Published in RNA on June 28, 2011
Evaluating our ability to predict the structural disruption of RNA by SNPs. BMC Genomics (2012) 1.19
The Azoarcus group I intron ribozyme misfolds and is accelerated for refolding by ATP-dependent RNA chaperone proteins. J Biol Chem (2011) 1.00
Evolutionary evidence for alternative structure in RNA sequence co-variation. PLoS Comput Biol (2013) 0.91
Attenuation of loop-receptor interactions with pseudoknot formation. Nucleic Acids Res (2011) 0.82
Understanding the role of three-dimensional topology in determining the folding intermediates of group I introns. Biophys J (2013) 0.80
Influence of ground-state structure and Mg2+ binding on folding kinetics of the guanine-sensing riboswitch aptamer domain. Nucleic Acids Res (2011) 0.79
RNA catalysis as a probe for chaperone activity of DEAD-box helicases. Methods Enzymol (2012) 0.78
Mapping the kinetic barriers of a Large RNA molecule's folding landscape. PLoS One (2014) 0.77
RNA folding pathways and kinetics using 2D energy landscapes. J Math Biol (2014) 0.77
Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme. Nucleic Acids Res (2015) 0.76
Formation of Tertiary Interactions during rRNA GTPase Center Folding. J Mol Biol (2015) 0.76
Trans-splicing with the group I intron ribozyme from Azoarcus. RNA (2013) 0.76
Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo. Biophys J (2017) 0.75
The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics (2002) 29.41
Crystal structure of a group I ribozyme domain: principles of RNA packing. Science (1996) 13.99
Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J Mol Biol (1990) 10.85
Evolutionarily conserved pathways of energetic connectivity in protein families. Science (1999) 9.12
Self-splicing of group I introns. Annu Rev Biochem (1990) 6.36
Mapping the transition state and pathway of protein folding by protein engineering. Nature (1989) 5.44
SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA (2005) 3.95
Crystal structure of a self-splicing group I intron with both exons. Nature (2004) 3.92
Characterization of the cytoplasm of Escherichia coli K-12 as a function of external osmolarity. Implications for protein-DNA interactions in vivo. J Mol Biol (1991) 3.73
RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science (1998) 3.67
Frequent use of the same tertiary motif by self-folding RNAs. EMBO J (1995) 3.63
Sequence-specific endoribonuclease activity of the Tetrahymena ribozyme: enhanced cleavage of certain oligonucleotide substrates that form mismatched ribozyme-substrate complexes. Biochemistry (1988) 3.33
Evolutionary information for specifying a protein fold. Nature (2005) 3.23
Structural conventions for group I introns. Nucleic Acids Res (1987) 3.12
Kinetic intermediates in RNA folding. Science (1994) 3.07
Crystal structure of a phage Twort group I ribozyme-product complex. Nat Struct Mol Biol (2004) 2.99
Higher order structure in ribosomal RNA. EMBO J (1986) 2.97
New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme. Chem Biol (1996) 2.81
Exploring the folding landscape of a structured RNA. Proc Natl Acad Sci U S A (2001) 2.78
Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 1. Kinetic description of the reaction of an RNA substrate complementary to the active site. Biochemistry (1990) 2.77
A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor. Nat Struct Biol (1998) 2.71
Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site. Mol Cell (2004) 2.68
A universal mode of helix packing in RNA. Nat Struct Biol (2001) 2.54
Improved methods for fitting sedimentation coefficient distributions derived by time-derivative techniques. Anal Biochem (2006) 2.36
Self-splicing introns in tRNA genes of widely divergent bacteria. Nature (1992) 2.35
Beyond kinetic traps in RNA folding. Curr Opin Struct Biol (2001) 2.32
Small angle X-ray scattering reveals a compact intermediate in RNA folding. Nat Struct Biol (2000) 2.27
Rules for RNA recognition of GNRA tetraloops deduced by in vitro selection: comparison with in vivo evolution. EMBO J (1997) 2.14
Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure. Biochemistry (1993) 2.13
A story: unpaired adenosine bases in ribosomal RNAs. J Mol Biol (2000) 1.92
Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins. Protein Sci (2005) 1.91
Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations. J Mol Biol (2004) 1.90
