John P. Ferguson

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We consider an Empirical Bayes method to correct for the Winner's Curse phenomenon in genome-wide association studies. Our method utilizes the collective distribution of all odds ratios (ORs) to determine the appropriate correction for a particular single-nucleotide polymorphism (SNP). We can show that this approach is squared error optimal provided that(More)
The Ashkenazi Jewish population has a several-fold higher prevalence of Crohn's disease (CD) compared with non-Jewish European ancestry populations and has a unique genetic history. Haplotype association is critical to CD etiology in this population, most notably at NOD2, in which three causal, uncommon and conditionally independent NOD2 variants reside on(More)
Recently there has been great interest in identifying rare variants associated with common diseases. We apply several collapsing-based and kernel-based single-gene association tests to Genetic Analysis Workshop 17 (GAW17) rare variant association data with unrelated individuals without knowledge of the simulation model. We also implement modified versions(More)
Genome-wide association studies (GWAS) in immune-mediated diseases have identified over 150 associated genomic loci. Many of these loci play a role in T cell responses, and regulation of T cell differentiation plays a critical role in immune-mediated diseases; however, the relationship between implicated disease loci and T cell differentiation is(More)
RNA-Seq technology measures the transcript abundance by generating sequence reads and counting their frequencies across different biological conditions. To identify differentially expressed genes between two conditions, it is important to consider the experimental design as well as the distributional property of the data. In many RNA-Seq studies, the(More)
Conservative statistical tests are often used in complex multiple testing settings in which computing the type I error may be difficult. In such tests, the reported p-value for a hypothesis can understate the evidence against the null hypothesis and consequently statistical power may be lost. False Discovery Rate adjustments, used in multiple comparison(More)
We argue that the performance benefits of interpersonal heterogeneity are subject to three common failure points. First, heterogeneous people tend to homogenize over time with repeated exposure, leading any benefits of interpersonal heterogeneity to decay with time. Second, groups composed of heterogeneous people tend to be fragile; they are both more(More)
Association studies using tag SNPs have been successful in detecting disease-associated common variants. However, common variants, with rare exceptions, explain only at most 5-10% of the heritability resulting from genetic factors, which leads to the common disease/rare variants assumption. Indeed, recent studies using sequencing technologies have(More)
We consider the application of Efron's empirical Bayes classification method to risk prediction in a genome-wide association study using the Genetic Analysis Workshop 17 (GAW17) data. A major advantage of using this method is that the effect size distribution for the set of possible features is empirically estimated and that all subsequent parameter(More)
The purpose of this note is to introduce you to today's world of work and to outline the skills, strategies, and actions you will need to contribute to and to prosper in it. You will be some of the best-prepared young people in the world. You bring to work a world-class scientific, mathematical, and technical education, and you will now complement that with(More)
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