Published in Plant J on June 01, 2010
starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res (2010) 3.99
miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments. Nucleic Acids Res (2011) 2.25
Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing. BMC Plant Biol (2011) 2.01
Apple miRNAs and tasiRNAs with novel regulatory networks. Genome Biol (2012) 1.61
Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing. BMC Genomics (2011) 1.51
PsRobot: a web-based plant small RNA meta-analysis toolbox. Nucleic Acids Res (2012) 1.43
Identification of conserved and novel microRNAs that are responsive to heat stress in Brassica rapa. J Exp Bot (2011) 1.33
High-throughput sequencing, characterization and detection of new and conserved cucumber miRNAs. PLoS One (2011) 1.25
High-throughput sequencing of small RNAs and analysis of differentially expressed microRNAs associated with pistil development in Japanese apricot. BMC Genomics (2012) 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
Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis. J Exp Bot (2013) 1.23
Small RNA and degradome sequencing reveal complex miRNA regulation during cotton somatic embryogenesis. J Exp Bot (2013) 1.22
Catalyzing plant science research with RNA-seq. Front Plant Sci (2013) 1.19
Cloning and characterization of maize miRNAs involved in responses to nitrogen deficiency. PLoS One (2012) 1.17
Identification of miRNAs and their targets using high-throughput sequencing and degradome analysis in cytoplasmic male-sterile and its maintainer fertile lines of Brassica juncea. BMC Genomics (2013) 1.12
Homology-independent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm. Proc Natl Acad Sci U S A (2012) 1.12
PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing. Nucleic Acids Res (2012) 1.12
Uncovering small RNA-mediated responses to cold stress in a wheat thermosensitive genic male-sterile line by deep sequencing. Plant Physiol (2012) 1.10
Genome-wide identification of miRNAs responsive to drought in peach (Prunus persica) by high-throughput deep sequencing. PLoS One (2012) 1.10
Genome-wide identification of Brassica napus microRNAs and their targets in response to cadmium. J Exp Bot (2012) 1.09
Characterization of the stress associated microRNAs in Glycine max by deep sequencing. BMC Plant Biol (2011) 1.08
SeqTar: an effective method for identifying microRNA guided cleavage sites from degradome of polyadenylated transcripts in plants. Nucleic Acids Res (2011) 1.06
Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing. BMC Genomics (2014) 1.04
Identification of wild soybean miRNAs and their target genes responsive to aluminum stress. BMC Plant Biol (2012) 1.04
Comparative analysis reveals dynamic changes in miRNAs and their targets and expression during somatic embryogenesis in longan (Dimocarpus longan Lour.). PLoS One (2013) 1.04
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
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
Identification and characterization of miRNA transcriptome in potato by high-throughput sequencing. PLoS One (2013) 1.03
High-throughput sequencing of RNA silencing-associated small RNAs in olive (Olea europaea L.). PLoS One (2011) 1.02
Analysis of the melon (Cucumis melo) small RNAome by high-throughput pyrosequencing. BMC Genomics (2011) 1.02
Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs. BMC Plant Biol (2012) 1.01
Genomic organization, phylogenetic comparison and differential expression of the SBP-box family genes in grape. PLoS One (2013) 1.00
Sculpting the maturation, softening and ethylene pathway: the influences of microRNAs on tomato fruits. BMC Genomics (2012) 0.98
Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon. Genome Biol (2013) 0.97
Identification of miRNAs and their targets from Brassica napus by high-throughput sequencing and degradome analysis. BMC Genomics (2012) 0.96
Genome-wide profiling of novel and conserved Populus microRNAs involved in pathogen stress response by deep sequencing. Planta (2011) 0.96
Identification and characterization of cold-responsive microRNAs in tea plant (Camellia sinensis) and their targets using high-throughput sequencing and degradome analysis. BMC Plant Biol (2014) 0.96
Dynamic expression of small RNA populations in larch (Larix leptolepis). Planta (2012) 0.95
Discovery and profiling of novel and conserved microRNAs during flower development in Carya cathayensis via deep sequencing. Planta (2012) 0.95
miRNA regulation in the early development of barley seed. BMC Plant Biol (2012) 0.94
Computational Prediction of miRNA Genes from Small RNA Sequencing Data. Front Bioeng Biotechnol (2015) 0.94
High-throughput sequencing and characterization of the small RNA transcriptome reveal features of novel and conserved microRNAs in Panax ginseng. PLoS One (2012) 0.94
Identification of chilling stress-responsive tomato microRNAs and their target genes by high-throughput sequencing and degradome analysis. BMC Genomics (2014) 0.94
