Published in Nature on February 13, 2003
Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proc Natl Acad Sci U S A (2011) 3.30
Topology of three-way junctions in folded RNAs. RNA (2006) 3.14
The building blocks and motifs of RNA architecture. Curr Opin Struct Biol (2006) 2.94
Ribozymes, riboswitches and beyond: regulation of gene expression without proteins. Nat Rev Genet (2007) 2.52
Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA. Nature (2010) 2.40
The kink-turn motif in RNA is dimorphic, and metal ion-dependent. RNA (2004) 2.08
Crystal structure of a bacterial ribonuclease P RNA. Proc Natl Acad Sci U S A (2005) 2.01
Ribonuclease P: the evolution of an ancient RNA enzyme. Crit Rev Biochem Mol Biol (2006) 1.97
Exploring RNA structural codes with SHAPE chemistry. Acc Chem Res (2011) 1.78
Influence of nucleotide identity on ribose 2'-hydroxyl reactivity in RNA. RNA (2009) 1.68
Of proteins and RNA: the RNase P/MRP family. RNA (2010) 1.67
Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications. RNA (2003) 1.64
On the significance of an RNA tertiary structure prediction. RNA (2010) 1.61
Time-resolved RNA SHAPE chemistry: quantitative RNA structure analysis in one-second snapshots and at single-nucleotide resolution. Nat Protoc (2009) 1.60
RNA misfolding and the action of chaperones. Front Biosci (2008) 1.59
Identification and analysis of ribonuclease P and MRP RNA in a broad range of eukaryotes. Nucleic Acids Res (2005) 1.56
The common and the distinctive features of the bulged-G motif based on a 1.04 A resolution RNA structure. Nucleic Acids Res (2003) 1.55
The interaction networks of structured RNAs. Nucleic Acids Res (2006) 1.45
Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA. Nature (2013) 1.45
Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns. Nucleic Acids Res (2004) 1.43
Predicting helical coaxial stacking in RNA multibranch loops. RNA (2007) 1.40
On the occurrence of the T-loop RNA folding motif in large RNA molecules. RNA (2003) 1.37
Slow conformational dynamics at C2'-endo nucleotides in RNA. J Am Chem Soc (2008) 1.35
SeqFold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data. Genome Res (2012) 1.30
R3D Align: global pairwise alignment of RNA 3D structures using local superpositions. Bioinformatics (2010) 1.28
Three-way RNA junctions with remote tertiary contacts: a recurrent and highly versatile fold. RNA (2009) 1.26
Structural implications of novel diversity in eucaryal RNase P RNA. RNA (2005) 1.25
Three-dimensional RNA structure refinement by hydroxyl radical probing. Nat Methods (2012) 1.20
Fingerprinting noncanonical and tertiary RNA structures by differential SHAPE reactivity. J Am Chem Soc (2012) 1.18
Identification of catalytic metal ion ligands in ribozymes. Methods (2009) 1.18
Principles for understanding the accuracy of SHAPE-directed RNA structure modeling. Biochemistry (2013) 1.16
C2'-endo nucleotides as molecular timers suggested by the folding of an RNA domain. Proc Natl Acad Sci U S A (2009) 1.16
Structural basis of UGUA recognition by the Nudix protein CFI(m)25 and implications for a regulatory role in mRNA 3' processing. Proc Natl Acad Sci U S A (2010) 1.15
Metal ion dependence, thermodynamics, and kinetics for intramolecular docking of a GAAA tetraloop and receptor connected by a flexible linker. Biochemistry (2006) 1.15
Comparison of mode analyses at different resolutions applied to nucleic acid systems. Biophys J (2005) 1.14
Eukaryotic ribonucleases P/MRP: the crystal structure of the P3 domain. EMBO J (2010) 1.10
Mapping metal-binding sites in the catalytic domain of bacterial RNase P RNA. RNA (2008) 1.09
Nucleic acid visualization with UCSF Chimera. Nucleic Acids Res (2006) 1.07
NMR structure and dynamics of the Specifier Loop domain from the Bacillus subtilis tyrS T box leader RNA. Nucleic Acids Res (2010) 1.01
Emerging structural themes in large RNA molecules. Curr Opin Struct Biol (2011) 1.00
