Published in Genetics on March 01, 1995
RSEARCH: finding homologs of single structured RNA sequences. BMC Bioinformatics (2003) 4.14
Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinformatics (2004) 3.60
Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag. PLoS Comput Biol (2008) 2.32
Maintenance of pre-mRNA secondary structure by epistatic selection. Proc Natl Acad Sci U S A (1995) 2.14
Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. BMC Bioinformatics (2006) 2.08
The evolution of ribosomal DNA: divergent paralogues and phylogenetic implications. Genetics (1997) 2.03
A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza A virus. Mol Biol Evol (2008) 1.96
The rate of compensatory evolution. Genetics (1996) 1.91
RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum-likelihood methods. Genetics (2001) 1.53
Selection intensity against deleterious mutations in RNA secondary structures and rate of compensatory nucleotide substitutions. Genetics (2001) 1.51
Detecting selection in noncoding regions of nucleotide sequences. Genetics (2004) 1.50
Site-directed mutations reveal long-range compensatory interactions in the Adh gene of Drosophila melanogaster. Proc Natl Acad Sci U S A (1997) 1.43
The relationship between third-codon position nucleotide content, codon bias, mRNA secondary structure and gene expression in the drosophilid alcohol dehydrogenase genes Adh and Adhr. Genetics (2001) 1.39
Compensatory evolution of a precursor messenger RNA secondary structure in the Drosophila melanogaster Adh gene. Proc Natl Acad Sci U S A (2003) 1.36
High apparent rate of simultaneous compensatory base-pair substitutions in ribosomal RNA. Genetics (1998) 1.33
Comparative sequence analysis and patterns of covariation in RNA secondary structures. Genetics (2000) 1.32
RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers. RNA (2006) 1.19
Evolutionary rates vary among rRNA structural elements. Nucleic Acids Res (2007) 1.12
Conservation patterns in angiosperm rDNA ITS2 sequences. Nucleic Acids Res (1996) 1.07
Causes of evolutionary rate variation among protein sites. Nat Rev Genet (2016) 1.03
Molecular phylogenetic evaluation of classification and scenarios of character evolution in calcareous sponges (Porifera, Class Calcarea). PLoS One (2012) 0.96
Molecular evolution of rDNA in early diverging Metazoa: first comparative analysis and phylogenetic application of complete SSU rRNA secondary structures in Porifera. BMC Evol Biol (2008) 0.95
Pitfalls of the most commonly used models of context dependent substitution. Biol Direct (2008) 0.92
Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses. J Virol (2013) 0.88
Phylogenetic analyses under secondary structure-specific substitution models outperform traditional approaches: case studies with diploblast LSU. J Mol Evol (2007) 0.88
Compensatory evolution in RNA secondary structures increases substitution rate variation among sites. Mol Biol Evol (2008) 0.81
A phylogenetic model for the detection of epistatic interactions. Mol Biol Evol (2013) 0.79
Strong epistatic selection on the RNA secondary structure of HIV. PLoS Pathog (2014) 0.79
Assessing the state of substitution models describing noncoding RNA evolution. Genome Biol Evol (2014) 0.76
Compensatory evolution in the human malaria parasite Plasmodium ovale. Genetics (2004) 0.76
Widespread Historical Contingency in Influenza Viruses. Genetics (2016) 0.75
Structural characterization of the internal transcribed spacer 2 (ITS2) of the ribosomal DNA (rDNA) cluster in Calyptratae (Diptera: Schizophora) and its implications for molecular phylogenetic analyses. J Mol Evol (2013) 0.75
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol (1980) 113.75
Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol (1981) 67.56
Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol (1993) 38.03
Comparative anatomy of 16-S-like ribosomal RNA. Prog Nucleic Acid Res Mol Biol (1985) 16.21
5S RNA secondary structure. Nature (1975) 10.58
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol (1994) 7.55
Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases. Mol Biol Evol (1992) 5.99
Secondary structure of the Tetrahymena ribosomal RNA intervening sequence: structural homology with fungal mitochondrial intervening sequences. Proc Natl Acad Sci U S A (1983) 4.78
The secondary structure of ribonuclease P RNA, the catalytic element of a ribonucleoprotein enzyme. Cell (1988) 4.41
Saccharomyces cerevisiae has a U1-like small nuclear RNA with unexpected properties. Science (1987) 2.64
Phylogenetic comparative analysis and the secondary structure of ribonuclease P RNA--a review. Gene (1989) 2.45
Testing for equality of evolutionary rates. Genetics (1992) 2.25
Ribonuclease P: function and variation. J Biol Chem (1990) 2.07
RNA folding in Drosophila shows a distance effect for compensatory fitness interactions. Genetics (1993) 1.94
Evolution of compensatory substitutions through G.U intermediate state in Drosophila rRNA. Proc Natl Acad Sci U S A (1991) 1.73
Rates and patterns of base change in the small subunit ribosomal RNA gene. Genetics (1993) 1.34
Constraints on the evolution of plastid introns: the group II intron in the gene encoding tRNA-Val(UAC). Mol Biol Evol (1992) 1.08
Structure and evolution of ribonuclease P RNA. Biochimie (1991) 0.99