Published in PLoS Genet on December 05, 2008
A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet (2009) 30.09
Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nat Genet (2010) 23.08
Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature (2010) 16.86
Genotype imputation for genome-wide association studies. Nat Rev Genet (2010) 14.59
Practical aspects of imputation-driven meta-analysis of genome-wide association studies. Hum Mol Genet (2008) 13.26
Genotype imputation with thousands of genomes. G3 (Bethesda) (2011) 8.77
Genotype-imputation accuracy across worldwide human populations. Am J Hum Genet (2009) 7.28
Genome-wide efficient mixed-model analysis for association studies. Nat Genet (2012) 6.62
DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol (2011) 6.48
DNase I sensitivity QTLs are a major determinant of human expression variation. Nature (2012) 6.17
Web-based, participant-driven studies yield novel genetic associations for common traits. PLoS Genet (2010) 5.02
Meta-analyses of genome-wide association studies identify multiple loci associated with pulmonary function. Nat Genet (2009) 4.56
Validating, augmenting and refining genome-wide association signals. Nat Rev Genet (2009) 4.56
Bayesian statistical methods for genetic association studies. Nat Rev Genet (2009) 4.37
Genome-wide association study identifies five loci associated with lung function. Nat Genet (2009) 4.10
Sex-stratified genome-wide association studies including 270,000 individuals show sexual dimorphism in genetic loci for anthropometric traits. PLoS Genet (2013) 2.83
Identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue. PLoS Genet (2011) 2.68
Dissecting the regulatory architecture of gene expression QTLs. Genome Biol (2012) 2.51
A statin-dependent QTL for GATM expression is associated with statin-induced myopathy. Nature (2013) 2.46
Chapter 11: Genome-wide association studies. PLoS Comput Biol (2012) 2.46
Genome-wide association of lipid-lowering response to statins in combined study populations. PLoS One (2010) 2.43
Efficiency and power as a function of sequence coverage, SNP array density, and imputation. PLoS Comput Biol (2012) 2.29
A comparison of approaches to account for uncertainty in analysis of imputed genotypes. Genet Epidemiol (2011) 2.19
Accuracy of genome-wide imputation of untyped markers and impacts on statistical power for association studies. BMC Genet (2009) 2.16
Controls of nucleosome positioning in the human genome. PLoS Genet (2012) 2.14
Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a Breast Cancer Consortium. PLoS Genet (2011) 1.94
The relationship between imputation error and statistical power in genetic association studies in diverse populations. Am J Hum Genet (2009) 1.89
Strain screen and haplotype association mapping of wheel running in inbred mouse strains. J Appl Physiol (1985) (2010) 1.88
The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study. PLoS Genet (2015) 1.87
Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders. Nat Genet (2013) 1.72
Bayesian test for colocalisation between pairs of genetic association studies using summary statistics. PLoS Genet (2014) 1.71
Interactions between glucocorticoid treatment and cis-regulatory polymorphisms contribute to cellular response phenotypes. PLoS Genet (2011) 1.49
Evaluation of imputation-based association in and around the integrin-alpha-M (ITGAM) gene and replication of robust association between a non-synonymous functional variant within ITGAM and systemic lupus erythematosus (SLE). Hum Mol Genet (2009) 1.46
Strong Selection at MHC in Mexicans since Admixture. PLoS Genet (2016) 1.41
Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels. PLoS Genet (2014) 1.39
A comparison of multivariate genome-wide association methods. PLoS One (2014) 1.38
Integrative modeling of eQTLs and cis-regulatory elements suggests mechanisms underlying cell type specificity of eQTLs. PLoS Genet (2013) 1.34
Practical considerations for imputation of untyped markers in admixed populations. Genet Epidemiol (2010) 1.33
The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels. PLoS Genet (2012) 1.25
Genome-wide analysis of BMI in adolescents and young adults reveals additional insight into the effects of genetic loci over the life course. Hum Mol Genet (2013) 1.23
Imputation and quality control steps for combining multiple genome-wide datasets. Front Genet (2014) 1.21
