Published in Planta on April 06, 2007
Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Res (2008) 2.89
A microRNA superfamily regulates nucleotide binding site-leucine-rich repeats and other mRNAs. Plant Cell (2012) 2.32
Genome-wide Medicago truncatula small RNA analysis revealed novel microRNAs and isoforms differentially regulated in roots and nodules. Plant Cell (2009) 1.66
Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: new functional implications for MITEs. Genome Res (2008) 1.63
Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis. J Exp Bot (2013) 1.23
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
Identification and characterization of 27 conserved microRNAs in citrus. Planta (2009) 1.17
Identification and characterization of microRNAs and their targets in the bioenergy plant switchgrass (Panicum virgatum). Planta (2010) 1.13
A combined approach of high-throughput sequencing and degradome analysis reveals tissue specific expression of microRNAs and their targets in cucumber. PLoS One (2012) 1.03
Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics. Nucleic Acids Res (2010) 1.01
Sculpting the maturation, softening and ethylene pathway: the influences of microRNAs on tomato fruits. BMC Genomics (2012) 0.98
Genomic organization, phylogenetic comparison and differential expression of the SBP-box family of transcription factors in tomato. Planta (2011) 0.96
Characterisation and expression of microRNAs in developing wings of the neotropical butterfly Heliconius melpomene. BMC Genomics (2011) 0.95
Identification of chilling stress-responsive tomato microRNAs and their target genes by high-throughput sequencing and degradome analysis. BMC Genomics (2014) 0.94
A simple and efficient method for isolating small RNAs from different plant species. Plant Methods (2011) 0.93
Diverse correlation patterns between microRNAs and their targets during tomato fruit development indicates different modes of microRNA actions. Planta (2012) 0.92
Identification of microRNAs in Caragana intermedia by high-throughput sequencing and expression analysis of 12 microRNAs and their targets under salt stress. Plant Cell Rep (2013) 0.87
MicroRNAs suppress NB domain genes in tomato that confer resistance to Fusarium oxysporum. PLoS Pathog (2014) 0.87
Small RNA and degradome deep sequencing reveals drought-and tissue-specific micrornas and their important roles in drought-sensitive and drought-tolerant tomato genotypes. Plant Biotechnol J (2016) 0.85
Small RNAs in plants: recent development and application for crop improvement. Front Plant Sci (2015) 0.85
Tuning LeSPL-CNR expression by SlymiR157 affects tomato fruit ripening. Sci Rep (2015) 0.83
Functional genomics of tomato in a post-genome-sequencing phase. Breed Sci (2013) 0.82
Microarray-based identification of tomato microRNAs and time course analysis of their response to Cucumber mosaic virus infection. J Zhejiang Univ Sci B (2011) 0.81
Small RNA analysis in Sindbis virus infected human HEK293 cells. PLoS One (2013) 0.79
Small RNA analysis in Petunia hybrida identifies unusual tissue-specific expression patterns of conserved miRNAs and of a 24mer RNA. RNA (2009) 0.79
miRNA expression during prickly pear cactus fruit development. Planta (2014) 0.79
Identification of Arbuscular Mycorrhiza (AM)-Responsive microRNAs in Tomato. Front Plant Sci (2016) 0.79
Molecular cloning and characterisation of SlAGO family in tomato. BMC Plant Biol (2013) 0.77
Identification of microRNAs in the Toxigenic Dinoflagellate Alexandrium catenella by High-Throughput Illumina Sequencing and Bioinformatic Analysis. PLoS One (2015) 0.77
Discovery of Novel Leaf Rust Responsive microRNAs in Wheat and Prediction of Their Target Genes. J Nucleic Acids (2014) 0.76
Genome-wide identification of reverse complementary microRNA genes in plants. PLoS One (2012) 0.76
Diversity, expression and mRNA targeting abilities of Argonaute-targeting miRNAs among selected vascular plants. BMC Genomics (2014) 0.76
Parsing the Regulatory Network between Small RNAs and Target Genes in Ethylene Pathway in Tomato. Front Plant Sci (2017) 0.75
High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute. Int J Genomics (2015) 0.75
Rosaceae Fruit Development, Ripening and Post-harvest: An Epigenetic Perspective. Front Plant Sci (2017) 0.75
A uniform system for microRNA annotation. RNA (2003) 20.28
MicroRNAs in plants. Genes Dev (2002) 20.12
Vienna RNA secondary structure server. Nucleic Acids Res (2003) 19.69
The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res (2003) 18.69
Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science (2002) 18.37
CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr Biol (2002) 15.13
microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell (2005) 14.81
MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol (2006) 14.44
Genetic and functional diversification of small RNA pathways in plants. PLoS Biol (2004) 12.21
A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev (2006) 11.71
Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell (2003) 11.69
Control of leaf morphogenesis by microRNAs. Nature (2003) 11.36
Endogenous and silencing-associated small RNAs in plants. Plant Cell (2002) 10.07
Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell (2004) 9.18
Elucidation of the small RNA component of the transcriptome. Science (2005) 8.66
SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev (2004) 8.18
Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell (2004) 7.68
Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell (2005) 7.58
Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat Genet (2004) 6.34
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
EMBL Nucleotide Sequence Database: developments in 2005. Nucleic Acids Res (2006) 5.13
RNA silencing genes control de novo DNA methylation. Science (2004) 5.11
Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs. Curr Biol (2005) 4.98
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics (2004) 4.95
A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus. Science (2002) 4.90
The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center. Cell (2006) 4.82
A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat Genet (2006) 4.59
Genetic regulation of fruit development and ripening. Plant Cell (2004) 4.20
MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. Genome Res (2006) 4.08
DRB4-dependent TAS3 trans-acting siRNAs control leaf morphology through AGO7. Curr Biol (2006) 3.90
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
The SOL Genomics Network: a comparative resource for Solanaceae biology and beyond. Plant Physiol (2005) 3.65
Conservation and divergence of plant microRNA genes. Plant J (2006) 3.64
Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell (2005) 3.18
Deductions about the number, organization, and evolution of genes in the tomato genome based on analysis of a large expressed sequence tag collection and selective genomic sequencing. Plant Cell (2002) 2.97
The early extra petals1 mutant uncovers a role for microRNA miR164c in regulating petal number in Arabidopsis. Curr Biol (2005) 2.51
Regulation of Arabidopsis shoot apical meristem and lateral organ formation by microRNA miR166g and its AtHD-ZIP target genes. Development (2005) 2.24
Comprehensive EST analysis of tomato and comparative genomics of fruit ripening. Plant J (2004) 2.11
Metabolic regulation underlying tomato fruit development. J Exp Bot (2006) 2.01
Analysis of short RNAs in the malaria parasite and its red blood cell host. FEBS Lett (2006) 1.60
Functional analysis of cymbidium ringspot virus genome. Virology (1993) 1.48
Pathways through the small RNA world of plants. FEBS Lett (2005) 1.30
The Pfam protein families database. Nucleic Acids Res (2004) 56.46
Pfam: clans, web tools and services. Nucleic Acids Res (2006) 34.83
Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res (2005) 25.49
RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics (2010) 9.49
Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol (2003) 8.51
The European Nucleotide Archive. Nucleic Acids Res (2010) 6.48
Mutations in the seed region of human miR-96 are responsible for nonsyndromic progressive hearing loss. Nat Genet (2009) 3.72
An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice. Nat Genet (2009) 3.05
Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Res (2008) 2.89
A toolkit for analysing large-scale plant small RNA datasets. Bioinformatics (2008) 2.80
The cartilage specific microRNA-140 targets histone deacetylase 4 in mouse cells. FEBS Lett (2006) 2.79
Facing growth in the European Nucleotide Archive. Nucleic Acids Res (2012) 2.67
Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis. Plant J (2010) 2.46
High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genomics (2008) 2.31
Fleshy fruit expansion and ripening are regulated by the Tomato SHATTERPROOF gene TAGL1. Plant Cell (2009) 2.05
Sulphur starvation induces the expression of microRNA-395 and one of its target genes but in different cell types. Plant J (2008) 2.01
Specific requirements of MRFs for the expression of muscle specific microRNAs, miR-1, miR-206 and miR-133. Dev Biol (2008) 1.99
Major submissions tool developments at the European Nucleotide Archive. Nucleic Acids Res (2011) 1.94
The expression and function of microRNAs in chondrogenesis and osteoarthritis. Arthritis Rheum (2011) 1.92
Bounding the number of hybridisation events for a consistent evolutionary history. J Math Biol (2005) 1.80
The role of small RNAs in abiotic stress. FEBS Lett (2007) 1.73
RNAcentral: A vision for an international database of RNA sequences. RNA (2011) 1.73
The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets. Bioinformatics (2012) 1.69
Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns. Plant J (2011) 1.65
Using consensus networks to visualize contradictory evidence for species phylogeny. Mol Biol Evol (2004) 1.65
The Tomato Sequencing Project, the first cornerstone of the International Solanaceae Project (SOL). Comp Funct Genomics (2005) 1.63
Analysis of short RNAs in the malaria parasite and its red blood cell host. FEBS Lett (2006) 1.60
Consistency of topological moves based on the balanced minimum evolution principle of phylogenetic inference. IEEE/ACM Trans Comput Biol Bioinform (2009) 1.58
A comparison of RNA folding measures. BMC Bioinformatics (2005) 1.54
