Published in Bioinformatics on June 24, 2004
Principles of microRNA-target recognition. PLoS Biol (2005) 23.70
Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci U S A (2005) 8.15
miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res (2011) 5.83
Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. Genome Res (2006) 5.23
MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res (2007) 3.69
Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics (2005) 3.69
MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries. Stem Cells (2008) 3.14
Cloning and characterization of microRNAs from wheat (Triticum aestivum L.). Genome Biol (2007) 3.02
Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals. Genome Biol (2005) 2.94
The expansion of the metazoan microRNA repertoire. BMC Genomics (2006) 2.80
Identification of clustered microRNAs using an ab initio prediction method. BMC Bioinformatics (2005) 2.76
Human microRNA prediction through a probabilistic co-learning model of sequence and structure. Nucleic Acids Res (2005) 2.48
LNCipedia: a database for annotated human lncRNA transcript sequences and structures. Nucleic Acids Res (2012) 2.40
Repertoire of microRNAs in epithelial ovarian cancer as determined by next generation sequencing of small RNA cDNA libraries. PLoS One (2009) 2.37
Current tools for the identification of miRNA genes and their targets. Nucleic Acids Res (2009) 2.12
Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency. RNA (2005) 2.12
Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genet (2013) 2.07
Mouse microRNA profiles determined with a new and sensitive cloning method. Nucleic Acids Res (2006) 1.94
Unique folding of precursor microRNAs: quantitative evidence and implications for de novo identification. RNA (2006) 1.85
Repertoire and evolution of miRNA genes in four divergent nematode species. Genome Res (2009) 1.64
Identification of soybean microRNAs and their targets. Planta (2008) 1.64
Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response. BMC Genomics (2009) 1.62
miROrtho: computational survey of microRNA genes. Nucleic Acids Res (2008) 1.60
Direct evolution of genetic robustness in microRNA. Proc Natl Acad Sci U S A (2006) 1.59
A comparison of RNA folding measures. BMC Bioinformatics (2005) 1.54
Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing. BMC Genomics (2011) 1.51
Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast. BMC Genomics (2009) 1.42
Discrete clusters of virus-encoded micrornas are associated with complementary strands of the genome and the 7.2-kilobase stable intron in murine cytomegalovirus. J Virol (2007) 1.39
Identification of real microRNA precursors with a pseudo structure status composition approach. PLoS One (2015) 1.36
Characterization of 43 non-protein-coding mRNA genes in Arabidopsis, including the MIR162a-derived transcripts. Plant Physiol (2006) 1.35
Age-related changes in microRNA levels in serum. Aging (Albany NY) (2013) 1.35
Identification and characterization of microRNAs from peanut (Arachis hypogaea L.) by high-throughput sequencing. PLoS One (2011) 1.32
De novo prediction of structured RNAs from genomic sequences. Trends Biotechnol (2009) 1.31
Origins and evolution of microRNA genes in Drosophila species. Genome Biol Evol (2010) 1.31
Identification and characterization of maize microRNAs involved in the very early stage of seed germination. BMC Genomics (2011) 1.30
A global analysis of evolutionary conservation among known and predicted gammaherpesvirus microRNAs. J Virol (2009) 1.30
uShuffle: a useful tool for shuffling biological sequences while preserving the k-let counts. BMC Bioinformatics (2008) 1.30
A family of microRNAs present in plants and animals. Plant Cell (2006) 1.30
Monitoring genomic sequences during SELEX using high-throughput sequencing: neutral SELEX. PLoS One (2010) 1.28
Complete probabilistic analysis of RNA shapes. BMC Biol (2006) 1.27
Ab initio identification of human microRNAs based on structure motifs. BMC Bioinformatics (2007) 1.27
MicroRNAs in common human diseases. Genomics Proteomics Bioinformatics (2012) 1.25
MicroRNA: biological and computational perspective. Genomics Proteomics Bioinformatics (2005) 1.23
Molecular mechanisms of chlorhexidine tolerance in Burkholderia cenocepacia biofilms. Antimicrob Agents Chemother (2011) 1.22
Identification of novel small RNAs in tomato (Solanum lycopersicum). Planta (2007) 1.22
Small RNA and degradome sequencing reveal complex miRNA regulation during cotton somatic embryogenesis. J Exp Bot (2013) 1.22
