Published in Genetics on September 15, 2004
Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet (2009) 9.16
Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet (2008) 8.92
Recent human effective population size estimated from linkage disequilibrium. Genome Res (2007) 6.79
Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans. Nat Genet (2007) 6.63
Ascertainment bias in studies of human genome-wide polymorphism. Genome Res (2005) 6.63
Genomic scans for selective sweeps using SNP data. Genome Res (2005) 6.43
African genetic diversity: implications for human demographic history, modern human origins, and complex disease mapping. Annu Rev Genomics Hum Genet (2008) 6.06
Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proc Natl Acad Sci U S A (2005) 5.94
Localizing recent adaptive evolution in the human genome. PLoS Genet (2007) 5.11
Genomic regions exhibiting positive selection identified from dense genotype data. Genome Res (2005) 4.81
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Testing for ancient admixture between closely related populations. Mol Biol Evol (2011) 3.56
Darwinian and demographic forces affecting human protein coding genes. Genome Res (2009) 3.01
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Population differentiation as a test for selective sweeps. Genome Res (2010) 2.08
Controlling the false-positive rate in multilocus genome scans for selection. Genetics (2006) 2.00
Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica (2008) 1.92
Length distributions of identity by descent reveal fine-scale demographic history. Am J Hum Genet (2012) 1.91
Linkage disequilibrium and demographic history of wild and domestic canids. Genetics (2009) 1.79
Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds. Proc Natl Acad Sci U S A (2008) 1.75
Genome-wide insights into the patterns and determinants of fine-scale population structure in humans. Am J Hum Genet (2009) 1.64
An approximate Bayesian computation approach to overcome biases that arise when using amplified fragment length polymorphism markers to study population structure. Genetics (2008) 1.52
Correcting estimators of theta and Tajima's D for ascertainment biases caused by the single-nucleotide polymorphism discovery process. Genetics (2008) 1.44
Methods for human demographic inference using haplotype patterns from genomewide single-nucleotide polymorphism data. Genetics (2009) 1.42
Frequency spectrum neutrality tests: one for all and all for one. Genetics (2009) 1.39
Effects of ascertainment bias and marker number on estimations of barley diversity from high-throughput SNP genotype data. Theor Appl Genet (2010) 1.28
Efficient moment-based inference of admixture parameters and sources of gene flow. Mol Biol Evol (2013) 1.26
Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals. Nat Commun (2015) 1.23
SNP ascertainment bias in population genetic analyses: why it is important, and how to correct it. Bioessays (2013) 1.18
Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping. BMC Genomics (2011) 1.09
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Divergence and polymorphism under the nearly neutral theory of molecular evolution. J Mol Evol (2008) 1.01
Multiple advantageous amino acid variants in the NAT2 gene in human populations. PLoS One (2008) 1.00
Gene discovery in the threatened elkhorn coral: 454 sequencing of the Acropora palmata transcriptome. PLoS One (2011) 0.98
Microsatellite-based genetic diversity and population structure of domestic sheep in northern Eurasia. BMC Genet (2010) 0.96
Biased gene conversion skews allele frequencies in human populations, increasing the disease burden of recessive alleles. Am J Hum Genet (2014) 0.95
IMPROVING POPULATION-SPECIFIC ALLELE FREQUENCY ESTIMATES BY ADAPTING SUPPLEMENTAL DATA: AN EMPIRICAL BAYES APPROACH. Ann Appl Stat (2007) 0.95
The effect of recent admixture on inference of ancient human population history. Genetics (2010) 0.93
Disease-associated alleles in genome-wide association studies are enriched for derived low frequency alleles relative to HapMap and neutral expectations. BMC Med Genomics (2010) 0.90
Detecting directional selection in the presence of recent admixture in African-Americans. Genetics (2010) 0.88
Inferring population size changes with sequence and SNP data: lessons from human bottlenecks. Heredity (Edinb) (2013) 0.88
The effect of SNP discovery method and sample size on estimation of population genetic data for Chinese and Indian rhesus macaques (Macaca mulatta). Primates (2011) 0.88
Correcting coalescent analyses for panel-based SNP ascertainment. Genetics (2013) 0.86
A population genetic hidden Markov model for detecting genomic regions under selection. Mol Biol Evol (2010) 0.84
Correcting the site frequency spectrum for divergence-based ascertainment. PLoS One (2009) 0.83
Fine-scale map of encyclopedia of DNA elements regions in the Korean population. Genetics (2006) 0.82
Targeted Sequencing Reveals Large-Scale Sequence Polymorphism in Maize Candidate Genes for Biomass Production and Composition. PLoS One (2015) 0.82
Genome-wide insights into the genetic history of human populations. Investig Genet (2015) 0.81
Estimating population divergence time and phylogeny from single-nucleotide polymorphisms data with outgroup ascertainment bias. Mol Ecol (2011) 0.81
Mining the pig genome to investigate the domestication process. Heredity (Edinb) (2014) 0.79
Farmers without borders-genetic structuring in century old barley (Hordeum vulgare). Heredity (Edinb) (2014) 0.79
GBStools: A Statistical Method for Estimating Allelic Dropout in Reduced Representation Sequencing Data. PLoS Genet (2016) 0.78