Unexpected abundance of self-splicing introns in the genome of bacteriophage Twort: introns in multiple genes, a single gene with three introns, and exon skipping by group I ribozymes. Proc Natl Acad Sci U S A (1999) 1.85
Atomic level architecture of group I introns revealed. Trends Biochem Sci (2005) 1.82
Probing the folding landscape of the Tetrahymena ribozyme: commitment to form the native conformation is late in the folding pathway. J Mol Biol (2001) 1.80
Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme. Proc Natl Acad Sci U S A (2003) 1.75
Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 2. Kinetic description of the reaction of an RNA substrate that forms a mismatch at the active site. Biochemistry (1990) 1.63
The paradoxical behavior of a highly structured misfolded intermediate in RNA folding. J Mol Biol (2006) 1.61
New pathways in folding of the Tetrahymena group I RNA enzyme. J Mol Biol (1999) 1.58
Mg2+-dependent folding of a large ribozyme without kinetic traps. Nat Struct Biol (1999) 1.54
An optimal Mg(2+) concentration for kinetic folding of the tetrahymena ribozyme. Proc Natl Acad Sci U S A (1999) 1.53
Activity and thermostability of the small self-splicing group I intron in the pre-tRNA(lle) of the purple bacterium Azoarcus. RNA (1996) 1.51
Structure and assembly of group I introns. Curr Opin Struct Biol (2005) 1.43
A simple method for 3'-labeling of RNA. Nucleic Acids Res (1996) 1.43
Tertiary interactions determine the accuracy of RNA folding. J Am Chem Soc (2008) 1.40
Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule. J Mol Biol (2006) 1.38
Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins. Nucleic Acids Res (2006) 1.33
Concordant exploration of the kinetics of RNA folding from global and local perspectives. J Mol Biol (2005) 1.33
Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding. Proc Natl Acad Sci U S A (2007) 1.26
The P5abc peripheral element facilitates preorganization of the tetrahymena group I ribozyme for catalysis. Biochemistry (2000) 1.21
Comprehensive features of natural and in vitro selected GNRA tetraloop-binding receptors. Nucleic Acids Res (2007) 1.20
Structural specificity conferred by a group I RNA peripheral element. Proc Natl Acad Sci U S A (2005) 1.19
Structural requirement for Mg2+ binding in the group I intron core. J Mol Biol (2003) 1.16
Direct measurement of tertiary contact cooperativity in RNA folding. J Am Chem Soc (2008) 1.15
Concerted kinetic folding of a multidomain ribozyme with a disrupted loop-receptor interaction. J Mol Biol (2001) 1.15
Comparison of successive transition states for folding reveals alternative early folding pathways of two homologous proteins. Proc Natl Acad Sci U S A (2008) 1.10
Perturbation of the hierarchical folding of a large RNA by the destabilization of its Scaffold's tertiary structure. J Mol Biol (2005) 1.10
Kinetic barriers and the role of topology in protein and RNA folding. Protein Sci (2008) 1.07
Structural biology. Evolution of RNA architecture. Science (2004) 1.05
Monitoring structural changes in nucleic acids with single residue spatial and millisecond time resolution by quantitative hydroxyl radical footprinting. Nat Protoc (2008) 1.03
Multiple monovalent ion-dependent pathways for the folding of the L-21 Tetrahymena thermophila ribozyme. J Mol Biol (2003) 1.02
Self-splicing of the Tetrahymena intron from mRNA in mammalian cells. EMBO J (1999) 1.01
The UAA/GAN internal loop motif: a new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions. J Mol Biol (2006) 1.01
Toward predicting self-splicing and protein-facilitated splicing of group I introns. RNA (2008) 1.00
Structural metals in the group I intron: a ribozyme with a multiple metal ion core. J Mol Biol (2007) 1.00
Structural rearrangements linked to global folding pathways of the Azoarcus group I ribozyme. J Mol Biol (2009) 0.99
Deletion of the P5abc peripheral element accelerates early and late folding steps of the Tetrahymena group I ribozyme. Biochemistry (2007) 0.98
Reduced contact order and RNA folding rates. J Mol Biol (2004) 0.97
Self-splicing of the bacteriophage T4 group I introns requires efficient translation of the pre-mRNA in vivo and correlates with the growth state of the infected bacterium. J Bacteriol (2006) 0.89
Group I introns and GNRA tetraloops: remnants of 'The RNA world'? Mol Biol Rep (2007) 0.81
A comparative study on two GNRA-tetraloop receptors: 11-nt and IC3 motifs. J Biochem (2001) 0.81
Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell (2012) 12.32
