Phylogenetic comparative analysis of RNA secondary structure.

Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc Natl Acad Sci U S A (1994) 8.06

Stochastic context-free grammars for tRNA modeling. Nucleic Acids Res (1994) 6.29

Secondary structure of the 5' nontranslated regions of hepatitis C virus and pestivirus genomic RNAs. Nucleic Acids Res (1992) 4.58

RSEARCH: finding homologs of single structured RNA sequences. BMC Bioinformatics (2003) 4.14

The human immunodeficiency virus type 1 packaging signal and major splice donor region have a conserved stable secondary structure. J Virol (1992) 3.48

The 5' nontranslated region of hepatitis A virus RNA: secondary structure and elements required for translation in vitro. J Virol (1991) 2.83

Predicting oligonucleotide affinity to nucleic acid targets. RNA (1999) 2.67

A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison. Nucleic Acids Res (1991) 2.51

A cis-acting replication element in the sequence encoding the NS5B RNA-dependent RNA polymerase is required for hepatitis C virus RNA replication. J Virol (2004) 2.36

Noncoding RNA genes identified in AT-rich hyperthermophiles. Proc Natl Acad Sci U S A (2002) 2.33

Structure and function of a bacterial mRNA stabilizer: analysis of the 5' untranslated region of ompA mRNA. J Bacteriol (1991) 1.90

A comparative method for finding and folding RNA secondary structures within protein-coding regions. Nucleic Acids Res (2004) 1.89

Comparative analysis of ribonuclease P RNA using gene sequences from natural microbial populations reveals tertiary structural elements. Proc Natl Acad Sci U S A (1996) 1.85

Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element. RNA (1997) 1.68

A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation. Nucleic Acids Res (2006) 1.67

Specificity of RNA-RNA helix recognition. Proc Natl Acad Sci U S A (2002) 1.38

Tracing the evolution of RNA structure in ribosomes. Nucleic Acids Res (2002) 1.35

Computational approaches for RNA energy parameter estimation. RNA (2010) 1.33

High-affinity RNA ligands to basic fibroblast growth factor inhibit receptor binding. Proc Natl Acad Sci U S A (1993) 1.29

Leeway and constraints in the forced evolution of a regulatory RNA helix. EMBO J (1994) 1.19

A common core structure for U3 small nucleolar RNAs. Nucleic Acids Res (1994) 1.11

Computational methods in noncoding RNA research. J Math Biol (2007) 1.08

Grass evolution inferred from chromosomal rearrangements and geometrical and statistical features in RNA structure. J Mol Evol (2005) 1.01

Diversity of Geobacteraceae species inhabiting metal-polluted freshwater lake sediments ascertained by 16S rDNA analyses. Microb Ecol (2003) 0.97

Comparative structure analysis of vertebrate ribonuclease P RNA. Nucleic Acids Res (1998) 0.95

Prediction of alternative RNA secondary structures based on fluctuating thermodynamic parameters. Nucleic Acids Res (1993) 0.87

Duck Hepatitis A virus possesses a distinct type IV internal ribosome entry site element of picornavirus. J Virol (2011) 0.86

A computer method for finding common base paired helices in aligned sequences: application to the analysis of random sequences. Nucleic Acids Res (1991) 0.81

Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science (1996) 41.35

Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A (1985) 37.69

The RDP-II (Ribosomal Database Project). Nucleic Acids Res (2001) 27.07

Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science (1989) 24.75

Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol (1986) 22.39

Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial cells. J Bacteriol (1988) 21.38

Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol (1998) 21.35

The Ribosomal Database Project. Nucleic Acids Res (1994) 20.01

Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J Bacteriol (1991) 18.78

The ribosomal database project. Nucleic Acids Res (1993) 17.20

Differential amplification of rRNA genes by polymerase chain reaction. Appl Environ Microbiol (1992) 14.96

The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature (1997) 14.38

A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res (1999) 13.25

The RDP (Ribosomal Database Project). Nucleic Acids Res (1997) 12.94

CRITICA: coding region identification tool invoking comparative analysis. Mol Biol Evol (1999) 12.64

Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc Natl Acad Sci U S A (1994) 11.41

Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol (1998) 11.22

Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microbiol (1998) 10.17

The RDP (Ribosomal Database Project) continues. Nucleic Acids Res (2000) 10.03

The Ribosomal Database Project (RDP). Nucleic Acids Res (1996) 8.86

Mitochondrial origins. Proc Natl Acad Sci U S A (1985) 8.82

The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature (1998) 7.77

Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc Natl Acad Sci U S A (1996) 7.17

Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences. Science (1984) 7.06

Phylogenetic analysis using ribosomal RNA. Methods Enzymol (1988) 6.21

Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences. Appl Environ Microbiol (1985) 6.06

Evolutionary relationships among cyanobacteria and green chloroplasts. J Bacteriol (1988) 5.99

Tangential flow filtration and preliminary phylogenetic analysis of marine picoplankton. Appl Environ Microbiol (1990) 5.98

Conserved 5S rRNA complement to tRNA is not required for protein synthesis. Proc Natl Acad Sci U S A (1982) 5.54

Phylogenetic analysis of the hyperthermophilic pink filament community in Octopus Spring, Yellowstone National Park. Appl Environ Microbiol (1994) 5.46

Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev (2000) 5.44

Structure and synthesis of the ribosomal ribonucleic acid of prokaryotes. Bacteriol Rev (1973) 4.88

