Published in Mol Biol Evol on January 16, 2008
Signals of recent positive selection in a worldwide sample of human populations. Genome Res (2009) 8.38
Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genet (2009) 4.02
Pervasive natural selection in the Drosophila genome? PLoS Genet (2009) 3.27
High rate of recent transposable element-induced adaptation in Drosophila melanogaster. PLoS Biol (2008) 1.52
Genome-wide patterns of adaptation to temperate environments associated with transposable elements in Drosophila. PLoS Genet (2010) 1.24
Shifting fitness landscapes in response to altered environments. Evolution (2013) 1.15
The adaptive role of transposable elements in the Drosophila genome. Gene (2009) 1.14
High genetic differentiation between the M and S molecular forms of Anopheles gambiae in Africa. PLoS One (2008) 1.08
The evolution of transposable elements in natural populations of self-fertilizing Arabidopsis thaliana and its outcrossing relative Arabidopsis lyrata. BMC Evol Biol (2010) 1.08
Patterns and processes of genome-wide divergence between North American and African Drosophila melanogaster. Genetics (2010) 0.94
A recent adaptive transposable element insertion near highly conserved developmental loci in Drosophila melanogaster. Mol Biol Evol (2009) 0.92
Inferring the strength of selection in Drosophila under complex demographic models. Mol Biol Evol (2008) 0.85
Haplotype structure and expression divergence at the Drosophila cellular immune gene eater. Mol Biol Evol (2010) 0.82
Patterns of selection and polymorphism of innate immunity genes in bumblebees (Hymenoptera: Apidae). Genetica (2012) 0.78
Statistical significance for genomewide studies. Proc Natl Acad Sci U S A (2003) 88.64
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics (1989) 73.50
On the number of segregating sites in genetical models without recombination. Theor Popul Biol (1975) 60.96
Detection of large-scale variation in the human genome. Nat Genet (2004) 49.18
Evolutionary relationship of DNA sequences in finite populations. Genetics (1983) 40.67
The hitch-hiking effect of a favourable gene. Genet Res (1974) 34.74
Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics (2002) 34.50
DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics (2003) 32.63
A map of recent positive selection in the human genome. PLoS Biol (2006) 29.19
Fine-scale structural variation of the human genome. Nat Genet (2005) 24.31
Detecting recent positive selection in the human genome from haplotype structure. Nature (2002) 22.00
Structural variation in the human genome. Nat Rev Genet (2006) 21.40
The "hitchhiking effect" revisited. Genetics (1989) 17.72
Hitchhiking under positive Darwinian selection. Genetics (2000) 14.72
Mobile elements: drivers of genome evolution. Science (2004) 11.78
The coalescent process in models with selection. Genetics (1988) 10.14
The effect of change in population size on DNA polymorphism. Genetics (1989) 9.10
Molecular signatures of natural selection. Annu Rev Genet (2005) 7.51
The coalescent process in models with selection and recombination. Genetics (1988) 7.49
The effects of artificial selection on the maize genome. Science (2005) 6.20
The signature of positive selection at randomly chosen loci. Genetics (2002) 6.06
African and North American populations of Drosophila melanogaster are very different at the DNA level. Nature (1993) 6.02
FlyBase: anatomical data, images and queries. Nucleic Acids Res (2006) 6.01
Soft sweeps: molecular population genetics of adaptation from standing genetic variation. Genetics (2005) 5.99
A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature (2006) 5.98
Genetic traces of ancient demography. Proc Natl Acad Sci U S A (1998) 5.48
A single p450 allele associated with insecticide resistance in Drosophila. Science (2002) 5.34
Genetic variation of Drosophila melanogaster natural populations. Trends Genet (1988) 4.62
The signature of positive selection on standing genetic variation. Evolution (2005) 4.17
How reliable are empirical genomic scans for selective sweeps? Genome Res (2006) 4.14
Haldane's sieve and adaptation from the standing genetic variation. Genetics (2001) 4.02
Organization, transcription, and regulation in the animal genome. Q Rev Biol (1973) 3.95
A test for the role of natural selection in the stabilization of transposable element copy number in a population of Drosophila melanogaster. Genet Res (1987) 3.82