Clinical assessment incorporating a personal genome. Lancet (2010) 10.18
The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science (2008) 8.52
The incidentalome: a threat to genomic medicine. JAMA (2006) 7.24
Genetics. Genomic research and human subject privacy. Science (2004) 6.56
PharmGKB: the Pharmacogenetics Knowledge Base. Nucleic Acids Res (2002) 6.40
A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci U S A (2003) 6.19
Toward interoperable bioscience data. Nat Genet (2012) 4.72
Common genetic variation in the HLA region is associated with late-onset sporadic Parkinson's disease. Nat Genet (2010) 4.47
From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource. Biomark Med (2011) 4.05
Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO). Bioinformatics (2003) 3.97
SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA (2005) 3.95
Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature. Genome Res (2002) 3.77
Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics (2002) 3.65
Health-information altruists--a potentially critical resource. N Engl J Med (2005) 3.61
The RNA Ontology Consortium: an open invitation to the RNA community. RNA (2006) 3.60
Creating an online dictionary of abbreviations from MEDLINE. J Am Med Inform Assoc (2002) 3.32
Genetic variants associated with warfarin dose in African-American individuals: a genome-wide association study. Lancet (2013) 3.21
Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genet (2011) 3.20
Data-driven prediction of drug effects and interactions. Sci Transl Med (2012) 2.93
Challenges in the clinical application of whole-genome sequencing. Lancet (2010) 2.92
Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Genome Res (2004) 2.84
PharmGKB: a logical home for knowledge relating genotype to drug response phenotype. Nat Genet (2007) 2.65
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA (2009) 2.63
Disease-associated mutations that alter the RNA structural ensemble. PLoS Genet (2010) 2.54
A novel signal detection algorithm for identifying hidden drug-drug interactions in adverse event reports. J Am Med Inform Assoc (2011) 2.53
Clinical implementation of pharmacogenomics: overcoming genetic exceptionalism. Lancet Oncol (2010) 2.52
The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge. Nucleic Acids Res (2007) 2.45
The Pharmacogenomics Research Network Translational Pharmacogenetics Program: overcoming challenges of real-world implementation. Clin Pharmacol Ther (2013) 2.39
Bioinformatics challenges for personalized medicine. Bioinformatics (2011) 2.28
Time to organize the bioinformatics resourceome. PLoS Comput Biol (2005) 2.25
MScanner: a classifier for retrieving Medline citations. BMC Bioinformatics (2008) 2.24
Using binning to maintain confidentiality of medical data. Proc AMIA Symp (2002) 2.23
Web-scale pharmacovigilance: listening to signals from the crowd. J Am Med Inform Assoc (2013) 2.19
Using text to build semantic networks for pharmacogenomics. J Biomed Inform (2010) 2.19
Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text. BMC Bioinformatics (2009) 2.15
PharmGKB: understanding the effects of individual genetic variants. Drug Metab Rev (2008) 2.09
GAPSCORE: finding gene and protein names one word at a time. Bioinformatics (2004) 2.05
Pharmacogenomics: challenges and opportunities. Ann Intern Med (2006) 1.96
Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery. Genome Res (2004) 1.92
Pharmacogenomics and bioinformatics: PharmGKB. Pharmacogenomics (2010) 1.91
Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations. J Mol Biol (2004) 1.90
Recent progress in automatically extracting information from the pharmacogenomic literature. Pharmacogenomics (2010) 1.88
Automating data acquisition into ontologies from pharmacogenetics relational data sources using declarative object definitions and XML. Pac Symp Biocomput (2002) 1.81
PharmGKB: the Pharmacogenomics Knowledge Base. Methods Mol Biol (2013) 1.81
PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base. Methods Mol Biol (2005) 1.80
High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis. Nucleic Acids Res (2008) 1.78
Using text analysis to identify functionally coherent gene groups. Genome Res (2002) 1.71
The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications. BMC Genomics (2008) 1.64
Finding haplotype tagging SNPs by use of principal components analysis. Am J Hum Genet (2004) 1.61
