Natural Selection Affects Multiple Aspects of Genetic Variation at Putatively Neutral Sites across the Human Genome

Estimation of allele frequency and association mapping using next-generation sequencing data

(2011) Su Kim et al.   BMC BIOINFORMATICS

Classic Selective Sweeps Were Rare in Recent Human Evolution

(2011) R. D. Hernandez et al.   SCIENCE

The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation

(2010) Jonathan K. Pritchard et al.   CURRENT BIOLOGY

Design of association studies with pooled or un-pooled next-generation sequencing data

(2010) Su Yeon Kim et al.   GENETIC EPIDEMIOLOGY

Characterizing Recurrent Positive Selection at Fast-Evolving Genes in Drosophila miranda and Drosophila pseudoobscura

(2010) J. D. Jensen et al.   Genome Biology and Evolution

A Continuous-State Coalescent and the Impact of Weak Selection on the Structure of Gene Genealogies

(2010) B. D. O'Fallon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Determinants of Synonymous and Nonsynonymous Variability in Three Species of Drosophila

(2010) Penelope R. Haddrill et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fine-scale recombination rate differences between sexes, populations and individuals

(2010) Augustine Kong et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes

(2010) Michael F Hammer et al.   NATURE GENETICS

Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants

(2010) Yingrui Li et al.   NATURE GENETICS

Adaptation – not by sweeps alone

(2010) Jonathan K. Pritchard et al.   NATURE REVIEWS GENETICS

Genetic hitchhiking versus background selection: the controversy and its implications

(2010) W. Stephan   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

What can we learn about the distribution of fitness effects of new mutations from DNA sequence data?

(2010) P. D. Keightley et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Adaptations to new environments in humans: the role of subtle allele frequency shifts

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

A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection

(2010) S. R. Grossman et al.   SCIENCE

Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes

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

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Methods for Human Demographic Inference Using Haplotype Patterns From Genomewide Single-Nucleotide Polymorphism Data

(2009) K. E. Lohmueller et al.   GENETICS

Gene Genealogies Strongly Distorted by Weakly Interfering Mutations in Constant Environments

(2009) J. Seger et al.   GENETICS

Constructing genomic maps of positive selection in humans: Where do we go from here?

(2009) J. M. Akey   GENOME RESEARCH

Signals of recent positive selection in a worldwide sample of human populations

(2009) J. K. Pickrell et al.   GENOME RESEARCH

Darwinian and demographic forces affecting human protein coding genes

(2009) R. Nielsen et al.   GENOME RESEARCH

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Natural Selection on Synonymous and Nonsynonymous Mutations Shapes Patterns of Polymorphism in Populus tremula

(2009) P. K. Ingvarsson   MOLECULAR BIOLOGY AND EVOLUTION

Estimating the Rate of Adaptive Molecular Evolution in the Presence of Slightly Deleterious Mutations and Population Size Change

(2009) A. Eyre-Walker et al.   MOLECULAR BIOLOGY AND EVOLUTION

Detecting Ancient Admixture and Estimating Demographic Parameters in Multiple Human Populations

(2009) Jeffrey D. Wall et al.   MOLECULAR BIOLOGY AND EVOLUTION

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

(2009) R. Drmanac et al.   SCIENCE

Evolutionary Processes Acting on Candidate cis-Regulatory Regions in Humans Inferred from Patterns of Polymorphism and Divergence

(2009) Dara G. Torgerson et al.   PLoS Genetics

Widespread Genomic Signatures of Natural Selection in Hominid Evolution

(2009) Graham McVicker et al.   PLoS Genetics

Pervasive Natural Selection in the Drosophila Genome?

(2009) Guy Sella et al.   PLoS Genetics

Pervasive Hitchhiking at Coding and Regulatory Sites in Humans

(2009) James J. Cai et al.   PLoS Genetics

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

The Role of Geography in Human Adaptation

(2009) Graham Coop et al.   PLoS Genetics

Positive Selection in the Human Genome: From Genome Scans to Biological Significance

(2008) Joanna L. Kelley et al.   Annual Review of Genomics and Human Genetics

A flexible forward simulator for populations subject to selection and demography

(2008) R. D. Hernandez   BIOINFORMATICS

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

Similar rates of protein adaptation in Drosophila miranda and D. melanogaster, two species with different current effective population sizes

(2008) Doris Bachtrog   BMC EVOLUTIONARY BIOLOGY

Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals

(2008) I. Hellmann et al.   GENOME RESEARCH

Estimation of Hominoid Ancestral Population Sizes under Bayesian Coalescent Models Incorporating Mutation Rate Variation and Sequencing Errors

(2008) Ralph Burgess et al.   MOLECULAR BIOLOGY AND EVOLUTION

Patterns of Divergence among Conifer ESTs and Polymorphism in Pinus sylvestris Identify Putative Selective Sweeps

(2008) A. E. Palme et al.   MOLECULAR BIOLOGY AND EVOLUTION

The complete genome of an individual by massively parallel DNA sequencing

(2008) David A. Wheeler et al.   NATURE

Proportionally more deleterious genetic variation in European than in African populations

(2008) Kirk E. Lohmueller et al.   NATURE

Evolution of protein-coding genes in Drosophila

(2008) Amanda M. Larracuente 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

Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome

(2008) Adam R. Boyko et al.   PLoS Genetics