Published in Nat Rev Genet on January 19, 2016
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
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Res (2016) 1.18
Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes. PLoS Biol (2016) 0.80
A Comparison of One-Rate and Two-Rate Inference Frameworks for Site-Specific dN/dS Estimation. Genetics (2016) 0.80
Improved insights into protein thermal stability: from the molecular to the structurome scale. Philos Trans A Math Phys Eng Sci (2016) 0.79
Dissecting the roles of local packing density and longer-range effects in protein sequence evolution. Proteins (2016) 0.77
Intermediate divergence levels maximize the strength of structure-sequence correlations in enzymes and viral proteins. Protein Sci (2016) 0.77
Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes. Mol Biol Evol (2016) 0.76
Extensively Parameterized Mutation-Selection Models Reliably Capture Site-Specific Selective Constraint. Mol Biol Evol (2016) 0.76
Sequence amplification via cell passaging creates spurious signals of positive adaptation in influenza virus H3N2 hemagglutinin. Virus Evol (2016) 0.76
Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants. Mol Biol Evol (2017) 0.76
Chemosensory adaptations of the mountain fly Drosophila nigrosparsa (Insecta: Diptera) through genomics' and structural biology's lenses. Sci Rep (2017) 0.75
Computational prediction of the tolerance to amino-acid deletion in green-fluorescent protein. PLoS One (2017) 0.75
Accelerated simulation of evolutionary trajectories in origin-fixation models. J R Soc Interface (2017) 0.75
Susceptibility to type 2 diabetes may be modulated by haplotypes in G6PC2, a target of positive selection. BMC Evol Biol (2017) 0.75
Non-Markovian effects on protein sequence evolution due to site dependent substitution rates. BMC Bioinformatics (2016) 0.75
Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models. Biol Direct (2017) 0.75
Phylogenetic analyses reveal molecular signatures associated with functional divergence among Subtilisin like Serine Proteases are linked to lifestyle transitions in Hypocreales. BMC Evol Biol (2016) 0.75
Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. J R Soc Interface (2017) 0.75
Calculating site-specific evolutionary rates at the amino-acid or codon level yields similar rate estimates. PeerJ (2017) 0.75
SubVis: an interactive R package for exploring the effects of multiple substitution matrices on pairwise sequence alignment. PeerJ (2017) 0.75
BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol (2007) 74.13
PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol (2007) 45.68
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol (1986) 36.06
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol (1994) 24.04
A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol (1994) 19.91
HyPhy: hypothesis testing using phylogenies. Bioinformatics (2004) 17.33
Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature (1988) 15.05
Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics (2000) 14.84
Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol (2000) 13.01
Bayes empirical bayes inference of amino acid sites under positive selection. Mol Biol Evol (2005) 11.26
Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics (1998) 11.25
A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol (1985) 10.67
Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol (2005) 10.21
Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol (2002) 9.74
A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol (2004) 7.34
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol (2011) 7.33
Why highly expressed proteins evolve slowly. Proc Natl Acad Sci U S A (2005) 6.19
Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics (2010) 6.14
Relating three-dimensional structures to protein networks provides evolutionary insights. Science (2006) 5.50
Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol Evol (1996) 5.21
Positive selection on the H3 hemagglutinin gene of human influenza virus A. Mol Biol Evol (1999) 4.97
On some principles governing molecular evolution. Proc Natl Acad Sci U S A (1974) 4.97
Analysis of catalytic residues in enzyme active sites. J Mol Biol (2002) 4.90
Rewiring the specificity of two-component signal transduction systems. Cell (2008) 4.80
Scoring residue conservation. Proteins (2002) 4.66
Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics (2002) 4.54
Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci U S A (2011) 4.08
PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics (2011) 3.89
Detecting individual sites subject to episodic diversifying selection. PLoS Genet (2012) 3.77
Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. Mol Biol Evol (2004) 3.62
High-resolution mapping of protein sequence-function relationships. Nat Methods (2010) 3.47
Predicting functionally important residues from sequence conservation. Bioinformatics (2007) 3.42
Modeling protein evolution with several amino acid replacement matrices depending on site rates. Mol Biol Evol (2012) 3.35
Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature (2004) 3.29
Statistical methods for testing functional divergence after gene duplication. Mol Biol Evol (1999) 3.06
Alternative packing arrangements in the hydrophobic core of lambda repressor. Nature (1989) 2.89
Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. PLoS Comput Biol (2009) 2.82
Mapping mutations on phylogenies. Syst Biol (2002) 2.75
FUBAR: a fast, unconstrained bayesian approximation for inferring selection. Mol Biol Evol (2013) 2.73
Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci U S A (2005) 2.69
Simultaneous amino acid substitutions at antigenic sites drive influenza A hemagglutinin evolution. Proc Natl Acad Sci U S A (2007) 2.67
Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction. Proc Biol Sci (1990) 2.53