miR398 and miR408 are up-regulated in response to water deficit in Medicago truncatula. Planta (2009) 1.53
Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning. BMC Bioinformatics (2009) 1.42
Identification of new central nervous system specific mouse microRNAs. FEBS Lett (2006) 1.40
Spectronet: a package for computing spectra and median networks. Appl Bioinformatics (2002) 1.38
Reconstructing the evolutionary history of polyploids from multilabeled trees. Mol Biol Evol (2006) 1.38
A simplified method for cloning of short interfering RNAs from Brassica juncea infected with Turnip mosaic potyvirus and Turnip crinkle carmovirus. J Virol Methods (2006) 1.32
High throughput sequencing of microRNAs in chicken somites. FEBS Lett (2009) 1.31
Experimental identification of microRNA-140 targets by silencing and overexpressing miR-140. RNA (2008) 1.29
Structural and functional analysis of viral siRNAs. PLoS Pathog (2010) 1.28
Genetics and epigenetics of fruit development and ripening. Curr Opin Plant Biol (2007) 1.28
A SEPALLATA gene is involved in the development and ripening of strawberry (Fragaria x ananassa Duch.) fruit, a non-climacteric tissue. J Exp Bot (2010) 1.26
Regulation of multiple target genes by miR-1 and miR-206 is pivotal for C2C12 myoblast differentiation. J Cell Sci (2012) 1.26
Inferring polyploid phylogenies from multiply-labeled gene trees. BMC Evol Biol (2009) 1.24
Using supernetworks to distinguish hybridization from lineage-sorting. BMC Evol Biol (2008) 1.23
A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction. Bioinformatics (2003) 1.20
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
QNet: an agglomerative method for the construction of phylogenetic networks from weighted quartets. Mol Biol Evol (2006) 1.19
MicroRNA regulation of the paired-box transcription factor Pax3 confers robustness to developmental timing of myogenesis. Proc Natl Acad Sci U S A (2011) 1.17
Interplay of SLIM1 and miR395 in the regulation of sulfate assimilation in Arabidopsis. Plant J (2011) 1.15
FGF-4 signaling is involved in mir-206 expression in developing somites of chicken embryos. Dev Dyn (2006) 1.14
PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing. Nucleic Acids Res (2012) 1.12
Untangling complex histories of genome mergings in high polyploids. Syst Biol (2007) 1.11
A SQUAMOSA MADS box gene involved in the regulation of anthocyanin accumulation in bilberry fruits. Plant Physiol (2010) 1.11
Endogenous short RNAs generated by Dicer 2 and RNA-dependent RNA polymerase 1 regulate mRNAs in the basal fungus Mucor circinelloides. Nucleic Acids Res (2010) 1.09
Analyzing mRNA expression identifies Smad3 as a microRNA-140 target regulated only at protein level. RNA (2010) 1.09
Orthology relations, symbolic ultrametrics, and cographs. J Math Biol (2012) 1.09
The complexity of deriving multi-labeled trees from bipartitions. J Comput Biol (2008) 1.08
Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction. PLoS One (2009) 1.08
Genetic identification and genomic organization of factors affecting fruit texture. J Exp Bot (2002) 1.08
PADRE: a package for analyzing and displaying reticulate evolution. Bioinformatics (2009) 1.06
Biogenesis of Y RNA-derived small RNAs is independent of the microRNA pathway. FEBS Lett (2012) 1.04
Deep sequencing analysis of viral short RNAs from an infected Pinot Noir grapevine. Virology (2010) 1.04
Mosaic genomes of the six major primate lentivirus lineages revealed by phylogenetic analyses. J Virol (2003) 1.03
Visualizing conflicting evolutionary hypotheses in large collections of trees: using consensus networks to study the origins of placentals and hexapods. Syst Biol (2005) 1.02
Evidence for targeting common siRNA hotspots and GC preference by plant Dicer-like proteins. FEBS Lett (2007) 1.00
Estimating parameters for generalized mass action models using constraint propagation. Math Biosci (2006) 1.00
In situ detection of animal and plant microRNAs. DNA Cell Biol (2007) 1.00
Boltzmann probability of RNA structural neighbors and riboswitch detection. Bioinformatics (2007) 0.99
Regulation of leaf morphology by microRNA394 and its target LEAF CURLING RESPONSIVENESS. Plant Cell Physiol (2012) 0.99
Flexible tools for gene expression and silencing in tomato. Plant Physiol (2009) 0.97
SuperQ: computing supernetworks from quartets. IEEE/ACM Trans Comput Biol Bioinform (2013) 0.97
Unbiased descriptor and parameter selection confirms the potential of proteochemometric modelling. BMC Bioinformatics (2005) 0.96
Metrics on multilabeled trees: interrelationships and diameter bounds. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.96
Characterisation and expression of microRNAs in developing wings of the neotropical butterfly Heliconius melpomene. BMC Genomics (2011) 0.95
A novel exploratory method for visual recombination detection. Genome Biol (2003) 0.94
RNAbor: a web server for RNA structural neighbors. Nucleic Acids Res (2007) 0.93
Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Improved consensus network techniques for genome-scale phylogeny. Mol Biol Evol (2005) 0.92
Diverse correlation patterns between microRNAs and their targets during tomato fruit development indicates different modes of microRNA actions. Planta (2012) 0.92