Molecular phylogeny of the animal kingdom. Science (1988) 4.76

Evolutionary relationships among sulfur- and iron-oxidizing eubacteria. J Bacteriol (1992) 4.43

The secondary structure of ribonuclease P RNA, the catalytic element of a ribonucleoprotein enzyme. Cell (1988) 4.41

Sulfur-oxidizing bacterial endosymbionts: analysis of phylogeny and specificity by 16S rRNA sequences. J Bacteriol (1988) 4.35

Archaebacterial phylogeny: perspectives on the urkingdoms. Syst Appl Microbiol (1986) 4.10

Specific ribosomal DNA sequences from diverse environmental settings correlate with experimental contaminants. Appl Environ Microbiol (1998) 4.08

The small-subunit ribosomal RNA gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata. Mol Biol Evol (1985) 3.95

Ribonuclease P: unity and diversity in a tRNA processing ribozyme. Annu Rev Biochem (1998) 3.73

Phylogenetic analysis of Aquaspirillum magnetotacticum using polymerase chain reaction-amplified 16S rRNA-specific DNA. Int J Syst Bacteriol (1991) 3.30

The largest bacterium. Nature (1993) 3.29

Identifying microbial diversity in the natural environment: a molecular phylogenetic approach. Trends Biotechnol (1996) 3.26

A phylogenetic analysis of Aquifex pyrophilus. Syst Appl Microbiol (1992) 3.26

Nucleotide sequence of 5 S ribosomal RNA precursor from Bacillus subtilis. J Biol Chem (1976) 3.20

Sequence of the 16S rRNA gene from the thermoacidophilic archaebacterium Sulfolobus solfataricus and its evolutionary implications. J Mol Evol (1985) 3.20

Campylobacter pylori, the spiral bacterium associated with human gastritis, is not a true Campylobacter sp. J Bacteriol (1987) 3.17

Environmental diversity of bacteria and archaea. Syst Biol (2001) 3.12

Ribosomal RNA phylogeny and the primary lines of evolutionary descent. Cell (1986) 2.92

Role of the protein moiety of ribonuclease P, a ribonucleoprotein enzyme. Science (1988) 2.86

Wide diversity of Crenarchaeota. Nature (1996) 2.84

The excision of intervening sequences from Salmonella 23S ribosomal RNA. Cell (1990) 2.75

Ribonuclease P RNA and protein subunits from bacteria. Nucleic Acids Res (1992) 2.72

Phylogenetic analysis and evolution of RNase P RNA in proteobacteria. J Bacteriol (1991) 2.71

An unusual 5S rRNA, from Sulfolobus acidocaldarius, and its implications for a general 5S rRNA structure. Nucleic Acids Res (1981) 2.66

Phylogenetic analysis of the genera Thiobacillus and Thiomicrospira by 5S rRNA sequences. J Bacteriol (1985) 2.62

An archaeal genomic signature. Proc Natl Acad Sci U S A (2000) 2.53

Compilation and analysis of intein sequences. Nucleic Acids Res (1997) 2.46

Mapping the active site of ribonuclease P RNA using a substrate containing a photoaffinity agent. EMBO J (1990) 2.46

Phylogenetic comparative analysis and the secondary structure of ribonuclease P RNA--a review. Gene (1989) 2.45

Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of bacteria. Appl Environ Microbiol (2000) 2.44

Multiple magnesium ions in the ribonuclease P reaction mechanism. Biochemistry (1993) 2.42

Structure of the 5.8S RNA component of the 5.8S-28S ribosomal RNA junction complex. Biochemistry (1977) 2.42

A reconstruction of the metabolism of Methanococcus jannaschii from sequence data. Gene (1997) 2.35

Detection of DNA contamination in Taq polymerase. Biotechniques (1991) 2.32

In vitro synthesis of an infectious mutant RNA with a normal RNA replicase. Science (1966) 2.30

The RNA component of the Bacillus subtilis RNase P. Sequence, activity, and partial secondary structure. J Biol Chem (1986) 2.28

The synthesis of infectious RNA with a replicase purified according to its size and density. Proc Natl Acad Sci U S A (1966) 2.27

The ability of persons with Alzheimer disease (AD) to make a decision about taking an AD treatment. Neurology (2005) 2.27

Long-range structure in ribonuclease P RNA. Science (1991) 2.22

Influence of metal ions on the ribonuclease P reaction. Distinguishing substrate binding from catalysis. J Biol Chem (1992) 2.18

The design and catalytic properties of a simplified ribonuclease P RNA. Science (1989) 2.17

Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. Proc Natl Acad Sci U S A (1999) 2.14

The in vitro synthesis of a noninfectious complex containing biologically active viral RNA. Proc Natl Acad Sci U S A (1966) 2.10

Do persons with dementia vote? Neurology (2002) 2.04

Further perspective on the catalytic core and secondary structure of ribonuclease P RNA. Proc Natl Acad Sci U S A (1994) 2.00

Use of photoaffinity crosslinking and molecular modeling to analyze the global architecture of ribonuclease P RNA. EMBO J (1994) 1.99

Ion dependence of the Bacillus subtilis RNase P reaction. J Biol Chem (1985) 1.94

The varieties of ribonuclease P. Trends Biochem Sci (1992) 1.93

Circularly permuted tRNAs as specific photoaffinity probes of ribonuclease P RNA structure. Science (1993) 1.93

Reverse transcriptase sequencing of ribosomal RNA for phylogenetic analysis. Methods Enzymol (1988) 1.92