Evolutionary rate heterogeneity in proteins with long disordered regions. J Mol Evol (2002) 2.46
Prevalence of epistasis in the evolution of influenza A surface proteins. PLoS Genet (2011) 2.41
Accelerated evolution in the reactive centre regions of serine protease inhibitors. Nature (1987) 2.40
Heterotachy, an important process of protein evolution. Mol Biol Evol (2002) 2.34
Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag. PLoS Comput Biol (2008) 2.32
Flexibility and packing in proteins. Proc Natl Acad Sci U S A (2002) 2.22
A method for localizing ligand binding pockets in protein structures. Proteins (2006) 2.16
The spatial architecture of protein function and adaptation. Nature (2012) 2.14
Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics (1998) 2.05
Deep mutational scanning: a new style of protein science. Nat Methods (2014) 2.05
Evolutionary analyses of DNA sequences subject to constraints of secondary structure. Genetics (1995) 1.99
Disentangling direct from indirect co-evolution of residues in protein alignments. PLoS Comput Biol (2010) 1.98
Estimating synonymous and nonsynonymous substitution rates. Mol Biol Evol (1996) 1.95
An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope. PLoS Comput Biol (2007) 1.82
Comparison of solvent-inaccessible cores of homologous proteins: definitions useful for protein modelling. Protein Eng (1987) 1.81
Protein elastic network models and the ranges of cooperativity. Proc Natl Acad Sci U S A (2009) 1.76
Evolutionary biochemistry: revealing the historical and physical causes of protein properties. Nat Rev Genet (2013) 1.76
Structural determinants of the rate of protein evolution in yeast. Mol Biol Evol (2006) 1.75
Evolutionary conservation of the folding nucleus. J Mol Biol (2001) 1.68
A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences. Mol Biol Evol (2006) 1.63
Do viral proteins possess unique biophysical features? Trends Biochem Sci (2008) 1.60
Fragment ranking in modelling of protein structure. Conformationally constrained environmental amino acid substitution tables. J Mol Biol (1993) 1.60
A biophysical protein folding model accounts for most mutational fitness effects in viruses. Proc Natl Acad Sci U S A (2011) 1.56
The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci (2012) 1.54
Structural determinants of protein evolution are context-sensitive at the residue level. Mol Biol Evol (2009) 1.53
Distinguishing structural and functional restraints in evolution in order to identify interaction sites. J Mol Biol (2004) 1.52
Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica. Mol Biol Evol (2000) 1.43
A simple hierarchical approach to modeling distributions of substitution rates. Mol Biol Evol (2004) 1.42
Comparing models of evolution for ordered and disordered proteins. Mol Biol Evol (2009) 1.42
Structural determinant of protein designability. Phys Rev Lett (2003) 1.41
Amino acid coevolution induces an evolutionary Stokes shift. Proc Natl Acad Sci U S A (2012) 1.35
Structural and functional constraints in the evolution of protein families. Nat Rev Mol Cell Biol (2009) 1.35
Evolution. Systematic humanization of yeast genes reveals conserved functions and genetic modularity. Science (2015) 1.32
Protein folding and protein evolution: common folding nucleus in different subfamilies of c-type cytochromes? J Mol Biol (1998) 1.31
A gamma mixture model better accounts for among site rate heterogeneity. Bioinformatics (2005) 1.30
Quantifying the effect of burial of amino acid residues on protein stability. Proteins (2004) 1.29
Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes. Philos Trans R Soc Lond B Biol Sci (2008) 1.29
Protein misinteraction avoidance causes highly expressed proteins to evolve slowly. Proc Natl Acad Sci U S A (2012) 1.29
Inferring stabilizing mutations from protein phylogenies: application to influenza hemagglutinin. PLoS Comput Biol (2009) 1.26
The relationship between relative solvent accessibility and evolutionary rate in protein evolution. Genetics (2011) 1.25
Solvent exposure imparts similar selective pressures across a range of yeast proteins. Mol Biol Evol (2009) 1.24
Deriving protein dynamical properties from weighted protein contact number. Proteins (2008) 1.23
Protein structure and evolutionary history determine sequence space topology. Genome Res (2005) 1.22
Protein sequence entropy is closely related to packing density and hydrophobicity. Protein Eng Des Sel (2005) 1.20
An experimentally determined evolutionary model dramatically improves phylogenetic fit. Mol Biol Evol (2014) 1.19
Exploring among-site rate variation models in a maximum likelihood framework using empirical data: effects of model assumptions on estimates of topology, branch lengths, and bootstrap support. Syst Biol (2001) 1.19
Maximum allowed solvent accessibilites of residues in proteins. PLoS One (2013) 1.18
Context-dependent optimal substitution matrices. Protein Eng (1995) 1.17
Why time matters: codon evolution and the temporal dynamics of dN/dS. Mol Biol Evol (2013) 1.16
The pattern of amino acid replacements in alpha/beta-barrels. Mol Biol Evol (2002) 1.16
Integrating sequence variation and protein structure to identify sites under selection. Mol Biol Evol (2012) 1.15
Sequence evolution correlates with structural dynamics. Mol Biol Evol (2012) 1.14
Contact density affects protein evolutionary rate from bacteria to animals. J Mol Evol (2008) 1.10
Determinants of the rate of protein sequence evolution. Nat Rev Genet (2015) 1.09
A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility. BMC Evol Biol (2014) 1.07
Site-specific structural constraints on protein sequence evolutionary divergence: local packing density versus solvent exposure. Mol Biol Evol (2013) 1.07
A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny. BMC Evol Biol (2008) 1.06
Dissecting enzyme function with microfluidic-based deep mutational scanning. Proc Natl Acad Sci U S A (2015) 1.05