Published in Nature on March 06, 2008
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Higher-order cellular information processing with synthetic RNA devices. Science (2008) 3.64
Atomic accuracy in predicting and designing noncanonical RNA structure. Nat Methods (2010) 3.07
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA (2009) 2.63
Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis. Nat Struct Mol Biol (2010) 2.63
iFoldRNA: three-dimensional RNA structure prediction and folding. Bioinformatics (2008) 2.03
A single-base substitution in the seed region of miR-184 causes EDICT syndrome. Invest Ophthalmol Vis Sci (2012) 1.95
Architecture of human telomerase RNA. Proc Natl Acad Sci U S A (2011) 1.93
SMN2 splice modulators enhance U1-pre-mRNA association and rescue SMA mice. Nat Chem Biol (2015) 1.93
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Automated 3D structure composition for large RNAs. Nucleic Acids Res (2012) 1.85
ModeRNA: a tool for comparative modeling of RNA 3D structure. Nucleic Acids Res (2011) 1.85
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Engineering biological systems with synthetic RNA molecules. Mol Cell (2011) 1.80
New metrics for comparing and assessing discrepancies between RNA 3D structures and models. RNA (2009) 1.78
A cytoplasmic complex mediates specific mRNA recognition and localization in yeast. PLoS Biol (2011) 1.78
Improved RNA secondary structure prediction by maximizing expected pair accuracy. RNA (2009) 1.78
Frameworks for programming biological function through RNA parts and devices. Chem Biol (2009) 1.74
On the significance of an RNA tertiary structure prediction. RNA (2010) 1.61
Plant secondary siRNA production determined by microRNA-duplex structure. Proc Natl Acad Sci U S A (2012) 1.59
Controlling the specificity of modularly assembled small molecules for RNA via ligand module spacing: targeting the RNAs that cause myotonic muscular dystrophy. J Am Chem Soc (2009) 1.54
Developing three-dimensional models of putative-folding intermediates of the HDV ribozyme. Structure (2010) 1.49
5'-UTR G-quadruplex structures acting as translational repressors. Nucleic Acids Res (2010) 1.49
NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers. Proc Natl Acad Sci U S A (2013) 1.48
Discrete RNA libraries from pseudo-torsional space. J Mol Biol (2012) 1.46
Model-guided design of ligand-regulated RNAi for programmable control of gene expression. Mol Syst Biol (2008) 1.46
Design principles for riboswitch function. PLoS Comput Biol (2009) 1.44
The ligand-free state of the TPP riboswitch: a partially folded RNA structure. J Mol Biol (2009) 1.39
Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA. RNA (2013) 1.37
Visualizing transient low-populated structures of RNA. Nature (2012) 1.36
Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics. J Am Chem Soc (2009) 1.33
RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures. RNA (2015) 1.30
Computational approaches to RNA structure prediction, analysis, and design. Curr Opin Struct Biol (2011) 1.28
Turning limited experimental information into 3D models of RNA. RNA (2010) 1.27
A probabilistic model of RNA conformational space. PLoS Comput Biol (2009) 1.22
Structurally conserved five nucleotide bulge determines the overall topology of the core domain of human telomerase RNA. Proc Natl Acad Sci U S A (2010) 1.22
Physics-based de novo prediction of RNA 3D structures. J Phys Chem B (2011) 1.21
Annotation of tertiary interactions in RNA structures reveals variations and correlations. RNA (2008) 1.21
An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling. Proc Natl Acad Sci U S A (2011) 1.21
Three-dimensional RNA structure refinement by hydroxyl radical probing. Nat Methods (2012) 1.20
Predicting helical topologies in RNA junctions as tree graphs. PLoS One (2013) 1.20
RNA and protein 3D structure modeling: similarities and differences. J Mol Model (2011) 1.19
Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling. Nucleic Acids Res (2009) 1.18
Folding and finding RNA secondary structure. Cold Spring Harb Perspect Biol (2010) 1.18
A method for helical RNA global structure determination in solution using small-angle x-ray scattering and NMR measurements. J Mol Biol (2009) 1.16
