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PLINK: a tool set for whole-genome association and population-based linkage analyses.
TLDR
This work introduces PLINK, an open-source C/C++ WGAS tool set, and describes the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation, which focuses on the estimation and use of identity- by-state and identity/descent information in the context of population-based whole-genome studies.
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
TLDR
The GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.
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.
A framework for variation discovery and genotyping using next-generation DNA sequencing data
TLDR
A unified analytic framework to discover and genotype variation among multiple samples simultaneously that achieves sensitive and specific results across five sequencing technologies and three distinct, canonical experimental designs is presented.
PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
TLDR
An analytical strategy is introduced, Gene Set Enrichment Analysis, designed to detect modest but coordinate changes in the expression of groups of functionally related genes, which identifies a set of genes involved in oxidative phosphorylation whose expression is coordinately decreased in human diabetic muscle.
The Structure of Haplotype Blocks in the Human Genome
TLDR
It is shown that the human genome can be parsed objectively into haplotype blocks: sizable regions over which there is little evidence for historical recombination and within which only a few common haplotypes are observed.
Parametric and nonparametric linkage analysis: a unified multipoint approach.
TLDR
It is shown that NPL is robust to uncertainty about mode of inheritance, is much more powerful than commonly used nonparametric methods, and loses little power relative to parametric linkage analysis, and appears to be the method of choice for pedigree studies of complex traits.
A second generation human haplotype map of over 3.1 million SNPs
TLDR
The Phase II HapMap is described, which characterizes over 3.1 million human single nucleotide polymorphisms genotyped in 270 individuals from four geographically diverse populations and includes 25–35% of common SNP variation in the populations surveyed, and increased differentiation at non-synonymous, compared to synonymous, SNPs is demonstrated.
Efficiency and power in genetic association studies
TLDR
A haplotype-based tagging method is demonstrated that uniformly outperforms single-marker tests and methods for prioritization that markedly increase tagging efficiency, and is robust to the completeness of the reference panel from which tags are selected.
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