BAYESIAN METHODS FOR GENETIC ASSOCIATION ANALYSIS WITH HETEROGENEOUS SUBGROUPS: FROM META-ANALYSES TO GENE-ENVIRONMENT INTERACTIONS. Ann Appl Stat (2015) 1.15
Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13). PLoS One (2012) 1.14
Integrated enrichment analysis of variants and pathways in genome-wide association studies indicates central role for IL-2 signaling genes in type 1 diabetes, and cytokine signaling genes in Crohn's disease. PLoS Genet (2013) 1.14
Analyses and comparison of imputation-based association methods. PLoS One (2010) 1.12
Detecting signatures of selection through haplotype differentiation among hierarchically structured populations. Genetics (2013) 1.10
Fine Mapping Causal Variants with an Approximate Bayesian Method Using Marginal Test Statistics. Genetics (2015) 1.07
Imputation aware meta-analysis of genome-wide association studies. Genet Epidemiol (2010) 1.05
Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to risk for carotid artery disease. Lipids Health Dis (2009) 1.03
EMINIM: an adaptive and memory-efficient algorithm for genotype imputation. J Comput Biol (2010) 1.03
Re-ranking sequencing variants in the post-GWAS era for accurate causal variant identification. PLoS Genet (2013) 1.00
Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data. PLoS One (2012) 0.98
APOE is not associated with Alzheimer disease: a cautionary tale of genotype imputation. Ann Hum Genet (2010) 0.97
Quantile-specific penetrance of genes affecting lipoproteins, adiposity and height. PLoS One (2012) 0.93
New genetic evidence for involvement of the dopamine system in migraine with aura. Hum Genet (2009) 0.93
Detecting structure of haplotypes and local ancestry. Genetics (2014) 0.92
Bayesian variable selection in searching for additive and dominant effects in genome-wide data. PLoS One (2012) 0.90
fcGENE: a versatile tool for processing and transforming SNP datasets. PLoS One (2014) 0.89
Optimal methods for meta-analysis of genome-wide association studies. Genet Epidemiol (2011) 0.88
Genome-wide association study based on multiple imputation with low-depth sequencing data: application to biofuel traits in reed canarygrass. G3 (Bethesda) (2015) 0.88
Genetic and nongenetic sources of variation in phospholipid transfer protein activity. J Lipid Res (2009) 0.87
SEQCHIP: a powerful method to integrate sequence and genotype data for the detection of rare variant associations. Bioinformatics (2012) 0.86
ATRIUM: testing untyped SNPs in case-control association studies with related individuals. Am J Hum Genet (2009) 0.85
Genetic, functional and molecular features of glucocorticoid receptor binding. PLoS One (2013) 0.85
Analytical methods for immunogenetic population data. Methods Mol Biol (2012) 0.84
Genotype imputation for African Americans using data from HapMap phase II versus 1000 genomes projects. Genet Epidemiol (2012) 0.83
Gene-wide characterization of common quantitative trait loci for ABCB1 mRNA expression in normal liver tissues in the Chinese population. PLoS One (2012) 0.81
Statistical analysis for genome-wide association study. J Biomed Res (2014) 0.80
Family-based association tests using genotype data with uncertainty. Biostatistics (2011) 0.80
Detecting local haplotype sharing and haplotype association. Genetics (2014) 0.80
Single-nucleotide polymorphism bioinformatics: a comprehensive review of resources. Circ Cardiovasc Genet (2009) 0.80
Finite adaptation and multistep moves in the metropolis-hastings algorithm for variable selection in genome-wide association analysis. PLoS One (2012) 0.80
Bayesian Polynomial Regression Models to Fit Multiple Genetic Models for Quantitative Traits. Bayesian Anal (2015) 0.80
Evaluation of the imputation performance of the program IMPUTE in an admixed sample from Mexico City using several model designs. BMC Med Genomics (2012) 0.80
Inbred Strain Variant Database (ISVdb): A Repository for Probabilistically Informed Sequence Differences Among the Collaborative Cross Strains and Their Founders. G3 (Bethesda) (2017) 0.79
Genome-wide physical activity interactions in adiposity - A meta-analysis of 200,452 adults. PLoS Genet (2017) 0.78
Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays. BMC Bioinformatics (2010) 0.78
Genotype imputation in a coalescent model with infinitely-many-sites mutation. Theor Popul Biol (2012) 0.77
Imputation of non-genotyped individuals based on genotyped relatives: assessing the imputation accuracy of a real case scenario in dairy cattle. Genet Sel Evol (2014) 0.77
