Published in Nucleic Acids Res on July 01, 2003
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A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell (2010) 12.27
Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak. PLoS Med (2006) 11.14
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RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA (2005) 3.80
A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res (2008) 3.74
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Comparative genomics of foot-and-mouth disease virus. J Virol (2005) 3.42
Systematic identification of microRNA functions by combining target prediction and expression profiling. Nucleic Acids Res (2006) 3.29
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Evolution and functional diversification of MIRNA genes. Plant Cell (2011) 3.07
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Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Plant Physiol (2009) 2.98
Widespread regulatory activity of vertebrate microRNA* species. RNA (2010) 2.97
Target prediction for small, noncoding RNAs in bacteria. Nucleic Acids Res (2006) 2.90
miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res (2009) 2.90
MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence. Nucleic Acids Res (2005) 2.87
Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. RNA (2004) 2.86
Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. RNA (2008) 2.86
The expansion of the metazoan microRNA repertoire. BMC Genomics (2006) 2.80
Searching for IRES. RNA (2006) 2.78
Rapid quantitative profiling of complex microbial populations. Nucleic Acids Res (2006) 2.75
Partition function and base pairing probabilities of RNA heterodimers. Algorithms Mol Biol (2006) 2.74
Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature (2009) 2.72
Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Res (2008) 2.70
R-Coffee: a method for multiple alignment of non-coding RNA. Nucleic Acids Res (2008) 2.69
Cloning and expression of new microRNAs from zebrafish. Nucleic Acids Res (2006) 2.58
Genomic organization, differential expression, and interaction of SQUAMOSA promoter-binding-like transcription factors and microRNA156 in rice. Plant Physiol (2006) 2.56
Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing. Genome Res (2007) 2.55
A Pumilio-induced RNA structure switch in p27-3' UTR controls miR-221 and miR-222 accessibility. Nat Cell Biol (2010) 2.53
Yeast telomerase RNA: a flexible scaffold for protein subunits. Proc Natl Acad Sci U S A (2004) 2.52
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
Structures of the human and Drosophila 80S ribosome. Nature (2013) 2.36
An enhanced RNA alignment benchmark for sequence alignment programs. Algorithms Mol Biol (2006) 2.35
Multiple small RNAs act additively to integrate sensory information and control quorum sensing in Vibrio harveyi. Genes Dev (2007) 2.33
MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. Plant Cell (2010) 2.22
miRDeepFinder: a miRNA analysis tool for deep sequencing of plant small RNAs. Plant Mol Biol (2012) 2.14
Characterization of the Melanoma miRNAome by Deep Sequencing. PLoS One (2010) 2.08
miTarget: microRNA target gene prediction using a support vector machine. BMC Bioinformatics (2006) 2.08
Revealing posttranscriptional regulatory elements through network-level conservation. PLoS Comput Biol (2005) 2.04
DNMT1-interacting RNAs block gene-specific DNA methylation. Nature (2013) 2.04
Overlapping codes within protein-coding sequences. Genome Res (2010) 2.02
RNA folding: conformational statistics, folding kinetics, and ion electrostatics. Annu Rev Biophys (2008) 2.00
Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution. Proc Natl Acad Sci U S A (2010) 1.99
Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C-miRNA complexes and the degradation of miRNA targets. Genome Res (2009) 1.98
Correlation of mRNA expression and protein abundance affected by multiple sequence features related to translational efficiency in Desulfovibrio vulgaris: a quantitative analysis. Genetics (2006) 1.96
Antisense transcripts of the expanded C9ORF72 hexanucleotide repeat form nuclear RNA foci and undergo repeat-associated non-ATG translation in c9FTD/ALS. Acta Neuropathol (2013) 1.95
Mouse microRNA profiles determined with a new and sensitive cloning method. Nucleic Acids Res (2006) 1.94
Pre-mRNA secondary structures influence exon recognition. PLoS Genet (2007) 1.92
Variations on RNA folding and alignment: lessons from Benasque. J Math Biol (2007) 1.91
Identification and characterization of the Schizosaccharomyces pombe TER1 telomerase RNA. Nat Struct Mol Biol (2007) 1.90
The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures. Nucleic Acids Res (2007) 1.88
CENTROIDFOLD: a web server for RNA secondary structure prediction. Nucleic Acids Res (2009) 1.86
Unique folding of precursor microRNAs: quantitative evidence and implications for de novo identification. RNA (2006) 1.85
RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer. Nature (2014) 1.84
Differential repression of alternative transcripts: a screen for miRNA targets. PLoS Comput Biol (2006) 1.82
A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation. Nucleic Acids Res (2009) 1.81
Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels. Bioinformatics (2010) 1.80
Engineering biological systems with synthetic RNA molecules. Mol Cell (2011) 1.80
Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign. BMC Bioinformatics (2007) 1.79
deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res (2009) 1.78
Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster. Genetics (2010) 1.78
The effect of central loops in miRNA:MRE duplexes on the efficiency of miRNA-mediated gene regulation. PLoS One (2008) 1.78
Effect of target secondary structure on RNAi efficiency. RNA (2007) 1.76
snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome. Nucleic Acids Res (2006) 1.73
Paradigms for computational nucleic acid design. Nucleic Acids Res (2004) 1.72
Numerous conserved and divergent microRNAs expressed by herpes simplex viruses 1 and 2. J Virol (2010) 1.71
mirTools: microRNA profiling and discovery based on high-throughput sequencing. Nucleic Acids Res (2010) 1.70
E-RNAi: a web application to design optimized RNAi constructs. Nucleic Acids Res (2005) 1.69
Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development. BMC Genomics (2010) 1.68
RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins. Mol Cell (2014) 1.68
Reducing ligation bias of small RNAs in libraries for next generation sequencing. Silence (2012) 1.68
A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation. Nucleic Acids Res (2006) 1.67
Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots. Nucleic Acids Res (2005) 1.66
Bioinformatic and functional analysis of RNA secondary structure elements among different genera of human and animal caliciviruses. Nucleic Acids Res (2008) 1.63
MiRenSVM: towards better prediction of microRNA precursors using an ensemble SVM classifier with multi-loop features. BMC Bioinformatics (2010) 1.63
Composite effects of gene determinants on the translation speed and density of ribosomes. Genome Biol (2011) 1.61
Apple miRNAs and tasiRNAs with novel regulatory networks. Genome Biol (2012) 1.61
Sequence characteristics of functional siRNAs. RNA (2005) 1.59
IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinformatics (2011) 1.59
Two antisense RNAs target the transcriptional regulator CsgD to inhibit curli synthesis. EMBO J (2010) 1.53
Predicting structures and stabilities for H-type pseudoknots with interhelix loops. RNA (2009) 1.51
MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets. Hum Mutat (2010) 1.51
Mammalian miRNA curation through next-generation sequencing. Front Genet (2013) 1.49
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