There is a high demand for developing a computational platform for global analysis of position- specific sequence variation within HIV-1 subtypes. Undesirable probe designs can …
The human genome exhibits a rich structure resulting from a long history of genomic changes, including single base-pair mutations and larger scale rearrangements such as …
Online stochastic combinatorial optimization problems are problems in which a decision maker is trying to minimize or maximize an objective by making a sequence of …
Ten years ago, the first RNA-seq study was published. Since then over 200 thousand RNA-seq studies have been published, spanning many different organisms, tissue types, …
Cancer is a disease resulting from genomic mutations that occur during an individual's lifetime and cause the uncontrolled growth of a collection of cells into …
Cancer is caused largely by the accumulation of somatic mutations throughout an individual's life. Recent advances in next generation sequencing (NGS) enable measurement of somatic …
Large graphs are ubiquitous in many diverse fields ranging from sociology and economics to biology and engineering. Applications in numerous areas such as transportation, geographical …
Determining the sequences of alleles co-inherited on a single chromosome, or haplotypes, is fundamentally important in genomics, molecular biology, and genomic medicine. Experimental methods for …
The study of the dynamics of liquid state systems has always been an intriguing problem in theoretical and computational chemistry. A perspective called geodesic theory …
Educational assessments are crucial for both instructors and education researchers to measure learning, troubleshoot student problems, evaluate pedagogy, and improve education. Unfortunately, creating and administering …
Analyzing huge datasets becomes prohibitively slow when the dataset does not fit in main memory. Approximations of the results of guaranteed high quality are sufficient …
Sampling based and randomized algorithms are powerful tools in studying big data problems. In this thesis we provide sampling based algorithms for mining graphs and …
Gene expression occurs when an organism produces proteins that correspond to genes in DNA. Interactions of these proteins cause many biological functions. Some types of …
The studies presented in this dissertation describe and apply methods for using biplanar videoradiography to study dynamic in vivo knee motion. The techniques presented in …
Many optimization problems involving graphs naturally feature road networks, grids, or other large planar graphs. By exploiting the special structure of planar graphs, it is …
Cancer is an evolutionary process where cells acquire somatic mutations over time. As a result of this process, tumors are often highly heterogeneous — containing …