Site frequency spectra from genomic SNP surveys. Theor Popul Biol (2009) 0.78
Inferring selection on amino acid preference in protein domains. Mol Biol Evol (2008) 0.77
Examination of disease-based selection, demographic history and population structure in European Y-chromosome haplogroup I. J Hum Genet (2010) 0.76
The population genomic signature of environmental selection in the widespread insect-pollinated tree species Frangula alnus at different geographical scales. Heredity (Edinb) (2015) 0.76
Adjusting heterogeneous ascertainment bias for genetic association analysis with extended families. BMC Med Genet (2015) 0.75
Genomic signatures of adaptive introgression from European mouflon into domestic sheep. Sci Rep (2017) 0.75
Detecting recent positive selection in the human genome from haplotype structure. Nature (2002) 22.00
An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature (2000) 19.19
Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science (1998) 18.23
Interrogating a high-density SNP map for signatures of natural selection. Genome Res (2002) 10.33
Haplotype variation and linkage disequilibrium in 313 human genes. Science (2001) 8.52
The application of molecular genetic approaches to the study of human evolution. Nat Genet (2003) 7.44
Two-locus sampling distributions and their application. Genetics (2001) 7.42
Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics (2000) 6.44
A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set. Am J Hum Genet (2003) 5.34
Mining SNPs from EST databases. Genome Res (1999) 4.31
SNP frequencies in human genes an excess of rare alleles and differing modes of selection. Trends Genet (2000) 3.78
Usefulness of single nucleotide polymorphism data for estimating population parameters. Genetics (2000) 3.78
The discovery of single-nucleotide polymorphisms--and inferences about human demographic history. Am J Hum Genet (2001) 3.50
Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium. Theor Popul Biol (2003) 2.73
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The SNP Consortium website: past, present and future. Nucleic Acids Res (2003) 2.08
New explicit expressions for relative frequencies of single-nucleotide polymorphisms with application to statistical inference on population growth. Genetics (2003) 1.97
The effect of single nucleotide polymorphism identification strategies on estimates of linkage disequilibrium. Mol Biol Evol (2003) 1.93
Finding the missing heritability of complex diseases. Nature (2009) 67.95
The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Genome-wide associations of gene expression variation in humans. PLoS Genet (2005) 17.27
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res (2009) 12.58
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature (2007) 11.66
Natural selection on protein-coding genes in the human genome. Nature (2005) 10.84
Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet (2008) 8.92
A high-resolution map of human evolutionary constraint using 29 mammals. Nature (2011) 8.67
Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res (2005) 8.38
A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol (2005) 8.32
Demographic history and rare allele sharing among human populations. Proc Natl Acad Sci U S A (2011) 7.36
Natural selection shaped regional mtDNA variation in humans. Proc Natl Acad Sci U S A (2002) 6.95
Ascertainment bias in studies of human genome-wide polymorphism. Genome Res (2005) 6.63
Proportionally more deleterious genetic variation in European than in African populations. Nature (2008) 6.61
Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover. Mol Biol Evol (2002) 6.44
Genomic scans for selective sweeps using SNP data. Genome Res (2005) 6.43
Evolutionary changes in cis and trans gene regulation. Nature (2004) 6.24
Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci U S A (2004) 6.08
Natural variation in human membrane transporter genes reveals evolutionary and functional constraints. Proc Natl Acad Sci U S A (2003) 5.77
Recent explosive human population growth has resulted in an excess of rare genetic variants. Science (2012) 5.58
A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set. Am J Hum Genet (2003) 5.34
Localizing recent adaptive evolution in the human genome. PLoS Genet (2007) 5.11
Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33. Proc Natl Acad Sci U S A (2008) 4.76
Patterns of positive selection in six Mammalian genomes. PLoS Genet (2008) 4.69
Recent and ongoing selection in the human genome. Nat Rev Genet (2007) 4.62
The functional spectrum of low-frequency coding variation. Genome Biol (2011) 4.42
Deep resequencing reveals excess rare recent variants consistent with explosive population growth. Nat Commun (2010) 4.39
Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS One (2008) 4.03
A simple genetic architecture underlies morphological variation in dogs. PLoS Biol (2010) 3.46
Linkage disequilibrium and the mapping of complex human traits. Trends Genet (2002) 3.38
Regulatory changes underlying expression differences within and between Drosophila species. Nat Genet (2008) 3.24
Dynamic evolution of the innate immune system in Drosophila. Nat Genet (2007) 3.09
Bayesian inference of ancient human demography from individual genome sequences. Nat Genet (2011) 3.03
Darwinian and demographic forces affecting human protein coding genes. Genome Res (2009) 3.01
Genes regulated by mating, sperm, or seminal proteins in mated female Drosophila melanogaster. Curr Biol (2004) 2.84
Y chromosome of D. pseudoobscura is not homologous to the ancestral Drosophila Y. Science (2004) 2.80
