(Q36937898)

17 August 2017

1 reference

title

The quest for natural selection in the age of comparative genomics (English)

1 reference

17 August 2017

1 reference

Anisimova M

1

1 reference

17 August 2017

Liberles DA

series ordinal

2

1 reference

17 August 2017

language of work or name

English

0 references

publication date

12 September 2007

1 reference

17 August 2017

1 reference

17 August 2017

volume

99

1 reference

17 August 2017

issue

6

1 reference

17 August 2017

page(s)

567-579

1 reference

FunShift: a database of function shift analysis on protein subfamilies

17 August 2017

cites work

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Large-scale prediction of function shift in protein families with a focus on enzymatic function

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Within- and between-species DNA sequence variation and the 'footprint' of natural selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Accuracy and power of bayes prediction of amino acid sites under positive selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Identifying sites under positive selection with uncertain parameter estimates

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Methods for selecting fixed-effect models for heterogeneous codon evolution, with comments on their application to gene and genome data.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

How to guarantee optimal stability for most representative structures in the Protein Data Bank.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Post-genomic science: converting primary structure into physiological function

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Tertiary Windowing to Detect Positive Diversifying Selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Thermodynamics of neutral protein evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Positive selection on the H3 hemagglutinin gene of human influenza virus A.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Natural selection on protein-coding genes in the human genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Maximum likelihood and Bayesian methods for estimating the distribution of selective effects among classes of mutations using DNA polymorphism data.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

The cost of inbreeding in Arabidopsis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Hearing silence: non-neutral evolution at synonymous sites in mammals

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Rhodopsin evolution in the dark

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Missense meanderings in sequence space: a biophysical view of protein evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Detecting coevolving amino acid sites using Bayesian mutational mapping

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Identifying dramatic selection shifts in phylogenetic trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

A model-based approach for detecting coevolving positions in a molecule.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Large-scale search for genes on which positive selection may operate

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

A Sliding Window-Based Method to Detect Selective Constraints in Protein-Coding Genes and Its Application to RNA Viruses

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Testing the neutral theory of molecular evolution with genomic data from Drosophila.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Long term trends in the evolution of H(3) HA1 human influenza type A

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

A codon-based model of host-specific selection in parasites, with an application to the influenza A virus

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Maximum-likelihood phylogenetic analysis under a covarion-like model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Markov-modulated Markov chains and the covarion process of molecular evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Predicting functional divergence in protein evolution by site-specific rate shifts

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

The structural basis of molecular adaptation

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Punctuated equilibrium comes of age.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Maximum-likelihood approach for gene family evolution under functional divergence.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Modeling the site-specific variation of selection patterns along lineages

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Compensatory vs. pseudocompensatory evolution in molecular and developmental interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Developmental gene regulatory network architecture across 500 million years of echinoderm evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Bayesian estimation of positively selected sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

A Dirichlet process model for detecting positive selection in protein-coding DNA sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

A new approach to protein fold recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

The KEGG resource for deciphering the genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

A "silent" polymorphism in the MDR1 gene changes substrate specificity

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Evolution at two levels in humans and chimpanzees

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

A genetic algorithm approach to detecting lineage-specific variation in selection pressure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Not so different after all: a comparison of methods for detecting amino acid sites under selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

HyPhy: hypothesis testing using phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Site-to-site variation of synonymous substitution rates

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Probabilistic reconstruction of ancestral protein sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Mutation matrices and physical-chemical properties: correlations and implications

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Evaluation of methods for determination of a reconstructed history of gene sequence evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Proportion of solvent-exposed amino acids in a protein and rate of protein evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Heterotachy, an important process of protein evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Being positive about selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Detecting amino acid sites under positive selection and purifying selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Using hidden Markov models and observed evolution to annotate viral genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Estimating the influence of selection on the variable amino acid sites of the cytochrome B protein functional domains

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Adaptive protein evolution at the Adh locus in Drosophila

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Episodic adaptive evolution of primate lysozymes

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Codon usage tabulated from international DNA sequence databases: status for the year 2000

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Statistical tests of selective neutrality in the age of genomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

A scan for positively selected genes in the genomes of humans and chimpanzees

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Bayesian estimation of ancestral character states on phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

The structurally constrained protein evolution model accounts for sequence patterns of the LbetaH superfamily

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Generality of the structurally constrained protein evolution model: assessment on representatives of the four main fold classes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Mathematical elegance with biochemical realism: the covarion model of molecular evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Evolution of myostatin in vertebrates: is there evidence for positive selection?