iMiRNA-SSF: Improving the Identification of MicroRNA Precursors by Combining Negative Sets with Different Distributions. Sci Rep (2016) 1.21
Mammalian microRNA prediction through a support vector machine model of sequence and structure. PLoS One (2007) 1.20
Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants. PLoS Comput Biol (2007) 1.16
Nucleotide bias observed with a short SELEX RNA aptamer library. Nucleic Acid Ther (2011) 1.15
Identification and characteristics of microRNAs from Bombyx mori. BMC Genomics (2008) 1.14
Characterization of statistical features for plant microRNA prediction. BMC Genomics (2011) 1.13
Deep sequencing of maize small RNAs reveals a diverse set of microRNA in dry and imbibed seeds. PLoS One (2013) 1.09
Computational methods in noncoding RNA research. J Math Biol (2007) 1.08
"A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids". BMC Genomics (2013) 1.07
Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum). Planta (2010) 1.05
Identification of microRNA-like RNAs in a plant pathogenic fungus Sclerotinia sclerotiorum by high-throughput sequencing. Mol Genet Genomics (2012) 1.05
Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human. BMC Evol Biol (2007) 1.05
Identification of drought-responsive and novel Populus trichocarpa microRNAs by high-throughput sequencing and their targets using degradome analysis. BMC Genomics (2013) 1.05
Global profiling of miRNAs and the hairpin precursors: insights into miRNA processing and novel miRNA discovery. Nucleic Acids Res (2013) 1.02
Computational analysis of noncoding RNAs. Wiley Interdiscip Rev RNA (2012) 1.01
In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity. BMC Genomics (2009) 1.01
Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment. Gigascience (2014) 1.00
Genome-wide discovery of small RNAs in Mycobacterium tuberculosis. PLoS One (2012) 1.00
A genome-wide identification analysis of small regulatory RNAs in Mycobacterium tuberculosis by RNA-Seq and conservation analysis. PLoS One (2012) 1.00
Identification and characterization of microRNAs from Phaeodactylum tricornutum by high-throughput sequencing and bioinformatics analysis. BMC Genomics (2011) 0.99
From structure prediction to genomic screens for novel non-coding RNAs. PLoS Comput Biol (2011) 0.99
Computational Approaches for the Analysis of ncRNA through Deep Sequencing Techniques. Front Bioeng Biotechnol (2015) 0.96
Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach. PLoS One (2009) 0.96
Neutral evolution of robustness in Drosophila microRNA precursors. Mol Biol Evol (2011) 0.95
Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity. ISME J (2014) 0.95
Mapping of small RNAs in the human ENCODE regions. Am J Hum Genet (2008) 0.94
Evolution of MIR168 paralogs in Brassicaceae. BMC Evol Biol (2009) 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
Identification of microRNA-like RNAs in mycelial and yeast phases of the thermal dimorphic fungus Penicillium marneffei. PLoS Negl Trop Dis (2013) 0.93
Identification and classification of ncRNA molecules using graph properties. Nucleic Acids Res (2009) 0.93
Structured RNAs and synteny regions in the pig genome. BMC Genomics (2014) 0.92
Detecting miRNAs in deep-sequencing data: a software performance comparison and evaluation. Brief Bioinform (2012) 0.92
Comparative genome-wide analysis of small RNAs of major Gram-positive pathogens: from identification to application. Microb Biotechnol (2010) 0.91
Computational identification of miRNAs and their target genes from expressed sequence tags of tea (Camellia sinensis). Genomics Proteomics Bioinformatics (2010) 0.91
Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals. BMC Genomics (2013) 0.91
Testing hypotheses on the rate of molecular evolution in relation to gene expression using microRNAs. Proc Natl Acad Sci U S A (2011) 0.90
High throughput sequencing of two celery varieties small RNAs identifies microRNAs involved in temperature stress response. BMC Genomics (2014) 0.90
The discriminant power of RNA features for pre-miRNA recognition. BMC Bioinformatics (2014) 0.89
MicroRNA-205 directly regulates the tumor suppressor, interleukin-24, in human KB oral cancer cells. Mol Cells (2012) 0.88
Identification and analysis of red sea mangrove (Avicennia marina) microRNAs by high-throughput sequencing and their association with stress responses. PLoS One (2013) 0.88
Identification of potential microRNAs and their targets in Brassica rapa L. Mol Cells (2011) 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
