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PLINK: a tool set for whole-genome association and population-based linkage analyses.
Whole-genome association studies (WGAS) bring new computational, as well as analytic, challenges to researchers. Many existing genetic-analysis tools are not designed to handle such large data setsExpand
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The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among individuals. However, the massive data setsExpand
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MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations.
With the advent of RFLPs, genetic linkage maps are now being assembled for a number of organisms including both inbred experimental populations such as maize and outbred natural populations such asExpand
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Haploview: analysis and visualization of LD and haplotype maps
TLDR
Haploview is a software package that provides computation of linkage disequilibrium statistics and population haplotype patterns from primary genotype data in a visually appealing and interactive interface. Expand
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A framework for variation discovery and genotyping using next-generation DNA sequencing data
Recent advances in sequencing technology make it possible to comprehensively catalog genetic variation in population samples, creating a foundation for understanding human disease, ancestry andExpand
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PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
DNA microarrays can be used to identify gene expression changes characteristic of human disease. This is challenging, however, when relevant differences are subtle at the level of individual genes.Expand
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The Structure of Haplotype Blocks in the Human Genome
Haplotype-based methods offer a powerful approach to disease gene mapping, based on the association between causal mutations and the ancestral haplotypes on which they arose. As part of The SNPExpand
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Parametric and nonparametric linkage analysis: a unified multipoint approach.
TLDR
In complex disease studies, it is crucial to perform multipoint linkage analysis with many markers and to use robust nonparametric methods that take account of all pedigree information. Expand
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A second generation human haplotype map of over 3.1 million SNPs
We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations andExpand
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Efficiency and power in genetic association studies
We investigated selection and analysis of tag SNPs for genome-wide association studies by specifically examining the relationship between investment in genotyping and statistical power. Do pairwiseExpand
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