A universal RNA structural motif docking the elbow of tRNA in the ribosome, RNAse P and T-box leaders. Nucleic Acids Res (2013) 1.00
Solution structure of RNase P RNA. RNA (2011) 0.99
Footprinting analysis demonstrates extensive similarity between eukaryotic RNase P and RNase MRP holoenzymes. RNA (2008) 0.99
Structure and function of the T-loop structural motif in noncoding RNAs. Wiley Interdiscip Rev RNA (2013) 0.99
Ionic interactions between PRNA and P protein in Bacillus subtilis RNase P characterized using a magnetocapture-based assay. RNA (2004) 0.96
Structure-function analysis of the ribozymes of chrysanthemum chlorotic mottle viroid: a loop-loop interaction motif conserved in most natural hammerheads. Nucleic Acids Res (2008) 0.96
The ancient history of the structure of ribonuclease P and the early origins of Archaea. BMC Bioinformatics (2010) 0.96
Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility. Nucleic Acids Res (2014) 0.95
Bcheck: a wrapper tool for detecting RNase P RNA genes. BMC Genomics (2010) 0.95
Predicting and modeling RNA architecture. Cold Spring Harb Perspect Biol (2011) 0.95
Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin. Nucleic Acids Res (2007) 0.93
The Mrs1 splicing factor binds the bI3 group I intron at each of two tetraloop-receptor motifs. PLoS One (2010) 0.93
Comparisons between chemical mapping and binding to isoenergetic oligonucleotide microarrays reveal unexpected patterns of binding to the Bacillus subtilis RNase P RNA specificity domain. Biochemistry (2010) 0.92
The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50s ribosomal subunits. Biochemistry (2006) 0.92
Extended structures in RNA folding intermediates are due to nonnative interactions rather than electrostatic repulsion. J Mol Biol (2010) 0.92
A surprisingly large RNase P RNA in Candida glabrata. RNA (2005) 0.90
An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA. Biochemistry (2006) 0.88
RNA synthesis by in vitro selected ribozymes for recreating an RNA world. Life (Basel) (2015) 0.88
Characterization of conserved sequence elements in eukaryotic RNase P RNA reveals roles in holoenzyme assembly and tRNA processing. RNA (2005) 0.88
Fluorescence competition and optical melting measurements of RNA three-way multibranch loops provide a revised model for thermodynamic parameters. Biochemistry (2011) 0.87
Substrate recognition by ribonucleoprotein ribonuclease MRP. RNA (2010) 0.87
Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics. J Chem Theory Comput (2015) 0.85
SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data. RNA (2015) 0.84
Characterization of the kinetic and thermodynamic landscape of RNA folding using a novel application of isothermal titration calorimetry. Nucleic Acids Res (2011) 0.83
Microarrays for identifying binding sites and probing structure of RNAs. Nucleic Acids Res (2014) 0.83
Progress and Current Challenges in Modeling Large RNAs. J Mol Biol (2015) 0.83
Change of RNase P RNA function by single base mutation correlates with perturbation of metal ion binding in P4 as determined by NMR spectroscopy. Nucleic Acids Res (2004) 0.83
Secondary structure of a conserved domain in an intron of influenza A M1 mRNA. Biochemistry (2014) 0.82
Modular architecture of eukaryotic RNase P and RNase MRP revealed by electron microscopy. Nucleic Acids Res (2011) 0.82
Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy. J Am Chem Soc (2010) 0.82
Deciphering RNA structural diversity and systematic phylogeny from microbial metagenomes. Nucleic Acids Res (2007) 0.82
Bacterial transfer RNAs. FEMS Microbiol Rev (2015) 0.81
Self-Folding of Naked Segment 8 Genomic RNA of Influenza A Virus. PLoS One (2016) 0.81
A second eukaryotic group with mitochondrion-encoded tmRNA: in silico identification and experimental confirmation. RNA Biol (2013) 0.80
Principles of ion recognition in RNA: insights from the group II intron structures. RNA (2014) 0.80
Structural analysis of protein-RNA interactions with mass spectrometry. Methods Mol Biol (2008) 0.80