Genetics of Type 2 Diabetes in African Americans. Curr Diab Rep (2015) 0.77
Generalized admixture mapping for complex traits. G3 (Bethesda) (2013) 0.77
Prediction of LDL cholesterol response to statin using transcriptomic and genetic variation. Genome Biol (2014) 0.76
A targeted association study of immunity genes and networks suggests novel associations with placental malaria infection. PLoS One (2011) 0.76
Genetic Architecture of Transcription and Chromatin Regulation. Genomics Inform (2015) 0.75
Ascertainment bias from imputation methods evaluation in wheat. BMC Genomics (2016) 0.75
SNP imputation bias reduces effect size determination. Front Genet (2015) 0.75
Application of computational methods in genetic study of inflammatory bowel disease. World J Gastroenterol (2016) 0.75
Incorporating Functional Annotations for Fine-Mapping Causal Variants in a Bayesian Framework Using Summary Statistics. Genetics (2016) 0.75
Variation in Recombination Rate and Its Genetic Determinism in Sheep Populations. Genetics (2017) 0.75
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature (2007) 144.95
Statistical significance for genomewide studies. Proc Natl Acad Sci U S A (2003) 88.64
A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39
A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet (2007) 52.68
A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science (2007) 43.16
A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet (2006) 28.32
Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet (2007) 24.68
Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics (2003) 17.73
Imputation-based analysis of association studies: candidate regions and quantitative traits. PLoS Genet (2007) 15.55
Low LDL cholesterol in individuals of African descent resulting from frequent nonsense mutations in PCSK9. Nat Genet (2005) 12.12
Effect of statin therapy on C-reactive protein levels: the pravastatin inflammation/CRP evaluation (PRINCE): a randomized trial and cohort study. JAMA (2001) 5.54
Simple and efficient analysis of disease association with missing genotype data. Am J Hum Genet (2008) 4.52
A method to address differential bias in genotyping in large-scale association studies. PLoS Genet (2007) 4.51
Bayes factors for genome-wide association studies: comparison with P-values. Genet Epidemiol (2009) 4.33
A Bayesian measure of the probability of false discovery in genetic epidemiology studies. Am J Hum Genet (2007) 4.21
Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive protein. Am J Hum Genet (2008) 3.61
Imputation methods to improve inference in SNP association studies. Genet Epidemiol (2006) 2.41
Quantifying the amount of missing information in genetic association studies. Genet Epidemiol (2006) 2.01
A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res (2008) 62.07
Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics (2003) 53.11
A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet (2006) 28.32
Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics (2003) 17.73
Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27
Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature (2010) 16.86
Imputation-based analysis of association studies: candidate regions and quantitative traits. PLoS Genet (2007) 15.55
Genes mirror geography within Europe. Nature (2008) 14.23
A comparison of phasing algorithms for trios and unrelated individuals. Am J Hum Genet (2006) 12.45
Traces of human migrations in Helicobacter pylori populations. Science (2003) 11.92
Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat Genet (2012) 11.29
Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour (2009) 10.81
Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes (2007) 10.11
High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet (2008) 9.68
Genotype imputation with thousands of genomes. G3 (Bethesda) (2011) 8.77
Interpreting principal component analyses of spatial population genetic variation. Nat Genet (2008) 8.49
Evidence for substantial fine-scale variation in recombination rates across the human genome. Nat Genet (2004) 6.99
Genome-wide efficient mixed-model analysis for association studies. Nat Genet (2012) 6.62
DNase I sensitivity QTLs are a major determinant of human expression variation. Nature (2012) 6.17
Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive protein. Am J Hum Genet (2008) 3.61
