Published in Annu Rev Genet on January 01, 2005
Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol (2007) 6.18
Constructing genomic maps of positive selection in humans: where do we go from here? Genome Res (2009) 5.88
The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet (2010) 5.75
Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science (2009) 5.64
Patterns of positive selection in six Mammalian genomes. PLoS Genet (2008) 4.69
LOSITAN: a workbench to detect molecular adaptation based on a Fst-outlier method. BMC Bioinformatics (2008) 4.43
Counting labeled transitions in continuous-time Markov models of evolution. J Math Biol (2007) 4.18
A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biol (2007) 3.71
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature (2013) 3.45
Mechanistic approaches to the study of evolution: the functional synthesis. Nat Rev Genet (2007) 3.43
Stacks: an analysis tool set for population genomics. Mol Ecol (2013) 3.29
Pervasive natural selection in the Drosophila genome? PLoS Genet (2009) 3.27
Genomics and the future of conservation genetics. Nat Rev Genet (2010) 3.23
Independently evolving species in asexual bdelloid rotifers. PLoS Biol (2007) 3.05
Darwinian and demographic forces affecting human protein coding genes. Genome Res (2009) 3.01
From evolutionary genetics to human immunology: how selection shapes host defence genes. Nat Rev Genet (2009) 2.98
Crop genomics: advances and applications. Nat Rev Genet (2011) 2.72
Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science (2009) 2.68
Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context. Proc Natl Acad Sci U S A (2007) 2.55
Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles. Mol Ecol (2012) 2.42
Evolutionary dynamics of human Toll-like receptors and their different contributions to host defense. PLoS Genet (2009) 2.35
Experimental illumination of a fitness landscape. Proc Natl Acad Sci U S A (2011) 2.25
Evolutionary conflicts between viruses and restriction factors shape immunity. Nat Rev Immunol (2012) 2.10
Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput Biol (2007) 2.07
More genes underwent positive selection in chimpanzee evolution than in human evolution. Proc Natl Acad Sci U S A (2007) 2.00
Efficient approximate Bayesian computation coupled with Markov chain Monte Carlo without likelihood. Genetics (2009) 1.90
Selective sweep at a quantitative trait locus in the presence of background genetic variation. Genetics (2008) 1.86
Natural selection constrains neutral diversity across a wide range of species. PLoS Biol (2015) 1.85
Morphological evolution caused by many subtle-effect substitutions in regulatory DNA. Nature (2011) 1.83
Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation. PLoS Biol (2008) 1.80
Genomic divergence during speciation: causes and consequences. Philos Trans R Soc Lond B Biol Sci (2012) 1.80
Polymorphic members of the lag gene family mediate kin discrimination in Dictyostelium. Curr Biol (2009) 1.77
Evolutionary biochemistry: revealing the historical and physical causes of protein properties. Nat Rev Genet (2013) 1.76
Evolution and diversity of clonal bacteria: the paradigm of Mycobacterium tuberculosis. PLoS One (2008) 1.62
Genomic hotspots for adaptation: the population genetics of Müllerian mimicry in Heliconius erato. PLoS Genet (2010) 1.61
The genomic signature of parallel adaptation from shared genetic variation. Mol Ecol (2014) 1.58
Genome-wide patterns of latitudinal differentiation among populations of Drosophila melanogaster from North America. Mol Ecol (2012) 1.57
Formulating a historical and demographic model of recent human evolution based on resequencing data from noncoding regions. PLoS One (2010) 1.55
The genomic rate of molecular adaptation of the human influenza A virus. Mol Biol Evol (2011) 1.48
Natural selection and infectious disease in human populations. Nat Rev Genet (2014) 1.48
Positive and negative selection on noncoding DNA in Drosophila simulans. Mol Biol Evol (2008) 1.47
Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula. Proc Natl Acad Sci U S A (2011) 1.46
Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. Mol Ecol (2010) 1.44
Pervasive adaptive protein evolution apparent in diversity patterns around amino acid substitutions in Drosophila simulans. PLoS Genet (2011) 1.43
Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae. Genetics (2008) 1.43
The dynamic genetic repertoire of microbial communities. FEMS Microbiol Rev (2008) 1.42
Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia. Genome Res (2014) 1.42
Stable epigenetic effects impact adaptation in allopolyploid orchids (Dactylorhiza: Orchidaceae). Mol Biol Evol (2010) 1.42
Constraints and plasticity in genome and molecular-phenome evolution. Nat Rev Genet (2010) 1.41
Understanding the origin of species with genome-scale data: modelling gene flow. Nat Rev Genet (2013) 1.41
Fundamental concepts in genetics: genetics and the understanding of selection. Nat Rev Genet (2009) 1.41
Quantifying population genetic differentiation from next-generation sequencing data. Genetics (2013) 1.41
Impact of amplified fragment length polymorphism size homoplasy on the estimation of population genetic diversity and the detection of selective loci. Genetics (2008) 1.40