Exploring the electrostatic energy landscape for tetraloop-receptor docking. Phys Chem Chem Phys (2013) 0.79
Interactions of a Pop5/Rpp1 heterodimer with the catalytic domain of RNase MRP. RNA (2011) 0.79
Footprinting analysis of interactions between the largest eukaryotic RNase P/MRP protein Pop1 and RNase P/MRP RNA components. RNA (2015) 0.79
An in vitro-selected RNA receptor for the GAAC loop: modular receptor for non-GNRA-type tetraloop. Nucleic Acids Res (2013) 0.78
'Z-DNA like' fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response. Nucleic Acids Res (2016) 0.78
Twist-joints and double twist-joints in RNA structure. RNA (2012) 0.77
The bacterial ribonuclease P holoenzyme requires specific, conserved residues for efficient catalysis and substrate positioning. Nucleic Acids Res (2012) 0.76
Conformational entropy of the RNA phosphate backbone and its contribution to the folding free energy. Biophys J (2014) 0.75
Discovery of a mini-RNase P in archaea. Proc Natl Acad Sci U S A (2010) 0.75
Bacterial type B RNase P: functional characterization of the L5.1-L15.1 tertiary contact and antisense inhibition. RNA (2016) 0.75
Essential is not irreplaceable: fitness dynamics of experimental E. coli RNase P RNA heterologous replacement. J Mol Evol (2014) 0.75
Pharmacologic disruption of Polycomb-repressive complex 2-mediated gene repression selectively induces apoptosis in cancer cells. Genes Dev (2007) 6.71
N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol (2011) 5.96
An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell (2010) 4.45
Tissue-specific differences in human transfer RNA expression. PLoS Genet (2006) 4.10
Molecular basis of metal-ion selectivity and zeptomolar sensitivity by CueR. Science (2003) 3.08
Codon-usage-based inhibition of HIV protein synthesis by human schlafen 11. Nature (2012) 2.98
Basis for structural diversity in homologous RNAs. Science (2004) 2.70
Innate immune and chemically triggered oxidative stress modifies translational fidelity. Nature (2009) 2.50
Selective charging of tRNA isoacceptors induced by amino-acid starvation. EMBO Rep (2005) 2.48
DACT3 is an epigenetic regulator of Wnt/beta-catenin signaling in colorectal cancer and is a therapeutic target of histone modifications. Cancer Cell (2008) 2.46
DNA methylation screening identifies driver epigenetic events of cancer cell survival. Cancer Cell (2012) 2.45
Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA. Nature (2010) 2.40
Leucine-tRNA initiates at CUG start codons for protein synthesis and presentation by MHC class I. Science (2012) 2.30
Independent movement, dimerization and stability of tandem repeats of chicken brain alpha-spectrin. J Mol Biol (2004) 2.27
Crystal structure of the RNA component of bacterial ribonuclease P. Nature (2005) 2.10
tRNA over-expression in breast cancer and functional consequences. Nucleic Acids Res (2009) 2.08
Diversity of tRNA genes in eukaryotes. Nucleic Acids Res (2006) 2.05
Structure and function of plant photoreceptors. Annu Rev Plant Biol (2010) 1.93
DNA methylation directly silences genes with non-CpG island promoters and establishes a nucleosome occupied promoter. Hum Mol Genet (2011) 1.83
Exploring the regulation of tRNA distribution on the genomic scale. J Mol Biol (2004) 1.80
The AlkB domain of mammalian ABH8 catalyzes hydroxylation of 5-methoxycarbonylmethyluridine at the wobble position of tRNA. Angew Chem Int Ed Engl (2010) 1.76
Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme. Proc Natl Acad Sci U S A (2004) 1.69
Automated crystallographic system for high-throughput protein structure determination. Acta Crystallogr D Biol Crystallogr (2003) 1.67
Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N6-methyladenosine. Nucleic Acids Res (2007) 1.66
Genome-wide analysis of tRNA charging and activation of the eIF2 kinase Gcn2p. J Biol Chem (2009) 1.64
A role for tRNA modifications in genome structure and codon usage. Cell (2012) 1.57