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Coevolving protein residues: maximum likelihood identification and relationship to structure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Evaluation of models for the evolution of protein sequences and functions under structural constraint

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Protein evolution with dependence among codons due to tertiary structure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Assessing site-interdependent phylogenetic models of sequence evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

A systematic search for positive selection in higher plants (Embryophytes)

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Detecting Site-Specific Physicochemical Selective Pressures: Applications to the Class I HLA of the Human Major Histocompatibility Complex and the SRK of the Plant Sporophytic Self-Incompatibility System

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Bayesian analysis suggests that most amino acid replacements in Drosophila are driven by positive selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Robust inference of positive selection from recombining coding sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

A Bayesian Model Comparison Approach to Inferring Positive Selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Adaptive protein evolution in Drosophila

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Predicting functional sites in proteins: site-specific evolutionary models and their application to neurotransmitter transporters

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

An Evolutionary Space-Time Model with Varying Among-Site Dependencies

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Myostatin rapid sequence evolution in ruminants predates domestication.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Modeling the covarion hypothesis of nucleotide substitution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Fitting Discrete Probability Distributions to Evolutionary Events

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Testing for covarion-like evolution in protein sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Statistical tests of neutrality in the age of weak selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Assessing the accuracy of ancestral protein reconstruction methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Estimating diversifying selection and functional constraint in the presence of recombination

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Identification of physicochemical selective pressure on protein encoding nucleotide sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

What amino acid properties affect protein evolution?

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Reevaluation of amino acid variability of the human immunodeficiency virus type 1 gp120 envelope glycoprotein and prediction of new discontinuous epitopes

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Among-site rate variation and its impact on phylogenetic analyses

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Statistical methods for detecting molecular adaptation

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Bayes empirical bayes inference of amino acid sites under positive selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

A composite-likelihood approach for detecting directional selection from DNA sequence data

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Site-specific amino acid replacement matrices from structurally constrained protein evolution simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Computational method for predicting protein functional sites with the use of specificity determinants

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Evaluation of Whether Accelerated Protein Evolution in Chordates Has Occurred before, after, or Simultaneously with Gene Duplication

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Evidence for Purifying Selection Against Synonymous Mutations in Mammalian Exonic Splicing Enhancers

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

7 January 2021

Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

7 January 2021

A systematic analysis of lineage-specific evolution in metabolic pathways

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

7 January 2021

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

7 January 2021

Modeling residue usage in aligned protein sequences via maximum likelihood

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

7 January 2021

Statistical methods for testing functional divergence after gene duplication

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

7 January 2021

Testing a covariotide model of DNA substitution

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

7 January 2021

Context-dependent optimal substitution matrices

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

7 January 2021

Annotation of selection strengths in viral genomes

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

7 January 2021

Mapping mutations on phylogenies

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

7 January 2021

A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

7 January 2021

Structural constraints and emergence of sequence patterns in protein evolution

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

7 January 2021

Site interdependence attributed to tertiary structure in amino acid sequence evolution

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

7 January 2021

A method for detecting positive selection at single amino acid sites

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

7 January 2021

Exploring variation in the d(N)/d(S) ratio among sites and lineages using mutational mappings: applications to the influenza virus

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

7 January 2021

Frequent false detection of positive selection by the likelihood method with branch-site models

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

7 January 2021

Small-sample tests of episodic adaptive evolution: a case study of primate lysozymes

1 reference

https://api.crossref.org/works/10.1038%2FSJ.HDY.6801052

7 January 2021

Identifiers

DOI

10.1038/SJ.HDY.6801052

1 reference

Dimensions Publication ID

17 August 2017

1021047823

0 references

1 reference