Identification of the conserved and novel miRNAs in Mulberry by high-throughput sequencing. PLoS One (2014) 0.88
Identification of negative cis-acting elements in response to copper in the chloroplastic iron superoxide dismutase gene of the moss Barbula unguiculata. Plant Physiol (2008) 0.88
Identification and characterization of microRNAs in white and brown alpaca skin. BMC Genomics (2012) 0.87
Analysis of phytoplasma-responsive sRNAs provide insight into the pathogenic mechanisms of mulberry yellow dwarf disease. Sci Rep (2014) 0.87
Evolutionary relationships between miRNA genes and their activity. BMC Genomics (2012) 0.87
Non-coding RNA prediction and verification in Saccharomyces cerevisiae. PLoS Genet (2009) 0.87
Deep sequencing and microarray hybridization identify conserved and species-specific microRNAs during somatic embryogenesis in hybrid yellow poplar. PLoS One (2012) 0.86
Computational methods for ab initio detection of microRNAs. Front Genet (2012) 0.86
Genome-wide identification and comparative analysis of conserved and novel microRNAs in grafted watermelon by high-throughput sequencing. PLoS One (2013) 0.86
Finding microRNA targets in plants: current status and perspectives. Genomics Proteomics Bioinformatics (2012) 0.86
Stable stem enabled Shannon entropies distinguish non-coding RNAs from random backgrounds. BMC Bioinformatics (2012) 0.86
Characterization of RNA silencing components in the plant pathogenic fungus Fusarium graminearum. Sci Rep (2015) 0.86
The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science (2007) 8.12
The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet (2010) 8.07
The European database on small subunit ribosomal RNA. Nucleic Acids Res (2002) 7.80
Opinion: Re-evaluating prokaryotic species. Nat Rev Microbiol (2005) 7.19
The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature (2008) 6.70
PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res (2002) 6.43
A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS One (2007) 5.62
The hidden duplication past of Arabidopsis thaliana. Proc Natl Acad Sci U S A (2002) 5.00
Modeling gene and genome duplications in eukaryotes. Proc Natl Acad Sci U S A (2005) 5.00
The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature (2011) 4.94
Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science (2007) 4.89
The Norway spruce genome sequence and conifer genome evolution. Nature (2013) 4.74
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet (2011) 4.65
Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc Natl Acad Sci U S A (2006) 4.52
Genome duplication, a trait shared by 22000 species of ray-finned fish. Genome Res (2003) 4.19
A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. J Comput Biol (2002) 4.05
Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science (2009) 4.05
Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc Natl Acad Sci U S A (2004) 3.97
Genome-wide analysis of core cell cycle genes in Arabidopsis. Plant Cell (2002) 3.91
From 2R to 3R: evidence for a fish-specific genome duplication (FSGD). Bioessays (2005) 3.91
RnaViz 2: an improved representation of RNA secondary structure. Bioinformatics (2003) 3.89
The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature (2010) 3.60
The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl Acad Sci U S A (2007) 3.58
Genome duplication and the origin of angiosperms. Trends Ecol Evol (2005) 3.46
The genome of Tetranychus urticae reveals herbivorous pest adaptations. Nature (2011) 3.29
Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc Natl Acad Sci U S A (2009) 3.13
Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates. Proc Natl Acad Sci U S A (2004) 3.13
Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res (2002) 3.12
Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications. Genome Res (2004) 3.02
Genome-wide characterization of the lignification toolbox in Arabidopsis. Plant Physiol (2003) 2.90
Obligate biotrophy features unraveled by the genomic analysis of rust fungi. Proc Natl Acad Sci U S A (2011) 2.84
Genome sequence of the recombinant protein production host Pichia pastoris. Nat Biotechnol (2009) 2.67
Robust biomarker identification for cancer diagnosis with ensemble feature selection methods. Bioinformatics (2009) 2.66
Evidence that rice and other cereals are ancient aneuploids. Plant Cell (2003) 2.62
Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc Natl Acad Sci U S A (2006) 2.61