Evidence for pervasive adaptive protein evolution in wild mice. PLoS Genet (2010) 1.39
Clonal interference in the evolution of influenza. Genetics (2012) 1.37
Localization of canine brachycephaly using an across breed mapping approach. PLoS One (2010) 1.33
Distinguishing between selective sweeps from standing variation and from a de novo mutation. PLoS Genet (2012) 1.31
Phenotypic plasticity in evolutionary rescue experiments. Philos Trans R Soc Lond B Biol Sci (2013) 1.30
Shotgun sequencing analysis of Trypanosoma cruzi I Sylvio X10/1 and comparison with T. cruzi VI CL Brener. PLoS Negl Trop Dis (2011) 1.30
A genome-wide signature of positive selection in ancient and recent invasive expansions of the honey bee Apis mellifera. Proc Natl Acad Sci U S A (2008) 1.30
Genetic resources, genome mapping and evolutionary genomics of the pig (Sus scrofa). Int J Biol Sci (2007) 1.29
Speciation genetics: current status and evolving approaches. Philos Trans R Soc Lond B Biol Sci (2010) 1.28
Human population differentiation is strongly correlated with local recombination rate. PLoS Genet (2010) 1.28
Gene mapping in the wild with SNPs: guidelines and future directions. Genetica (2008) 1.27
Detecting selection in population trees: the Lewontin and Krakauer test extended. Genetics (2010) 1.27
Population genomics and speciation. Genetica (2008) 1.26
USING POPULATION GENOMICS TO DETECT SELECTION IN NATURAL POPULATIONS: KEY CONCEPTS AND METHODOLOGICAL CONSIDERATIONS. Int J Plant Sci (2010) 1.23
Evolutionary adaptations to dietary changes. Annu Rev Nutr (2010) 1.23
Genome-wide scans provide evidence for positive selection of genes implicated in Lassa fever. Philos Trans R Soc Lond B Biol Sci (2012) 1.23
A genomic portrait of human microsatellite variation. Mol Biol Evol (2010) 1.21
Integrating evolutionary and functional approaches to infer adaptation at specific loci. Evolution (2010) 1.21
Parallel adaptive evolution of Atlantic cod on both sides of the Atlantic Ocean in response to temperature. Proc Biol Sci (2010) 1.19
Molecular evolution and population genetic analysis of candidate female reproductive genes in Drosophila. Genetics (2006) 1.19
Prospective identification of malaria parasite genes under balancing selection. PLoS One (2009) 1.18
Signatures of purifying and local positive selection in human miRNAs. Am J Hum Genet (2009) 1.18
Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms. BMC Evol Biol (2012) 1.18
Population genomics of the honey bee reveals strong signatures of positive selection on worker traits. Proc Natl Acad Sci U S A (2014) 1.17
A hierarchical Bayesian model for next-generation population genomics. Genetics (2011) 1.17
Establishment of new mutations under divergence and genome hitchhiking. Philos Trans R Soc Lond B Biol Sci (2012) 1.17
Genesis of a fungal non-self recognition repertoire. PLoS One (2007) 1.17
Selection on haemagglutinin imposes a bottleneck during mammalian transmission of reassortant H5N1 influenza viruses. Nat Commun (2013) 1.17
The adaptive hypothesis of clinal variation revisited: single-locus clines as a result of spatially restricted gene flow. Genetics (2006) 1.17
Why time matters: codon evolution and the temporal dynamics of dN/dS. Mol Biol Evol (2013) 1.16
Structural and functional annotation of the porcine immunome. BMC Genomics (2013) 1.16
Nonlinear dynamics of nonsynonymous (dN) and synonymous (dS) substitution rates affects inference of selection. Genome Biol Evol (2009) 1.15
CRISPR-mediated phage resistance and the ghost of coevolution past. Proc Biol Sci (2010) 1.14
Genome-wide scan for signatures of human population differentiation and their relationship with natural selection, functional pathways and diseases. PLoS One (2009) 1.14
Testing for associations between loci and environmental gradients using latent factor mixed models. Mol Biol Evol (2013) 1.13
Plasmodium relictum infection and MHC diversity in the house sparrow (Passer domesticus). Proc Biol Sci (2010) 1.12
Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation. Genome Res (2013) 1.12
Natural selection and the genetics of adaptation in threespine stickleback. Philos Trans R Soc Lond B Biol Sci (2010) 1.12
Filaggrin-2 variation is associated with more persistent atopic dermatitis in African American subjects. J Allergy Clin Immunol (2013) 1.12
Molecular hyperdiversity and evolution in very large populations. Mol Ecol (2013) 1.11
Universal patterns of purifying selection at noncoding positions in bacteria. Genome Res (2007) 1.11
An investigation of the statistical power of neutrality tests based on comparative and population genetic data. Mol Biol Evol (2008) 1.11
A depauperate immune repertoire precedes evolution of sociality in bees. Genome Biol (2015) 1.11
Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data. BMC Bioinformatics (2013) 1.10
Bursts of nonsynonymous substitutions in HIV-1 evolution reveal instances of positive selection at conservative protein sites. Proc Natl Acad Sci U S A (2006) 1.10
Genome-wide detection of natural selection in African Americans pre- and post-admixture. Genome Res (2011) 1.09
Population genetic models of duplicated genes. Genetica (2009) 1.09