Linkage disequilibrium as a signature of selective sweeps. Genetics (2004) 3.52
Methods to detect selection in populations with applications to the human. Annu Rev Genomics Hum Genet (2000) 3.45
Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster. Genetics (2005) 3.31
Perspective: transposable elements, parasitic DNA, and genome evolution. Evolution (2001) 3.30
Demography and natural selection have shaped genetic variation in Drosophila melanogaster: a multi-locus approach. Genetics (2003) 3.28
The population genetics of Drosophila transposable elements. Annu Rev Genet (1989) 3.27
Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat Rev Genet (2002) 3.24
Pattern of polymorphism after strong artificial selection in a domestication event. Proc Natl Acad Sci U S A (2004) 3.09
Inferring the demographic history and rate of adaptive substitution in Drosophila. PLoS Genet (2006) 2.88
A genealogical interpretation of linkage disequilibrium. Genetics (2002) 2.78
Strong selective sweep associated with a transposon insertion in Drosophila simulans. Proc Natl Acad Sci U S A (2004) 2.65
Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila. Science (2005) 2.56
Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content. Genome Biol (2005) 2.41
Regions of lower crossing over harbor more rare variants in African populations of Drosophila melanogaster. Genetics (2001) 2.34
Inversion polymorphisms and nucleotide variability in Drosophila. Genet Res (2001) 2.00
The contribution of RNAs and retroposition to evolutionary novelties. Genetica (2003) 1.75
Progress and prospects in mapping recent selection in the genome. Heredity (Edinb) (2007) 1.71
Sure facts, speculations, and open questions about the evolution of transposable element copy number. Genetica (1999) 1.71
Size matters: non-LTR retrotransposable elements and ectopic recombination in Drosophila. Mol Biol Evol (2003) 1.68
Cis-regulatory elements in the Accord retrotransposon result in tissue-specific expression of the Drosophila melanogaster insecticide resistance gene Cyp6g1. Genetics (2006) 1.66
World-wide survey of an Accord insertion and its association with DDT resistance in Drosophila melanogaster. Mol Ecol (2004) 1.56
Effect of inversion polymorphism on the neutral nucleotide variability of linked chromosomal regions in Drosophila. Genetics (2000) 1.46
Recombination can initiate and terminate at a large number of sites within the rosy locus of Drosophila melanogaster. Genetics (1988) 1.45
Simulating genealogies of selected alleles in a population of variable size. Genet Res (2001) 1.40
Patterns of insertion and deletion in contrasting chromatin domains. Mol Biol Evol (2002) 1.38
Pseudogene evolution and natural selection for a compact genome. J Hered (2000) 1.33
On the identification of the rosy locus DNA in Drosophila melanogaster: intragenic recombination mapping of mutations associated with insertions and deletions. Genetics (1986) 1.23
Rates of movement and distribution of transposable elements in Drosophila melanogaster: in situ hybridization vs Southern blotting data. Genet Res (2001) 1.18
Evolutionary genetics: Mobile DNAs as sources of adaptive change? Curr Biol (2004) 0.88
Evidence for the adaptive significance of an LTR retrotransposon sequence in a Drosophila heterochromatic gene. BMC Evol Biol (2002) 0.86
Evolutionary forces generating sequence homogeneity and heterogeneity within retrotransposon families. Cytogenet Genome Res (2005) 0.85
African sequence variation accounts for most of the sequence polymorphism in non-African Drosophila melanogaster. Genetics (2005) 0.80
CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics (2007) 16.52
Genotype, haplotype and copy-number variation in worldwide human populations. Nature (2008) 12.40
Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proc Natl Acad Sci U S A (2005) 10.22
The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol (2005) 10.13
A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nat Genet (2006) 8.46
Evolutionary rate in the protein interaction network. Science (2002) 7.75
Genotype-imputation accuracy across worldwide human populations. Am J Hum Genet (2009) 7.28
Features of evolution and expansion of modern humans, inferred from genomewide microsatellite markers. Am J Hum Genet (2003) 5.14
Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol Evol (2009) 4.91
Genetic variation and population structure in native Americans. PLoS Genet (2007) 4.87