Real-time RNA profiling within a single bacterium. Proc Natl Acad Sci U S A (2005) 1.56
RNA folding: models and perspectives. Curr Opin Struct Biol (2003) 1.56
Intercellular transfer of the cellular prion protein. J Biol Chem (2002) 1.54
Structural basis for an unexpected mode of SERM-mediated ER antagonism. Mol Cell (2005) 1.50
Structures of the spectrin-ankyrin interaction binding domains. Blood (2009) 1.49
Structural insights into the stability and flexibility of unusual erythroid spectrin repeats. Structure (2004) 1.48
Genome-wide identification and quantitative analysis of cleaved tRNA fragments induced by cellular stress. J Biol Chem (2012) 1.47
Structure of a complex between E. coli DNA topoisomerase I and single-stranded DNA. Structure (2003) 1.39
Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases. EMBO J (2006) 1.39
On the occurrence of the T-loop RNA folding motif in large RNA molecules. RNA (2003) 1.37
Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA. RNA (2013) 1.37
Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures. Proc Natl Acad Sci U S A (2007) 1.36
Genome-wide analysis of N1-methyl-adenosine modification in human tRNAs. RNA (2010) 1.33
A multicenter application and evaluation of the oxford classification of IgA nephropathy in adult chinese patients. Am J Kidney Dis (2012) 1.32
Structure of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding. J Mol Biol (2005) 1.31
Cellular dynamics of RNA modification. Acc Chem Res (2011) 1.28
Structural studies of type I topoisomerases. Nucleic Acids Res (2008) 1.24
High levels of tRNA abundance and alteration of tRNA charging by bortezomib in multiple myeloma. Biochem Biophys Res Commun (2009) 1.23
A self-defeating anabolic program leads to β-cell apoptosis in endoplasmic reticulum stress-induced diabetes via regulation of amino acid flux. J Biol Chem (2013) 1.22
Structural basis for spectrin recognition by ankyrin. Blood (2010) 1.21
Tetrathiomolybdate inhibits copper trafficking proteins through metal cluster formation. Science (2009) 1.21
Integration of general amino acid control and target of rapamycin (TOR) regulatory pathways in nitrogen assimilation in yeast. J Biol Chem (2010) 1.20
Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription. J Nanobiotechnology (2013) 1.19
Phase-changing sacrificial materials for solvent bonding of high-performance polymeric capillary electrophoresis microchips. Anal Chem (2005) 1.19
Topoisomerase V relaxes supercoiled DNA by a constrained swiveling mechanism. Proc Natl Acad Sci U S A (2007) 1.18
High-resolution N(6) -methyladenosine (m(6) A) map using photo-crosslinking-assisted m(6) A sequencing. Angew Chem Int Ed Engl (2014) 1.18
Allelic methylation levels of the noncoding VTRNA2-1 located on chromosome 5q31.1 predict outcome in AML. Blood (2011) 1.17
N6-methyladenosine–encoded epitranscriptomics. Nat Struct Mol Biol (2016) 1.17
Structure of ribonuclease P--a universal ribozyme. Curr Opin Struct Biol (2006) 1.16
Automated real-space refinement of protein structures using a realistic backbone move set. Biophys J (2011) 1.16
Pyk2 activation is integral to acid stimulation of sodium/hydrogen exchanger 3. J Clin Invest (2004) 1.15
Profiling non-lysyl tRNAs in HIV-1. RNA (2009) 1.14
Functional analysis of human tRNA isodecoders. J Mol Biol (2009) 1.13
Crystal structure and functional interpretation of the erythrocyte spectrin tetramerization domain complex. Blood (2010) 1.11
Structural studies of E. coli topoisomerase III-DNA complexes reveal a novel type IA topoisomerase-DNA conformational intermediate. J Mol Biol (2007) 1.11
Novel catalytic mechanism of glycoside hydrolysis based on the structure of an NAD+/Mn2+ -dependent phospho-alpha-glucosidase from Bacillus subtilis. Structure (2004) 1.11
A systematic, ligation-based approach to study RNA modifications. RNA (2006) 1.10
Ribosomal protein S27-like, a p53-inducible modulator of cell fate in response to genotoxic stress. Cancer Res (2007) 1.09