Thrice out of Africa: ancient and recent expansions of the honey bee, Apis mellifera. Science (2006) 2.64
Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques. Science (2007) 2.62
Adaptive genic evolution in the Drosophila genomes. Proc Natl Acad Sci U S A (2007) 2.56
Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals. Genome Res (2008) 2.46
Genetic basis of natural variation in D. melanogaster antibacterial immunity. Science (2004) 2.38
Evolution of protein-coding genes in Drosophila. Trends Genet (2008) 2.36
Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters. Mol Cell Biol (2007) 2.33
Fine-scale heterogeneity in crossover rate in the garnet-scalloped region of the Drosophila melanogaster X chromosome. Genetics (2013) 2.17
Balancing selection maintains a form of ERAP2 that undergoes nonsense-mediated decay and affects antigen presentation. PLoS Genet (2010) 2.14
Mapping determinants of variation in energy metabolism, respiration and flight in Drosophila. Genetics (2003) 2.07
Genome-wide inference of natural selection on human transcription factor binding sites. Nat Genet (2013) 2.03
Sperm competitive ability in Drosophila melanogaster associated with variation in male reproductive proteins. Genetics (2004) 2.01
Population genetics: malaria variorum. Nature (2002) 1.97
Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence. PLoS Genet (2009) 1.97
Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila. Genetics (2005) 1.93
Population genetic structure of the people of Qatar. Am J Hum Genet (2010) 1.91
Full-exon resequencing reveals toll-like receptor variants contribute to human susceptibility to tuberculosis disease. PLoS One (2007) 1.89
Understanding the accuracy of statistical haplotype inference with sequence data of known phase. Genet Epidemiol (2007) 1.87
Contrasting infection strategies in generalist and specialist wasp parasitoids of Drosophila melanogaster. PLoS Pathog (2007) 1.82
Sequence diversity and haplotype structure in the human ABCB1 (MDR1, multidrug resistance transporter) gene. Pharmacogenetics (2003) 1.79
Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation. Am J Hum Genet (2012) 1.75
Tracing the evolutionary history of Drosophila regulatory regions with models that identify transcription factor binding sites. Mol Biol Evol (2003) 1.75
The evolutionary costs of immunological maintenance and deployment. BMC Evol Biol (2008) 1.74
Low conservation of gene content in the Drosophila Y chromosome. Nature (2008) 1.72
Targets of balancing selection in the human genome. Mol Biol Evol (2009) 1.69
Genomewide distribution of high-frequency, completely mismatching SNP haplotype pairs observed to be common across human populations. Am J Hum Genet (2003) 1.66
Extended linkage disequilibrium surrounding the hemoglobin E variant due to malarial selection. Am J Hum Genet (2004) 1.61
Polymorphisms in a human kidney xenobiotic transporter, OCT2, exhibit altered function. Pharmacogenetics (2002) 1.57
Conjuring SNPs to detect associations. Nat Genet (2007) 1.57
A genome-wide approach to identifying novel-imprinted genes. Hum Genet (2007) 1.55
Origin and evolution of Y chromosomes: Drosophila tales. Trends Genet (2009) 1.53
Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping. BMC Genet (2008) 1.53
Estrogen receptor genotypes and haplotypes associated with breast cancer risk. Cancer Res (2004) 1.52
Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla. Genome Res (2005) 1.51
Impact of microRNA regulation on variation in human gene expression. Genome Res (2012) 1.49
Y chromosome and other heterochromatic sequences of the Drosophila melanogaster genome: how far can we go? Genetica (2003) 1.49
Mapping multiple Quantitative Trait Loci by Bayesian classification. Genetics (2004) 1.46
Natural genetic variation in male reproductive genes contributes to nontransitivity of sperm competitive ability in Drosophila melanogaster. Mol Ecol (2012) 1.46
Independent effects of cis- and trans-regulatory variation on gene expression in Drosophila melanogaster. Genetics (2008) 1.45
Associations between sperm competition and natural variation in male reproductive genes on the third chromosome of Drosophila melanogaster. Genetics (2007) 1.45
Genetic variation in Drosophila melanogaster resistance to infection: a comparison across bacteria. Genetics (2006) 1.44
Methods for human demographic inference using haplotype patterns from genomewide single-nucleotide polymorphism data. Genetics (2009) 1.42
Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing. Nat Genet (2011) 1.41
Disentangling the relationship between sex-biased gene expression and X-linkage. Genome Res (2012) 1.40
The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern. Genome Res (2005) 1.40
Robustness of inference of haplotype block structure. J Comput Biol (2003) 1.38
Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster. Genome Biol Evol (2009) 1.36
Inferring genetic ancestry: opportunities, challenges, and implications. Am J Hum Genet (2010) 1.36
Post-mating gene expression profiles of female Drosophila melanogaster in response to time and to four male accessory gland proteins. Genetics (2008) 1.33
Genome sequencing reveals complex speciation in the Drosophila simulans clade. Genome Res (2012) 1.31
Knowledge-driven analysis identifies a gene-gene interaction affecting high-density lipoprotein cholesterol levels in multi-ethnic populations. PLoS Genet (2012) 1.31
Optimal haplotype block-free selection of tagging SNPs for genome-wide association studies. Genome Res (2004) 1.28
Genetic incompatibilities are widespread within species. Nature (2013) 1.28