Genome-wide comparison of microRNAs and their targeted transcripts among leaf, flower and fruit of sweet orange. BMC Genomics (2014) 0.93
Diverse correlation patterns between microRNAs and their targets during tomato fruit development indicates different modes of microRNA actions. Planta (2012) 0.92
Characterization of the small RNA component of leaves and fruits from four different cucurbit species. BMC Genomics (2012) 0.92
A comparison of performance of plant miRNA target prediction tools and the characterization of features for genome-wide target prediction. BMC Genomics (2014) 0.91
Identification and comparative profiling of miRNAs in an early flowering mutant of trifoliate orange and its wild type by genome-wide deep sequencing. PLoS One (2012) 0.91
Identification and characterization of microRNAs in the flag leaf and developing seed of wheat (Triticum aestivum L.). BMC Genomics (2014) 0.90
Boron stress responsive microRNAs and their targets in barley. PLoS One (2013) 0.90
Identification of novel Oryza sativa miRNAs in deep sequencing-based small RNA libraries of rice infected with Rice stripe virus. PLoS One (2012) 0.89
Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots. BMC Genomics (2013) 0.88
Identification and characterization of miRNAome in root, stem, leaf and tuber developmental stages of potato (Solanum tuberosum L.) by high-throughput sequencing. BMC Plant Biol (2014) 0.88
Transcriptome-wide identification and characterization of miRNAs from Pinus densata. BMC Genomics (2012) 0.88
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
Sexual dimorphism floral microRNA profiling and target gene expression in andromonoecious poplar (Populus tomentosa). PLoS One (2013) 0.87
RNA degradome--its biogenesis and functions. Nucleic Acids Res (2011) 0.87
Finding microRNA targets in plants: current status and perspectives. Genomics Proteomics Bioinformatics (2012) 0.86
The miRNAome of globe artichoke: conserved and novel micro RNAs and target analysis. BMC Genomics (2012) 0.86
Comparative profiling of miRNA expression in developing seeds of high linoleic and high oleic safflower (Carthamus tinctorius L.) plants. Front Plant Sci (2013) 0.86
Grapevine microRNAs responsive to exogenous gibberellin. BMC Genomics (2014) 0.85
Identification of microRNAs from Eugenia uniflora by high-throughput sequencing and bioinformatics analysis. PLoS One (2012) 0.85
Novel and Recently Evolved MicroRNA Clusters Regulate Expansive F-BOX Gene Networks through Phased Small Interfering RNAs in Wild Diploid Strawberry. Plant Physiol (2015) 0.85
Computational identification of conserved microRNAs and their putative targets in the Hypericum perforatum L. flower transcriptome. Plant Reprod (2013) 0.85
Deep sequencing discovery of novel and conserved microRNAs in wild type and a white-flesh mutant strawberry. Planta (2013) 0.84
Characterization of miRNAs associated with Botrytis cinerea infection of tomato leaves. BMC Plant Biol (2015) 0.84
Effects of drought on the microtranscriptome of field-grown sugarcane plants. Planta (2012) 0.84
MicroRNA-mediated regulation of gene expression in the response of rice plants to fungal elicitors. RNA Biol (2015) 0.84
Characterization of microRNAs identified in a table grapevine cultivar with validation of computationally predicted grapevine miRNAs by miR-RACE. PLoS One (2011) 0.83
Transcriptome/Degradome-wide discovery of microRNAs and transcript targets in two Paulownia australis genotypes. PLoS One (2014) 0.83
Identification of microRNAs and their targets in tomato infected with Cucumber mosaic virus based on deep sequencing. Planta (2014) 0.82
Introns targeted by plant microRNAs: a possible novel mechanism of gene regulation. Rice (N Y) (2013) 0.82
A global profiling of uncapped mRNAs under cold stress reveals specific decay patterns and endonucleolytic cleavages in Brachypodium distachyon. Genome Biol (2013) 0.82
Identification of miRNAs and their target genes in peach (Prunus persica L.) using high-throughput sequencing and degradome analysis. PLoS One (2013) 0.82
Small RNA and degradome sequencing reveals microRNAs and their targets involved in tomato pedicel abscission. Planta (2015) 0.82
Identification of miRNAs involved in fruit ripening in Cavendish bananas by deep sequencing. BMC Genomics (2015) 0.81
Transcriptome profiling of root microRNAs reveals novel insights into taproot thickening in radish (Raphanus sativus L.). BMC Plant Biol (2015) 0.81
Identification and characterization of microRNAs in the leaf of ma bamboo (Dendrocalamus latiflorus) by deep sequencing. PLoS One (2013) 0.81
Identification of novel drought-responsive microRNAs and trans-acting siRNAs from Sorghum bicolor (L.) Moench by high-throughput sequencing analysis. Front Plant Sci (2015) 0.81
Genome-Wide Characterization of miRNAs Involved in N Gene-Mediated Immunity in Response to Tobacco Mosaic Virus in Nicotiana benthamiana. Evol Bioinform Online (2015) 0.81
