The demand for novel molecularly targeted drugs will continue to rise as we make progress toward personalizing cancer treatments to the molecular signatures of individual tumors. While the collection and analysis of genomic data has become routine,...
Genome-wide association studies (GWAS) have identified more than 8,900 genetic variants, mainly single nucleotide polymorphisms (SNPs), associated with hundreds of human traits and diseases, which define risk-associated loci (Hindorff et al., 2012 ...
The identification and characterization of functional genetic variation is essential for future advances in molecular diagnostics, pharmacogenomics, and personalized medicine. Recent attempts at identifying nucleotide level variation (somatic...
Telecommunication -- Traffic -- Measurement -- Statistical methods. IEEE 802.11 (Standard). Universities and colleges -- Computer networks -- New Hampshire -- Hanover -- Case studies.
The edge of the Internet is increasingly wireless. Enterprises large and small, homeowners, and even whole cities have deployed Wi-Fi networks for their users, and many users never need to--or never bother to--use the wired network. With the advent...
Breast cancer is the most common cancer in women. The discovery of breast tumor subtypes and the subsequent development of treatments aimed at them has allowed a reduction in the mortality of breast cancer. However, tumors with similar...
We study the bijective combinatorics of reduced words. These are fundamental objects in the study of Coxeter groups. We restrict our focus to reduced words of permutations and signed permutations. Our results can all be situated within the context...
Leukemia represents a small percentage of human cancer, accounting for about 5% of all cases of cancer in adults, but, interestingly, for about 50% of all cases of cancer in children. The behavior of leukemia is often regulated by the chromosomal...
PDZ protein-protein interaction domains recognize short linear motif (SLiM) sequences typically at the extreme C-terminus of a target protein. These domains often act as scaffolds, connecting target proteins to additional interaction and catalytic...
The Mixed Lineage Leukemia (MLL1) gene was first cloned as a hot spot of chromosomal translocations in acute leukemia. More than 70 fusion proteins of MLL1 have been described in both lymphoid and myeloid leukemia and many are highly associated...
Although genome-wide association studies (GWAS) and other high-throughput initiatives have led to an information explosion in human genetics and genetic epidemiology, the mapping from genotype to phenotype remains challenging as most of the...
The focus of this thesis is the study of nuclearity and exactness for groupoid crossed product C*-algebras. In particular, we present generalizations of two well-known facts from group dynamical systems and crossed products to the groupoid setting....
Gene set testing has become a critical tool for interpreting the results of high-throughput genomic experiments. Despite the development of robust statistical methods and extensive gene set collections, however, the results from gene set testing...
In this thesis, we characterize and enumerate the permutations which are realized by the orbits of signed shifts, a family of discrete dynamical systems on words. The permutations, which are called patterns of the signed shifts, are given by the...
We present aligned hierarchies, a novel solution to the dimension reduction problem, representing high-dimensional and noisy sequential data as a low-dimensional object that encodes relevant information. In this thesis, we motivate our presentation...
In Chapter 2 we look at the distribution of permutation statistics in the context of pattern-avoiding permutations. The first part of this chapter deals with a recursively defined bijection of Robertson [37] between 123- and 132-avoiding...
How is concrete conceptual information represented in the brain? Little is known about the neural organization for details of concrete objects when presented as words. The goal of the first two studies was to investigate this. In the third study,...
The present thesis is focused on developing a better understanding of factors driving disease biology and overall risk using cancers of the bladder and breast as model systems. As no single approach was likely to unravel the complexities of these...
Digital integrated circuits -- Testing. Digital integrated circuits -- Testing -- Mathematical models. Digital integrated circuits -- Design and construction.
PDZ domains are protein:protein interaction domains that serve as molecular scaffolds, especially in the case of specialized cellular environments like polarized airway epithelial cells of the human lung. Historically the domains have been thought...
Computer input-output equipment. ; Computational grids (Computer systems). ; High performance computing. ; Electronic data processing -- Distributed processing.
High-performance computing increasingly occurs on computational grids composed of heterogeneous and geographically distributed systems of computers, networks, and storage devices that collectively act as a single virtual computer. A key challenge...
Information retrieval -- Mathematical models. ; Electronic information resource searching. ; Computer algorithms. ; Decision making -- Data processing. ; Mathematical optimization.
This thesis presents a unified method for simultaneous solution of three problems in Information Retrieval--metasearch (the fusion of ranked lists returned by retrieval systems to elicit improved performance), efficient system evaluation (the...
Nutrients play fundamental roles in biological systems, affecting plant growth and quality, community structure, and species interactions. Although the effects of nutrients on primary and secondary production have been well documented, their...
In order to most effectively investigate protein structure and improve protein function, it is necessary to carefully plan appropriate experiments. The combinatorial number of possible experiment plans demands effective criteria and efficient...
This thesis explores practical and theoretical aspects of several privacy-providing technologies, including tools for anonymous web-browsing, verifiable electronic voting schemes, and private information retrieval from databases. State-of-art...
I investigate the kinematics and space densities of the local cataclysmic variable (CV) population. CVs are close binary star systems composed of a white dwarf that accretes matter from a less compact companion star in Roche lobe overflow....
Polynomials. Finite fields (Algebra). Algebraic functions. Number theory.
The ring of univariate polynomials over a finite field shares many foundational arithmetic properties with the ring of rational integers. This similarity makes it possible for many problems in elementary number theory to be translated 'through the...