Functional and evolutionary genomics of Mycobacterium tuberculosis: insights from genomic deletions in 100 strains. Proc Natl Acad Sci U S A (2004) 4.78
High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol (2008) 4.74
Massively parallel functional dissection of mammalian enhancers in vivo. Nat Biotechnol (2012) 4.51
Hierarchical maintenance of MLL myeloid leukemia stem cells employs a transcriptional program shared with embryonic rather than adult stem cells. Cell Stem Cell (2009) 4.43
Noise minimization in eukaryotic gene expression. PLoS Biol (2004) 4.36
Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genet (2009) 4.02
Selection on codon bias. Annu Rev Genet (2008) 3.83
Discordance of species trees with their most likely gene trees. PLoS Genet (2006) 3.58
A framework for feature selection in clustering. J Am Stat Assoc (2010) 3.46
Pervasive natural selection in the Drosophila genome? PLoS Genet (2009) 3.27
ADZE: a rarefaction approach for counting alleles private to combinations of populations. Bioinformatics (2008) 3.06
Functional genomic analysis of the rates of protein evolution. Proc Natl Acad Sci U S A (2005) 3.04
Evidence that mutation is universally biased towards AT in bacteria. PLoS Genet (2010) 2.95
The application of statistical physics to evolutionary biology. Proc Natl Acad Sci U S A (2005) 2.69
Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila. Science (2005) 2.56
Evidence that adaptation in Drosophila is not limited by mutation at single sites. PLoS Genet (2010) 2.41
A simple dependence between protein evolution rate and the number of protein-protein interactions. BMC Evol Biol (2003) 2.38
Normalization, testing, and false discovery rate estimation for RNA-sequencing data. Biostatistics (2011) 2.36
The large genome constraint hypothesis: evolution, ecology and phenotype. Ann Bot (2005) 2.33
Genomic patterns of homozygosity in worldwide human populations. Am J Hum Genet (2012) 2.30
Robustness of the inference of human population structure: a comparison of X-chromosomal and autosomal microsatellites. Hum Genomics (2004) 2.22
Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Mol Biol Evol (2012) 2.20
Inference of unexpected genetic relatedness among individuals in HapMap Phase III. Am J Hum Genet (2010) 2.16
Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers. Genome Biol (2012) 2.12
Coevolution of gene expression among interacting proteins. Proc Natl Acad Sci U S A (2004) 1.96
Preferential duplication of conserved proteins in eukaryotic genomes. PLoS Biol (2004) 1.96
3'-end sequencing for expression quantification (3SEQ) from archival tumor samples. PLoS One (2010) 1.91
Genomewide spatial correspondence between nonsynonymous divergence and neutral polymorphism reveals extensive adaptation in Drosophila. Genetics (2007) 1.89
The relationship between imputation error and statistical power in genetic association studies in diverse populations. Am J Hum Genet (2009) 1.89
Drosophila melanogaster recombination rate calculator. Gene (2010) 1.78
Out of Africa: modern human origins special feature: explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa. Proc Natl Acad Sci U S A (2009) 1.76
Demographic history of european populations of Arabidopsis thaliana. PLoS Genet (2008) 1.72
Distinct changes of genomic biases in nucleotide substitution at the time of Mammalian radiation. Mol Biol Evol (2003) 1.72
General rules for optimal codon choice. PLoS Genet (2009) 1.71
Size matters: non-LTR retrotransposable elements and ectopic recombination in Drosophila. Mol Biol Evol (2003) 1.68
Pervasive and persistent redundancy among duplicated genes in yeast. PLoS Genet (2008) 1.66
Genomic heterogeneity of background substitutional patterns in Drosophila melanogaster. Genetics (2004) 1.61
Population genomics of rapid adaptation by soft selective sweeps. Trends Ecol Evol (2013) 1.60
The benefits of implant removal from the foot and ankle. J Bone Joint Surg Am (2012) 1.55
Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus). PLoS Genet (2012) 1.54
The impact of transposable elements in environmental adaptation. Mol Ecol (2013) 1.53
High rate of recent transposable element-induced adaptation in Drosophila melanogaster. PLoS Biol (2008) 1.52
Mathematical properties of the r2 measure of linkage disequilibrium. Theor Popul Biol (2008) 1.51
Comparing spatial maps of human population-genetic variation using Procrustes analysis. Stat Appl Genet Mol Biol (2010) 1.48