The paradoxical behavior of a highly structured misfolded intermediate in RNA folding. J Mol Biol (2006) 1.61
Local RNA structural changes induced by crystallization are revealed by SHAPE. RNA (2007) 1.55
MutDB: annotating human variation with functionally relevant data. Bioinformatics (2003) 1.54
Structural inference of native and partially folded RNA by high-throughput contact mapping. Proc Natl Acad Sci U S A (2008) 1.54
Doxorubicin pathways: pharmacodynamics and adverse effects. Pharmacogenet Genomics (2011) 1.53
Training the next generation of informaticians: the impact of "BISTI" and bioinformatics--a report from the American College of Medical Informatics. J Am Med Inform Assoc (2004) 1.53
Discovery and explanation of drug-drug interactions via text mining. Pac Symp Biocomput (2012) 1.53
Concerted binding and bending of DNA by Escherichia coli integration host factor. J Mol Biol (2002) 1.49
The computational analysis of scientific literature to define and recognize gene expression clusters. Nucleic Acids Res (2003) 1.44
Direct measurement of a pK(a) near neutrality for the catalytic cytosine in the genomic HDV ribozyme using Raman crystallography. J Am Chem Soc (2007) 1.43
Independent component analysis: mining microarray data for fundamental human gene expression modules. J Biomed Inform (2010) 1.39
A 1.9 A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage. Biochemistry (2010) 1.39
Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule. J Mol Biol (2006) 1.38
Metformin pathways: pharmacokinetics and pharmacodynamics. Pharmacogenet Genomics (2012) 1.38
A statistical approach to scanning the biomedical literature for pharmacogenetics knowledge. J Am Med Inform Assoc (2004) 1.37
Monovalent cations mediate formation of native tertiary structure of the Tetrahymena thermophila ribozyme. Nat Struct Biol (2002) 1.36
Structure of a tyrosyl-tRNA synthetase splicing factor bound to a group I intron RNA. Nature (2008) 1.36
WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures. Nucleic Acids Res (2003) 1.35
Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins. Nucleic Acids Res (2006) 1.33
A literature-based method for assessing the functional coherence of a gene group. Bioinformatics (2003) 1.33
Concordant exploration of the kinetics of RNA folding from global and local perspectives. J Mol Biol (2005) 1.33
Linkage of monovalent and divalent ion binding in the folding of the P4-P6 domain of the Tetrahymena ribozyme. Biochemistry (2002) 1.31
A call for the creation of personalized medicine databases. Nat Rev Drug Discov (2006) 1.30
Extracting and characterizing gene-drug relationships from the literature. Pharmacogenetics (2004) 1.30
Using ODIN for a PharmGKB revalidation experiment. Database (Oxford) (2012) 1.29
Integration and publication of heterogeneous text-mined relationships on the Semantic Web. J Biomed Semantics (2011) 1.29
Biomedical term mapping databases. Nucleic Acids Res (2005) 1.29
Very important pharmacogene summary: ABCB1 (MDR1, P-glycoprotein). Pharmacogenet Genomics (2011) 1.29
Informatics confronts drug-drug interactions. Trends Pharmacol Sci (2013) 1.28
Turning limited experimental information into 3D models of RNA. RNA (2010) 1.27
Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments. Nat Protoc (2008) 1.27
A new disease-specific machine learning approach for the prediction of cancer-causing missense variants. Genomics (2011) 1.27
PharmGKB summary: methotrexate pathway. Pharmacogenet Genomics (2011) 1.27
Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding. Proc Natl Acad Sci U S A (2007) 1.26
Pharmacogenomics: The relevance of emerging genotyping technologies. MLO Med Lab Obs (2006) 1.26
Productive folding to the native state by a group II intron ribozyme. J Mol Biol (2002) 1.26
Spatial arrangement of an RNA zipcode identifies mRNAs under post-transcriptional control. Genes Dev (2012) 1.26
Predicting drug side-effects by chemical systems biology. Genome Biol (2009) 1.26
Large scale study of protein domain distribution in the context of alternative splicing. Nucleic Acids Res (2003) 1.26
PharmGKB summary: very important pharmacogene information for cytochrome P450, family 2, subfamily C, polypeptide 19. Pharmacogenet Genomics (2012) 1.25
Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme. J Mol Biol (2004) 1.24
An alternative route for the folding of large RNAs: apparent two-state folding by a group II intron ribozyme. J Mol Biol (2003) 1.24