Published in Genetics on December 29, 2011
Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server. BMC Bioinformatics (2016) 1.39
Amino acid coevolution induces an evolutionary Stokes shift. Proc Natl Acad Sci U S A (2012) 1.35
An experimentally determined evolutionary model dramatically improves phylogenetic fit. Mol Biol Evol (2014) 1.19
The relationship between dN/dS and scaled selection coefficients. Mol Biol Evol (2015) 1.03
On the statistical interpretation of site-specific variables in phylogeny-based substitution models. Genetics (2012) 1.00
On the need for mechanistic models in computational genomics and metagenomics. Genome Biol Evol (2013) 0.99
The role of epistasis in protein evolution. Nature (2013) 0.96
A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data. Genetics (2014) 0.93
Contingency and entrenchment in protein evolution under purifying selection. Proc Natl Acad Sci U S A (2015) 0.92
Nonadaptive Amino Acid Convergence Rates Decrease over Time. Mol Biol Evol (2015) 0.91
Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Mol Biol Evol (2014) 0.89
Population size dependence of fitness effect distribution and substitution rate probed by biophysical model of protein thermostability. Genome Biol Evol (2013) 0.88
Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package. Bioinformatics (2013) 0.88
Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies. PLoS One (2015) 0.85
How to calculate the non-synonymous to synonymous rate ratio of protein-coding genes under the Fisher-Wright mutation-selection framework. Biol Lett (2015) 0.85
Comparative population genomics: power and principles for the inference of functionality. Trends Genet (2014) 0.84
Why do more divergent sequences produce smaller nonsynonymous/synonymous rate ratios in pairwise sequence comparisons? Genetics (2013) 0.81
A Comparison of One-Rate and Two-Rate Inference Frameworks for Site-Specific dN/dS Estimation. Genetics (2016) 0.80
Selection on metabolic pathway function in the presence of mutation-selection-drift balance leads to rate-limiting steps that are not evolutionarily stable. Biol Direct (2016) 0.77
Extensively Parameterized Mutation-Selection Models Reliably Capture Site-Specific Selective Constraint. Mol Biol Evol (2016) 0.76
The tangled bank of amino acids. Protein Sci (2016) 0.76
Estimating Gene Expression and Codon-Specific Translational Efficiencies, Mutation Biases, and Selection Coefficients from Genomic Data Alone. Genome Biol Evol (2015) 0.76
Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes. Mol Biol Evol (2016) 0.76
Triallelic Population Genomics for Inferring Correlated Fitness Effects of Same Site Nonsynonymous Mutations. Genetics (2016) 0.76
MtDNA analysis reveals enriched pathogenic mutations in Tibetan highlanders. Sci Rep (2016) 0.75
SENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage. Genome Biol Evol (2016) 0.75
Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models. Biol Direct (2017) 0.75
Finding Direction in the Search for Selection. J Mol Evol (2016) 0.75
Molecular Population Genetics. Genetics (2017) 0.75
Sequence entropy of folding and the absolute rate of amino acid substitutions. Nat Ecol Evol (2017) 0.75
Predicting Amino Acid Substitution Probabilities Using Single Nucleotide Polymorphisms. Genetics (2017) 0.75
phydms: software for phylogenetic analyses informed by deep mutational scanning. PeerJ (2017) 0.75
Evolution in Mendelian Populations. Genetics (1931) 138.42
Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol (1981) 67.56
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol (1985) 47.78
PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol (2007) 45.68
The hitch-hiking effect of a favourable gene. Genet Res (1974) 34.74
Evolutionary rate at the molecular level. Nature (1968) 33.15
Initial sequence of the chimpanzee genome and comparison with the human genome. Nature (2005) 25.67
The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics (1969) 22.59
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics (2004) 20.94
The effect of linkage on limits to artificial selection. Genet Res (1966) 16.21
Characterization of the 1918 influenza virus polymerase genes. Nature (2005) 15.73
Slightly deleterious mutant substitutions in evolution. Nature (1973) 13.79
The genomic and epidemiological dynamics of human influenza A virus. Nature (2008) 10.26
The selection-mutation-drift theory of synonymous codon usage. Genetics (1991) 8.59
Population genetics of polymorphism and divergence. Genetics (1992) 7.72
Positive and negative selection on the human genome. Genetics (2001) 7.25