Sex-specific and lineage-specific alternative splicing in primates. Genome Res (2009) 3.61
Assigning African elephant DNA to geographic region of origin: applications to the ivory trade. Proc Natl Acad Sci U S A (2004) 3.17
Automating resequencing-based detection of insertion-deletion polymorphisms. Nat Genet (2006) 2.61
Polygenic modeling with bayesian sparse linear mixed models. PLoS Genet (2013) 2.59
Dissecting the regulatory architecture of gene expression QTLs. Genome Biol (2012) 2.51
A statin-dependent QTL for GATM expression is associated with statin-induced myopathy. Nature (2013) 2.46
A statistical framework for joint eQTL analysis in multiple tissues. PLoS Genet (2013) 2.46
msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots. Bioinformatics (2006) 2.45
Genome-wide association of lipid-lowering response to statins in combined study populations. PLoS One (2010) 2.43
Absence of the TAP2 human recombination hotspot in chimpanzees. PLoS Biol (2004) 2.22
Conservation of hotspots for recombination in low-copy repeats associated with the NF1 microdeletion. Nat Genet (2006) 2.11
Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis. PLoS Genet (2010) 2.06
Global effect of PEG-IFN-alpha and ribavirin on gene expression in PBMC in vitro. J Interferon Cytokine Res (2004) 1.98
Using DNA to track the origin of the largest ivory seizure since the 1989 trade ban. Proc Natl Acad Sci U S A (2007) 1.56
Interactions between glucocorticoid treatment and cis-regulatory polymorphisms contribute to cellular response phenotypes. PLoS Genet (2011) 1.49
Next generation analytic tools for large scale genetic epidemiology studies of complex diseases. Genet Epidemiol (2011) 1.47
Variation in human recombination rates and its genetic determinants. PLoS One (2011) 1.39
Comparative RNA sequencing reveals substantial genetic variation in endangered primates. Genome Res (2011) 1.36
Combating the illegal trade in African elephant ivory with DNA forensics. Conserv Biol (2008) 1.34
Fast and accurate estimation of the population-scaled mutation rate, theta, from microsatellite genotype data. Genetics (2007) 1.32
The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels. PLoS Genet (2012) 1.25
Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13). PLoS One (2012) 1.14
Integrated enrichment analysis of variants and pathways in genome-wide association studies indicates central role for IL-2 signaling genes in type 1 diabetes, and cytokine signaling genes in Crohn's disease. PLoS Genet (2013) 1.14
USING LINEAR PREDICTORS TO IMPUTE ALLELE FREQUENCIES FROM SUMMARY OR POOLED GENOTYPE DATA. Ann Appl Stat (2010) 1.12
Functional comparison of innate immune signaling pathways in primates. PLoS Genet (2010) 1.09
Linkage disequilibrium-based quality control for large-scale genetic studies. PLoS Genet (2008) 1.03
Insights into recombination from population genetic variation. Curr Opin Genet Dev (2006) 1.01
Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data. PLoS One (2012) 0.98
The effects of genotype-dependent recombination, and transmission asymmetry, on linkage disequilibrium. Genetics (2005) 0.91
STATISTICAL INFERENCE OF TRANSMISSION FIDELITY OF DNA METHYLATION PATTERNS OVER SOMATIC CELL DIVISIONS IN MAMMALS. Ann Appl Stat (2010) 0.90
Epigenetic modifications are associated with inter-species gene expression variation in primates. Genome Biol (2014) 0.90
Genetic, functional and molecular features of glucocorticoid receptor binding. PLoS One (2013) 0.85
Probabilistic segmentation and intensity estimation for microarray images. Biostatistics (2005) 0.84
Statistical inference of in vivo properties of human DNA methyltransferases from double-stranded methylation patterns. PLoS One (2012) 0.80
Mapping gene-environment interactions at regulatory polymorphisms: insights into mechanisms of phenotypic variation. Transcription (2012) 0.78
False discovery rates: a new deal. Biostatistics (2016) 0.77
Response to Cavalli-Sforza interview [Human Biology 82(3):245-266 (June 2010)]. Hum Biol (2010) 0.76
Identification of biological relationships from text documents using efficient computational methods. J Bioinform Comput Biol (2003) 0.75
A multi-level text mining method to extract biological relationships. Proc IEEE Comput Soc Bioinform Conf (2002) 0.75
Correction: Visualizing the structure of RNA-seq expression data using grade of membership models. PLoS Genet (2017) 0.75