The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biol (2006) 2.58
PLAZA: a comparative genomics resource to study gene and genome evolution in plants. Plant Cell (2009) 2.43
CATMA: a complete Arabidopsis GST database. Nucleic Acids Res (2003) 2.34
Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature (2013) 2.26
An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens. BMC Evol Biol (2007) 2.17
The Mycobacterium tuberculosis regulatory network and hypoxia. Nature (2013) 2.04
Dissecting plant genomes with the PLAZA comparative genomics platform. Plant Physiol (2011) 1.98
Gene duplication and biased functional retention of paralogs in bacterial genomes. Trends Microbiol (2004) 1.94
Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. Mol Syst Biol (2010) 1.91
ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles. Bioinformatics (2008) 1.91
GenomeView: a next-generation genome browser. Nucleic Acids Res (2011) 1.91
Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks. Plant Physiol (2009) 1.90
Towards a prokaryotic genomic taxonomy. FEMS Microbiol Rev (2005) 1.87
Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. Genome Biol (2006) 1.85
Genome-wide identification of potential plant E2F target genes. Plant Physiol (2005) 1.85
Generic eukaryotic core promoter prediction using structural features of DNA. Genome Res (2007) 1.80
A transgenic mouse marking live replicating cells reveals in vivo transcriptional program of proliferation. Dev Cell (2012) 1.72
EST data suggest that poplar is an ancient polyploid. New Phytol (2005) 1.70
i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles. Bioinformatics (2007) 1.68
Structural diversification and neo-functionalization during floral MADS-box gene evolution by C-terminal frameshift mutations. Nucleic Acids Res (2003) 1.54
i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets. Nucleic Acids Res (2011) 1.51
Computational approaches to identify promoters and cis-regulatory elements in plant genomes. Plant Physiol (2003) 1.50
Unbiased plasma proteomics for novel diagnostic biomarkers in cardiovascular disease: identification of quiescin Q6 as a candidate biomarker of acutely decompensated heart failure. Eur Heart J (2012) 1.48
Building genomic profiles for uncovering segmental homology in the twilight zone. Genome Res (2004) 1.48
SpliceMachine: predicting splice sites from high-dimensional local context representations. Bioinformatics (2004) 1.47
Choose your partners: dimerization in eukaryotic transcription factors. Trends Biochem Sci (2008) 1.43
Hydrogen peroxide-induced gene expression across kingdoms: a comparative analysis. Mol Biol Evol (2008) 1.40
Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks. BMC Syst Biol (2009) 1.40
Large-scale structural analysis of the core promoter in mammalian and plant genomes. Nucleic Acids Res (2005) 1.39
Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions. BMC Genomics (2013) 1.38
Module networks revisited: computational assessment and prioritization of model predictions. Bioinformatics (2009) 1.38
Investigating ancient duplication events in the Arabidopsis genome. J Struct Funct Genomics (2003) 1.38
Canalization without flux sensors: a traveling-wave hypothesis. Trends Plant Sci (2007) 1.36
Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress. Genome Biol (2009) 1.36
And then there were many: MADS goes genomic. Trends Plant Sci (2003) 1.35
How many genes are there in plants (... and why are they there)? Curr Opin Plant Biol (2007) 1.35
Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants. Proc Natl Acad Sci U S A (2013) 1.35
Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. BMC Genomics (2009) 1.34
TAPIR, a web server for the prediction of plant microRNA targets, including target mimics. Bioinformatics (2010) 1.34
The membrane-bound NAC transcription factor ANAC013 functions in mitochondrial retrograde regulation of the oxidative stress response in Arabidopsis. Plant Cell (2013) 1.34
Integrative genomic analysis implicates gain of PIK3CA at 3q26 and MYC at 8q24 in chronic lymphocytic leukemia. Clin Cancer Res (2012) 1.33
Automatic design of gene-specific sequence tags for genome-wide functional studies. Bioinformatics (2003) 1.33
AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling. Plant Physiol (2009) 1.33
In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation. BMC Bioinformatics (2007) 1.32
Large-scale event extraction from literature with multi-level gene normalization. PLoS One (2013) 1.30