Linking Great Apes Genome Evolution across Time Scales Using Polymorphism-Aware Phylogenetic Models

CodonPhyML: Fast Maximum Likelihood Phylogeny Estimation under Codon Substitution Models

(2013) Manuel Gil et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inference of Natural Selection from Interspersed Genomic Elements Based on Polymorphism and Divergence

(2013) Ilan Gronau et al.   MOLECULAR BIOLOGY AND EVOLUTION

Estimating Empirical Codon Hidden Markov Models

(2012) Nicola De Maio et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

(2012) David Bryant et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Fine-Scale Chimpanzee Genetic Map from Population Sequencing

(2012) A. Auton et al.   SCIENCE

The allele-frequency spectrum in a decoupled Moran model with mutation, drift, and directional selection, assuming small mutation rates

(2012) Claus Vogl et al.   THEORETICAL POPULATION BIOLOGY

A Method for Inferring the Rate of Occurrence and Fitness Effects of Advantageous Mutations

(2011) Adrian Schneider et al.   GENETICS

Comparative and demographic analysis of orang-utan genomes

(2011) Devin P. Locke et al.   NATURE

Variation in the mutation rate across mammalian genomes

(2011) Alan Hodgkinson et al.   NATURE REVIEWS GENETICS

A Population Genetics-Phylogenetics Approach to Inferring Natural Selection in Coding Sequences

(2011) Daniel J. Wilson et al.   PLoS Genetics

Estimating Divergence Time and Ancestral Effective Population Size of Bornean and Sumatran Orangutan Subspecies Using a Coalescent Hidden Markov Model

(2011) Thomas Mailund et al.   PLoS Genetics

The evolution of transcription-associated biases of mutations across vertebrates

(2010) Paz Polak et al.   BMC EVOLUTIONARY BIOLOGY

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Detecting positive selection within genomes: the problem of biased gene conversion

(2010) A. Ratnakumar et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Rate, molecular spectrum, and consequences of human mutation

(2010) M. Lynch   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes

(2009) Laurent Duret et al.   Annual Review of Genomics and Human Genetics

Estimating Selection Intensity on Synonymous Codon Usage in a Nonequilibrium Population

(2009) K. Zeng et al.   GENETICS

Ancestral Population Genomics: The Coalescent Hidden Markov Model Approach

(2009) J. Y. Dutheil et al.   GENETICS

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

(2009) K. D. Pruitt et al.   GENOME RESEARCH

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

Statistical Comparison of Nucleotide, Amino Acid, and Codon Substitution Models for Evolutionary Analysis of Protein-Coding Sequences

(2009) Tae-Kun Seo et al.   SYSTEMATIC BIOLOGY

Mutation Patterns in the Human Genome: More Variable Than Expected

(2009) Laurent Duret   PLOS BIOLOGY

Cryptic Variation in the Human Mutation Rate

(2009) Alan Hodgkinson et al.   PLOS BIOLOGY

BEST: Bayesian estimation of species trees under the coalescent model

(2008) L. Liu   BIOINFORMATICS

A Two-Stage Pruning Algorithm for Likelihood Computation for a Population Tree

(2008) A. RoyChoudhury et al.   GENETICS

Transcription induces strand-specific mutations at the 5' end of human genes

(2008) P. Polak et al.   GENOME RESEARCH

Quantifying the Stationarity and Time Reversibility of the Nucleotide Substitution Process

(2008) F. Squartini et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage

(2008) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates

(2008) Nicolas Galtier et al.   TRENDS IN GENETICS

The effects of deleterious mutations on evolution in non-recombining genomes

(2008) Vera B. Kaiser et al.   TRENDS IN GENETICS

The Impact of Recombination on Nucleotide Substitutions in the Human Genome

(2008) Laurent Duret et al.   PLoS Genetics