Functional DNA demethylation is accompanied by chromatin accessibility. Nucleic Acids Res (2013) 1.09
Misacylation of tRNA with methionine in Saccharomyces cerevisiae. Nucleic Acids Res (2012) 1.08
Misacylation of specific nonmethionyl tRNAs by a bacterial methionyl-tRNA synthetase. Proc Natl Acad Sci U S A (2011) 1.07
Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch. Proc Natl Acad Sci U S A (2012) 1.07
Syntheses of two 5-hydroxymethyl-2'-deoxycytidine phosphoramidites with TBDMS as the 5-hydroxymethyl protecting group and their incorporation into DNA. J Org Chem (2011) 1.07
Synthesis and SAR of 1,2,3,4-tetrahydroisoquinolin-1-ones as novel G-protein-coupled receptor 40 (GPR40) antagonists. Bioorg Med Chem Lett (2009) 1.06
Reversible and rapid transfer-RNA deactivation as a mechanism of translational repression in stress. PLoS Genet (2013) 1.05
Affinity monolith-integrated poly(methyl methacrylate) microchips for on-line protein extraction and capillary electrophoresis. Anal Chem (2008) 1.04
A study of the lengthening and contractility of the surgical margins in digestive tract cancer. Am J Surg (2004) 1.01
An unusual mechanism of glycoside hydrolysis involving redox and elimination steps by a family 4 beta-glycosidase from Thermotoga maritima. J Am Chem Soc (2004) 1.01
Prion protein is ubiquitinated after developing protease resistance in the brains of scrapie-infected mice. J Pathol (2004) 1.01
Emerging structural themes in large RNA molecules. Curr Opin Struct Biol (2011) 1.00
Efficient fluorescence labeling of a large RNA through oligonucleotide hybridization. RNA (2004) 0.99
Structure and function of the T-loop structural motif in noncoding RNAs. Wiley Interdiscip Rev RNA (2013) 0.99
Combinatorial pharmacologic approaches target EZH2-mediated gene repression in breast cancer cells. Mol Cancer Ther (2009) 0.98
Maternal low-protein diet induces gender-dependent changes in epigenetic regulation of the glucose-6-phosphatase gene in newborn piglet liver. J Nutr (2012) 0.98
Affinity monolith preconcentrators for polymer microchip capillary electrophoresis. Electrophoresis (2008) 0.98
Folding of a universal ribozyme: the ribonuclease P RNA. Q Rev Biophys (2007) 0.98
RNA folding during transcription: protocols and studies. Methods Enzymol (2009) 0.97
Single-molecule nonequilibrium periodic Mg2+-concentration jump experiments reveal details of the early folding pathways of a large RNA. Proc Natl Acad Sci U S A (2008) 0.96
Regulation of chaperone effects on a yeast prion by cochaperone Sgt2. Mol Cell Biol (2012) 0.96
Environmental perturbations lift the degeneracy of the genetic code to regulate protein levels in bacteria. Proc Natl Acad Sci U S A (2012) 0.95
Picoliter-volume aqueous droplets in oil: electrochemical detection and yeast cell electroporation. Electrophoresis (2006) 0.95
Biochemical characterization of an invariant histidine involved in Escherichia coli DNA topoisomerase I catalysis. J Biol Chem (2002) 0.95
Langerhans' cell histiocytosis of the spine in children with soft tissue extension and chemotherapy. Int Orthop (2008) 0.95
Surface-modified poly(methyl methacrylate) capillary electrophoresis microchips for protein and peptide analysis. Anal Chem (2004) 0.95
Dimeric and monomeric Bacillus subtilis RNase P holoenzyme in the absence and presence of pre-tRNA substrates. Biochemistry (2002) 0.94
Crystal structure of a bacterial type IB DNA topoisomerase reveals a preassembled active site in the absence of DNA. J Biol Chem (2005) 0.93
Microvesicle-shuttled miR-130b reduces fat deposition in recipient primary cultured porcine adipocytes by inhibiting PPAR-g expression. J Cell Physiol (2014) 0.93
Extended structures in RNA folding intermediates are due to nonnative interactions rather than electrostatic repulsion. J Mol Biol (2010) 0.92
Mid-infrared spectroscopic measurement of ionic dissociative materials in the metabolic pathway. Appl Spectrosc (2003) 0.92