The hot pepper (Capsicum annuum) microRNA transcriptome reveals novel and conserved targets: a foundation for understanding MicroRNA functional roles in hot pepper. PLoS One (2013) 0.81
Identification of novel and salt-responsive miRNAs to explore miRNA-mediated regulatory network of salt stress response in radish (Raphanus sativus L.). BMC Genomics (2015) 0.81
MicroRNA-directed cleavage of targets: mechanism and experimental approaches. BMB Rep (2014) 0.81
Insilico profiling of microRNAs in Korean ginseng (Panax ginseng Meyer). J Ginseng Res (2013) 0.81
Identification of Nicotiana benthamiana microRNAs and their targets using high throughput sequencing and degradome analysis. BMC Genomics (2015) 0.80
Combined small RNA and degradome sequencing to identify miRNAs and their targets in response to drought in foxtail millet. BMC Genet (2016) 0.80
miRVine: a microRNA expression atlas of grapevine based on small RNA sequencing. BMC Genomics (2015) 0.80
High-throughput sequencing and degradome analysis reveal neutral evolution of Cercis gigantea microRNAs and their targets. Planta (2015) 0.79
Identification of microRNAs differentially expressed involved in male flower development. Funct Integr Genomics (2015) 0.79
MicroRNA from Moringa oleifera: Identification by High Throughput Sequencing and Their Potential Contribution to Plant Medicinal Value. PLoS One (2016) 0.79
Cascading cis-cleavage on transcript from trans-acting siRNA-producing locus 3. Int J Mol Sci (2013) 0.79
Trans-acting small interfering RNA4: key to nutraceutical synthesis in grape development? Trends Plant Sci (2013) 0.79
miRNA expression during prickly pear cactus fruit development. Planta (2014) 0.79
Identification of cold-inducible microRNAs in grapevine. Front Plant Sci (2015) 0.79
Identification and characterization of microRNAs from Chinese pollination constant non-astringent persimmon using high-throughput sequencing. BMC Plant Biol (2015) 0.79
Identification and Characterization of MicroRNAs in Ginkgo biloba var. epiphylla Mak. PLoS One (2015) 0.78
Microarray and degradome sequencing reveal microRNA differential expression profiles and their targets in Pinellia pedatisecta. PLoS One (2013) 0.78
Novel miRNA and phasiRNA biogenesis networks in soybean roots from two sister lines that are resistant and susceptible to SCN race 4. PLoS One (2014) 0.78
In silico search and biological validation of microRNAs related to drought response in peach and almond. Funct Integr Genomics (2016) 0.78
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
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
High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genomics (2008) 2.31
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
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
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
Regulation of multiple target genes by miR-1 and miR-206 is pivotal for C2C12 myoblast differentiation. J Cell Sci (2012) 1.26
Global and cell-type gene expression profiles in tomato plants colonized by an arbuscular mycorrhizal fungus. New Phytol (2009) 1.25
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
Identification of novel small RNAs in tomato (Solanum lycopersicum). Planta (2007) 1.22
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
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
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
In situ detection of animal and plant microRNAs. DNA Cell Biol (2007) 1.00
Estimating parameters for generalized mass action models using constraint propagation. Math Biosci (2006) 1.00
Evidence for targeting common siRNA hotspots and GC preference by plant Dicer-like proteins. FEBS Lett (2007) 1.00
Regulation of leaf morphology by microRNA394 and its target LEAF CURLING RESPONSIVENESS. Plant Cell Physiol (2012) 0.99
Boltzmann probability of RNA structural neighbors and riboswitch detection. Bioinformatics (2007) 0.99
SuperQ: computing supernetworks from quartets. IEEE/ACM Trans Comput Biol Bioinform (2013) 0.97
Metrics on multilabeled trees: interrelationships and diameter bounds. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.96
Unbiased descriptor and parameter selection confirms the potential of proteochemometric modelling. BMC Bioinformatics (2005) 0.96
Comparative analysis of expression profiles in shoots and roots of tomato systemically infected by Tomato spotted wilt virus reveals organ-specific transcriptional responses. Mol Plant Microbe Interact (2009) 0.95
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
From root to fruit: RNA-Seq analysis shows that arbuscular mycorrhizal symbiosis may affect tomato fruit metabolism. BMC Genomics (2014) 0.94
Genome-wide identification of viral and host transcripts targeted by viral siRNAs in Vitis vinifera. Mol Plant Pathol (2012) 0.93
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