Substantial regional variation in substitution rates in the human genome: importance of GC content, gene density, and telomere-specific effects. J Mol Evol (2005) 1.45
Properties of consensus methods for inferring species trees from gene trees. Syst Biol (2009) 1.43
Reduced selection leads to accelerated gene loss in Shigella. Genome Biol (2007) 1.41
Statistical tests of the coalescent model based on the haplotype frequency distribution and the number of segregating sites. Genetics (2005) 1.41
Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes. Genome Biol Evol (2010) 1.40
Do disparate mechanisms of duplication add similar genes to the genome? Trends Genet (2005) 1.39
Frequent adaptation and the McDonald-Kreitman test. Proc Natl Acad Sci U S A (2013) 1.37
Genomic microsatellites identify shared Jewish ancestry intermediate between Middle Eastern and European populations. BMC Genet (2009) 1.37
Strong purifying selection at synonymous sites in D. melanogaster. PLoS Genet (2013) 1.34
Rates of DNA duplication and mitochondrial DNA insertion in the human genome. J Mol Evol (2003) 1.34
Heterozygote advantage as a natural consequence of adaptation in diploids. Proc Natl Acad Sci U S A (2011) 1.33
Long runs of homozygosity are enriched for deleterious variation. Am J Hum Genet (2013) 1.32
Host species and environmental effects on bacterial communities associated with Drosophila in the laboratory and in the natural environment. PLoS One (2013) 1.30
Protein evolution in the context of Drosophila development. J Mol Evol (2005) 1.29
X-linked genes evolve higher codon bias in Drosophila and Caenorhabditis. Genetics (2005) 1.26
Genome-wide patterns of adaptation to temperate environments associated with transposable elements in Drosophila. PLoS Genet (2010) 1.24
Evolutionary rate depends on number of protein-protein interactions independently of gene expression level. BMC Evol Biol (2004) 1.23
An unbiased estimator of gene diversity in samples containing related individuals. Mol Biol Evol (2008) 1.18
A quantitative comparison of the similarity between genes and geography in worldwide human populations. PLoS Genet (2012) 1.17
A general mechanistic model for admixture histories of hybrid populations. Genetics (2011) 1.17
Lack of population diversity in commonly used human embryonic stem-cell lines. N Engl J Med (2009) 1.17
Molecular signatures from omics data: from chaos to consensus. Biotechnol J (2012) 1.17
Empirical validation of pooled whole genome population re-sequencing in Drosophila melanogaster. PLoS One (2012) 1.16
The relationship between F(ST) and the frequency of the most frequent allele. Genetics (2012) 1.15
Similar levels of X-linked and autosomal nucleotide variation in African and non-African populations of Drosophila melanogaster. BMC Evol Biol (2007) 1.15
The adaptive role of transposable elements in the Drosophila genome. Gene (2009) 1.14
[Use of a coronary risk score (the TIMI Risk Score) in a non-selected patient population assessed for chest pain at an emergency department]. Rev Esp Cardiol (2005) 1.13
Broker genes in human disease. Genome Biol Evol (2010) 1.13
Population genomics of transposable elements in Drosophila melanogaster. Mol Biol Evol (2010) 1.12
Population differentiation and migration: coalescence times in a two-sex island model for autosomal and X-linked loci. Theor Popul Biol (2008) 1.12
Runs of homozygosity and parental relatedness. Genet Med (2013) 1.10
Haplotype variation and genotype imputation in African populations. Genet Epidemiol (2011) 1.10
Origins and rates of aneuploidy in human blastomeres. Fertil Steril (2011) 1.10
T-lex: a program for fast and accurate assessment of transposable element presence using next-generation sequencing data. Nucleic Acids Res (2010) 1.09
Codon bias and noncoding GC content correlate negatively with recombination rate on the Drosophila X chromosome. J Mol Evol (2005) 1.09
Haplotypic background of a private allele at high frequency in the Americas. Mol Biol Evol (2009) 1.08
[Time intervals in primary angioplasty from onset of symptoms until restoration of blood flow]. Rev Esp Cardiol (2002) 1.07
Consistency properties of species tree inference by minimizing deep coalescences. J Comput Biol (2011) 1.07
[Program of coronary angioplasty in acute myocardial infarction in the region of Murcia (Spain). APRIMUR Registry]. Rev Esp Cardiol (2002) 1.07