The goal of determining which of hundreds of thousands of SNPs are associated with disease poses one of the most challenging multiple testing problems. Using the empirical Bayes approach, the local false discovery rate (LFDR) estimated using popular semiparametric models has enjoyed success in...

Genetic association studies are a powerful tool to detect genetic variants that predispose to human disease. Once an associated variant is identified, investigators are also interested in estimating the effect of the identified variant on disease risk. Estimates of the genetic effect based on...

Population-based case-control design has become one of the most popular approaches for conducting genome-wide association scans for rare diseases like cancer. In this article, we propose a novel method for improving the power of the widely used single-single-nucleotide polymorphism (SNP)...

Unequal growth rates between mutant and wild-type cells in a large population constitute a problem for the estimation of mutation rate. Over a period of cell growth, a selective advantage of one cell type over the other might lead to considerable error in the estimation of mutation rate if equal...

The factors that affect reliable estimations of mutation rates ([mu]) in cultured mammalian somatic cell populations by fluctuation analysis are studied experimentally and statistically. We analyze the differential effect of the final cell population size in each culture (Nt) and the number of...

A systematic comparison of 5 different statistical methods for the estimation of mutation rate ([mu]) in cultured Chinese hamster V79 cells is presented. Fluctuation tests were performed with several large batches of parallel cell cultures each allowed to grow for a different length of time in...

Linkage and association analysis are both tools for mapping the locations of genes responsible for human traits. A common approach for quantitative trait linkage analysis in human pedigrees involves the use of variance component models. In the first part of this dissertation, I extended the...

The Genome-Wide Association Study (GWAS) is the predominant tool to search for genetic risk variants that contribute to complex human disease. Despite the large number of GWAS findings, variants implicated by GWAS are themselves unlikely to fully explain the heritability of many diseases. In...

This is a seminar based on research literature. Papers covered are selected to illustrate important problems and approaches in the field of computational and systems biology, and provide students a framework from which to evaluate new developments. The MIT Initiative in Computational and Systems...