Analysis of mammalian overlapping reading frames and species composition in metagenomic samples

This dissertation addresses two seemingly unconnected biological questions: (1) understanding the evolution of overlapping reading frames (dual coding) in higher eukaryotes and (2) the development of approaches for delineating taxonomic representation of eukaryotic metagenomic samples, both of which reflect the timeline of my graduate study and the developments that have occurred in life sciences during the past five years. Before starting graduate school I was primarily trained as an experimental biologist and these skills were essential in the research project described in Chapters 2 and 4. In the course of my graduate studies, I realized that without proper computational background I would not be equipped to realize my potential as a proficient biologist. This became especially prominent with the advent of the next generation sequencing technologies that produce datasets that are beyond use for most experimentalists. In light of these new technologies, I decided to design my last project (Chapter 5) to utilize the next generation sequencing data.