabidopsis inbred populations are associated with modified expression of non-coding transcripts. PLoS One (2012) 0.85
Draft Genome Sequence of Erwinia toletana, a Bacterium Associated with Olive Knots Caused by Pseudomonas savastanoi pv. Savastanoi. Genome Announc (2013) 0.85
Heterologous expression of pyruvate decarboxylase in Geobacillus thermoglucosidasius. Biotechnol Lett (2008) 0.84
A Boolean model of the Pseudomonas syringae hrp regulon predicts a tightly regulated system. PLoS One (2010) 0.83
Using a viral vector to reveal the role of microRNA159 in disease symptom induction by a severe strain of Cucumber mosaic virus. Plant Physiol (2014) 0.83
NCD3G: a novel nine-cysteine domain in family 3 GPCRs. Trends Biochem Sci (2004) 0.82
Isolation of Salmonella mutants resistant to the inhibitory effect of Salicylidene acylhydrazides on flagella-mediated motility. PLoS One (2013) 0.82
Finding sRNA generative locales from high-throughput sequencing data with NiBLS. BMC Bioinformatics (2010) 0.81
Identification of possible virulence marker from Campylobacter jejuni isolates. Emerg Infect Dis (2014) 0.80
MANSC: a seven-cysteine-containing domain present in animal membrane and extracellular proteins. Trends Biochem Sci (2004) 0.80
Dissection of silencing signal movement in Arabidopsis. Plant Signal Behav (2007) 0.79
Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles. Genome Res (2015) 0.79
Genome characterization of a novel Burkholderia cepacia complex genomovar isolated from dieback affected mango orchards. World J Microbiol Biotechnol (2013) 0.78
Potato virus Y NIa protease activity is not sufficient for elicitation of Ry-mediated disease resistance in potato. Plant J (2003) 0.78
Marker development for the genetic study of natural variation in Arabidopsis thaliana. Bioinformatics (2007) 0.77