The distribution of fitness effects of new mutations. Nat Rev Genet (2007) 6.42
Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science (2008) 6.35
Estimating the pattern of nucleotide substitution. J Mol Evol (1994) 5.74
The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus. Proc Natl Acad Sci U S A (2004) 4.77
The distribution of fitness effects among beneficial mutations. Genetics (2003) 3.97
Genetic hitchhiking. Philos Trans R Soc Lond B Biol Sci (2000) 3.81
The cost of inbreeding in Arabidopsis. Nature (2002) 3.80
Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol Biol Evol (1994) 3.64
The distribution of fitness effects of new deleterious amino acid mutations in humans. Genetics (2006) 3.63
Demography and natural selection have shaped genetic variation in Drosophila melanogaster: a multi-locus approach. Genetics (2003) 3.28
Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies. Mol Biol Evol (1998) 2.82
The structure of human mitochondrial DNA variation. J Mol Evol (1991) 2.78
Quantifying the slightly deleterious mutation model of molecular evolution. Mol Biol Evol (2002) 2.65
Bayesian analysis suggests that most amino acid replacements in Drosophila are driven by positive selection. J Mol Evol (2003) 2.39
Distribution of the strength of selection against amino acid replacements in human proteins. Hum Mol Genet (2005) 2.34
Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA. Mol Biol Evol (2003) 2.29
Experimental illumination of a fitness landscape. Proc Natl Acad Sci U S A (2011) 2.25
Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol Biol Evol (2008) 2.25
An empirical codon model for protein sequence evolution. Mol Biol Evol (2007) 2.20
Within- and between-species DNA sequence variation and the 'footprint' of natural selection. Gene (1999) 2.06
Direct estimate of the mutation rate and the distribution of fitness effects in the yeast Saccharomyces cerevisiae. Genetics (2001) 2.03
Estimating the distribution of fitness effects from DNA sequence data: implications for the molecular clock. Proc Natl Acad Sci U S A (2003) 2.01
Mathematical elegance with biochemical realism: the covarion model of molecular evolution. J Mol Evol (2001) 1.84
Maximum-likelihood phylogenetic analysis under a covarion-like model. Mol Biol Evol (2001) 1.79
Multi-locus selection and the structure of variation at the white gene of Drosophila melanogaster. Genetics (1996) 1.70
Identifying changes in selective constraints: host shifts in influenza. PLoS Comput Biol (2009) 1.67
Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites. Mol Biol Evol (1996) 1.66
Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles. Proc Natl Acad Sci U S A (2010) 1.64
Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila. Proc Natl Acad Sci U S A (2007) 1.63
Homologous recombination is very rare or absent in human influenza A virus. J Virol (2008) 1.63
Maintenance of Genetic Variability under the Joint Effect of Mutation, Selection and Random Drift. Genetics (1978) 1.60
Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses. J Mol Evol (2006) 1.56
Assessing site-interdependent phylogenetic models of sequence evolution. Mol Biol Evol (2006) 1.42
Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes. Philos Trans R Soc Lond B Biol Sci (2008) 1.29
Models of natural mutations including site heterogeneity. Proteins (1998) 1.28
Distributions of beneficial fitness effects in RNA. Genetics (2005) 1.25
Quantification of tertiary structural conservation despite primary sequence drift in the globin fold. Protein Sci (1994) 1.12
Higher intensity of purifying selection on >90% of the human genes revealed by the intrinsic replacement mutation rates. Mol Biol Evol (2006) 1.12
Estimating translational selection in eukaryotic genomes. Mol Biol Evol (2008) 1.12
Using non-homogeneous models of nucleotide substitution to identify host shift events: application to the origin of the 1918 'Spanish' influenza pandemic virus. J Mol Evol (2009) 1.11
Population genetics without intraspecific data. Mol Biol Evol (2007) 1.08
Statistical potentials for improved structurally constrained evolutionary models. Mol Biol Evol (2010) 0.96
Charting the host adaptation of influenza viruses. Mol Biol Evol (2010) 0.96
What's in a likelihood? Simple models of protein evolution and the contribution of structurally viable reconstructions to the likelihood. Syst Biol (2011) 0.85
Perturbation analysis of a two-locus model with directional selection and recombination. J Math Biol (1995) 0.83