NMR-assisted prediction of RNA secondary structure: identification of a probable pseudoknot in the coding region of an R2 retrotransposon. J Am Chem Soc (2008) 1.14
Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler. J Mol Graph Model (2008) 1.14
Robust and generic RNA modeling using inferred constraints: a structure for the hepatitis C virus IRES pseudoknot domain. Biochemistry (2010) 1.13
Predicting RNA structure by multiple template homology modeling. Pac Symp Biocomput (2010) 1.12
MicroRNA-mediated loss of ADAR1 in metastatic melanoma promotes tumor growth. J Clin Invest (2013) 1.11
Automated and fast building of three-dimensional RNA structures. Sci Rep (2012) 1.10
Structure of the yeast U2/U6 snRNA complex. RNA (2012) 1.09
In silico selection of RNA aptamers. Nucleic Acids Res (2009) 1.09
Advances in RNA structure prediction from sequence: new tools for generating hypotheses about viral RNA structure-function relationships. J Virol (2009) 1.09
A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed. J Am Chem Soc (2013) 1.09
Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models. Bioinformatics (2009) 1.06
Targeting microRNAs with small molecules: from dream to reality. Clin Pharmacol Ther (2010) 1.04
Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation. Curr Opin Struct Biol (2011) 1.04
Recognition and coupling of A-to-I edited sites are determined by the tertiary structure of the RNA. Nucleic Acids Res (2009) 1.04
Optical melting measurements of nucleic acid thermodynamics. Methods Enzymol (2009) 1.03
Interfamilial recombination between viruses led to acquisition of a novel translation-enhancing RNA element that allows resistance breaking. New Phytol (2013) 1.03
A folding algorithm for extended RNA secondary structures. Bioinformatics (2011) 1.03
Predictions of RNA secondary structure by combining homologous sequence information. Bioinformatics (2009) 1.03
Multifunctional RNA nanoparticles. Nano Lett (2014) 1.03
Predicting loop-helix tertiary structural contacts in RNA pseudoknots. RNA (2010) 1.02
Modeling and design by hierarchical natural moves. Proc Natl Acad Sci U S A (2012) 1.02
Vfold: a web server for RNA structure and folding thermodynamics prediction. PLoS One (2014) 1.02
Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation. RNA (2011) 1.01
Computational analysis of noncoding RNAs. Wiley Interdiscip Rev RNA (2012) 1.01
Importance of the NCp7-like domain in the recognition of pre-let-7g by the pluripotency factor Lin28. Nucleic Acids Res (2011) 1.00
The cap-binding translation initiation factor, eIF4E, binds a pseudoknot in a viral cap-independent translation element. Structure (2011) 1.00
Long non-coding RNAs as targets for cytosine methylation. RNA Biol (2013) 1.00
RNA structure determination using SAXS data. J Phys Chem B (2010) 0.99
Clustering to identify RNA conformations constrained by secondary structure. Proc Natl Acad Sci U S A (2011) 0.98
Coarse-grained model for simulation of RNA three-dimensional structures. J Phys Chem B (2010) 0.98
Secondary structure is required for 3' splice site recognition in yeast. Nucleic Acids Res (2011) 0.98
Modeling nucleic acids. Curr Opin Struct Biol (2012) 0.98
CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction. Nucleic Acids Res (2013) 0.97
RNA internal loops with tandem AG pairs: the structure of the 5'GAGU/3'UGAG loop can be dramatically different from others, including 5'AAGU/3'UGAA. Biochemistry (2010) 0.97
A ribosome-binding, 3' translational enhancer has a T-shaped structure and engages in a long-distance RNA-RNA interaction. J Virol (2012) 0.95
Predicting and modeling RNA architecture. Cold Spring Harb Perspect Biol (2011) 0.95
Computational generation and screening of RNA motifs in large nucleotide sequence pools. Nucleic Acids Res (2010) 0.95
N(6)-Methyladenosine Modification in a Long Noncoding RNA Hairpin Predisposes Its Conformation to Protein Binding. J Mol Biol (2015) 0.95
Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges. J Phys Chem B (2014) 0.95
RNAlyzer--novel approach for quality analysis of RNA structural models. Nucleic Acids Res (2013) 0.95
β-Catenin recognizes a specific RNA motif in the cyclooxygenase-2 mRNA 3'-UTR and interacts with HuR in colon cancer cells. Nucleic Acids Res (2012) 0.94
A model for the structure of satellite tobacco mosaic virus. J Struct Biol (2012) 0.94
