Dissecting the spatial structure of overlapping transcription in budding yeast

This thesis presents a computational and algorithmic method for the analysis of high-resolution transcription data in the budding yeast Saccharomyces cerevisiae. We begin by describing a computational system for storing and retrieving spatiallymapped genomic data. This system forms the infrastructure for a novel algorithmic approach to detect and recover instances of same-strand overlapping transcripts in high resolution expression experiments. We then apply these algorithms to a set of transcription experiments in budding yeast, Saccharomyces cerevisiae, in order to identify potential sites of same-strand overlapping transcripts that may be involved in novel forms of transcriptional regulation. Thesis Supervisor: David K. Gifford Title: Professor