History can matter: non-Markovian behavior of ancestral lineages. Syst Biol (2011) 0.80
Why are proteins marginally stable? Proteins (2002) 2.74
Churchill, a zinc finger transcriptional activator, regulates the transition between gastrulation and neurulation. Cell (2003) 2.10
rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. J Mol Evol (2002) 2.06
Why are proteins so robust to site mutations? J Mol Biol (2002) 1.87
Statistical properties of the branch-site test of positive selection. Mol Biol Evol (2010) 1.85
Identifying changes in selective constraints: host shifts in influenza. PLoS Comput Biol (2009) 1.67
Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales. Curr Biol (2015) 1.66
Assessing the accuracy of ancestral protein reconstruction methods. PLoS Comput Biol (2006) 1.62
Changing selective pressure during antigenic changes in human influenza H3. PLoS Pathog (2008) 1.61
Myocardial perfusion and function: single photon emission computed tomography. J Nucl Cardiol (2007) 1.58
The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci (2012) 1.54
Amino acid coevolution induces an evolutionary Stokes shift. Proc Natl Acad Sci U S A (2012) 1.35
Myocardial perfusion and function single photon emission computed tomography. J Nucl Cardiol (2006) 1.27
Probing conformational changes in neurotransmitter transporters: a structural context. Eur J Pharmacol (2003) 1.17
Archaeology and evolution of transfer RNA genes in the Escherichia coli genome. RNA (2006) 1.15
Using non-homogeneous models of nucleotide substitution to identify host shift events: application to the origin of the 1918 'Spanish' influenza pandemic virus. J Mol Evol (2009) 1.11
Positron emission tomography myocardial perfusion and glucose metabolism imaging. J Nucl Cardiol (2006) 1.09
Optimization of a new score function for the generation of accurate alignments. Proteins (2002) 1.08
Detecting distant homologs using phylogenetic tree-based HMMs. Proteins (2003) 1.05
Dimerization in aminergic G-protein-coupled receptors: application of a hidden-site class model of evolution. Biochemistry (2003) 1.00
Performance of an iterated T-HMM for homology detection. Bioinformatics (2004) 0.98
Depicting a protein's two faces: GPCR classification by phylogenetic tree-based HMMs. FEBS Lett (2003) 0.97
Assessing predictors of changes in protein stability upon mutation using self-consistency. PLoS One (2012) 0.96
Charting the host adaptation of influenza viruses. Mol Biol Evol (2010) 0.96
A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data. Genetics (2014) 0.93
Analysis of host-parasite incongruence in papillomavirus evolution using importance sampling. Mol Biol Evol (2010) 0.92
Strong evidence for protein epistasis, weak evidence against it. Proc Natl Acad Sci U S A (2014) 0.90
Predicting functional sites in proteins: site-specific evolutionary models and their application to neurotransmitter transporters. J Mol Biol (2004) 0.86
Performance evaluation of a new algorithm for the detection of remote homologs with sequence comparison. Proteins (2002) 0.83
A model of the mechanisms of language extinction and revitalization strategies to save endangered languages. Hum Biol (2010) 0.80
Functionality and the evolution of marginal stability in proteins: inferences from lattice simulations. Evol Bioinform Online (2007) 0.80
Evolution of response dynamics underlying bacterial chemotaxis. BMC Evol Biol (2011) 0.80
The organization of two rRNA (rrn) operons of the slow-growing pathogen Mycobacterium celatum provides key insights into mycobacterial evolution. FEMS Microbiol Lett (2008) 0.80
Molecular evolutionary characterization of a V1R subfamily unique to strepsirrhine primates. Genome Biol Evol (2014) 0.80
Divergence, recombination and retention of functionality during protein evolution. Hum Genomics (2005) 0.79
Summary of the HESI consortium studies exploring circulating inhibin B as a potential biomarker of testis damage in the rat. Birth Defects Res B Dev Reprod Toxicol (2013) 0.78
A beginners guide to estimating the non-synonymous to synonymous rate ratio of all protein-coding genes in a genome. Methods Mol Biol (2015) 0.78
Using evolutionary methods to study G-protein coupled receptors. Pac Symp Biocomput (2002) 0.77
The inhibin B response in male rats treated with two drug candidates. Birth Defects Res B Dev Reprod Toxicol (2013) 0.76
Analytic markovian rates for generalized protein structure evolution. PLoS One (2012) 0.76
The evolution of collective restraint: policing and obedience among non-conjugative plasmids. PLoS Comput Biol (2013) 0.75
In silico biology. Pac Symp Biocomput (2010) 0.75