The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex. Nucleic Acids Res (2010) 0.94
The centrality of RNA for engineering gene expression. Biotechnol J (2013) 0.94
Aptamer Base: a collaborative knowledge base to describe aptamers and SELEX experiments. Database (Oxford) (2012) 0.94
Computational analysis of RNA structures with chemical probing data. Methods (2015) 0.93
Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities? J Phys Chem B (2010) 0.93
Prevalence of syn nucleobases in the active sites of functional RNAs. RNA (2011) 0.93
Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints. J Comput Chem (2011) 0.93
Stochastic sampling of the RNA structural alignment space. Nucleic Acids Res (2009) 0.93
New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation. Nucleic Acids Res (2011) 0.93
Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function. PLoS Comput Biol (2012) 0.92
Structural characterization of naturally occurring RNA single mismatches. Nucleic Acids Res (2010) 0.92
The core microprocessor component DiGeorge syndrome critical region 8 (DGCR8) is a nonspecific RNA-binding protein. J Biol Chem (2013) 0.92
Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding. J Mol Biol (2009) 0.91
RNAML: a standard syntax for exchanging RNA information. RNA (2002) 5.34
An E2F/miR-20a autoregulatory feedback loop. J Biol Chem (2006) 5.20
The RNA Ontology Consortium: an open invitation to the RNA community. RNA (2006) 3.60
Autism-related deficits via dysregulated eIF4E-dependent translational control. Nature (2012) 3.13
Staufen1 regulates diverse classes of mammalian transcripts. EMBO J (2007) 2.18
RNA canonical and non-canonical base pairing types: a recognition method and complete repertoire. Nucleic Acids Res (2002) 2.03
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. RNA (2012) 1.88
New metrics for comparing and assessing discrepancies between RNA 3D structures and models. RNA (2009) 1.78
Identification of a conserved RNA motif essential for She2p recognition and mRNA localization to the yeast bud. Mol Cell Biol (2005) 1.46
Genetic mapping of activity determinants within cellular prion proteins: N-terminal modules in PrPC offset pro-apoptotic activity of the Doppel helix B/B' region. J Biol Chem (2004) 1.23
Automated extraction and classification of RNA tertiary structure cyclic motifs. Nucleic Acids Res (2006) 1.15
Recognition and coupling of A-to-I edited sites are determined by the tertiary structure of the RNA. Nucleic Acids Res (2009) 1.04
Role of SLV in SLI substrate recognition by the Neurospora VS ribozyme. RNA (2008) 1.00
RNA structure determination using SAXS data. J Phys Chem B (2010) 0.99
A comparative analysis of the triloops in all high-resolution RNA structures reveals sequence structure relationships. RNA (2007) 0.95
RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles. Nucleic Acids Res (2010) 0.92
Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure. Bioinformatics (2012) 0.90
The ERPIN server: an interface to profile-based RNA motif identification. Nucleic Acids Res (2004) 0.89
Designing small multiple-target artificial RNAs. Nucleic Acids Res (2010) 0.88
Determining RNA three-dimensional structures using low-resolution data. J Struct Biol (2012) 0.87
Modeling RNA tertiary structure motifs by graph-grammars. Nucleic Acids Res (2007) 0.86
Molecular basis of TRAP-5'SL RNA interaction in the Bacillus subtilis trp operon transcription attenuation mechanism. RNA (2008) 0.86
RKB: a Semantic Web knowledge base for RNA. J Biomed Semantics (2010) 0.85
Ranking the factors that contribute to protein beta-sheet folding. Proteins (2007) 0.84
A 6374 unigene set corresponding to low abundance transcripts expressed following fertilization in Solanum chacoense Bitt, and characterization of 30 receptor-like kinases. Plant Mol Biol (2005) 0.83
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Identification of two distinct intracellular localization signals in STT3-B. Arch Biochem Biophys (2005) 0.78
A new catalog of protein beta-sheets. Proteins (2005) 0.78
Parametrization of a force field for metals complexed to biomacromolecules: applications to Fe(II), Cu(II) and Pb(II). J Comput Aided Mol Des (2003) 0.77
Modifications and deletions of helices within the hairpin ribozyme-substrate complex: an active ribozyme lacking helix 1. RNA (2004) 0.75