Computational tools for modeling and measuring chromosome structure

Abstract

DNA conformation within cells has many important biological implications, but there are challenges both in modeling DNA due to the need for specialized techniques, and experimentally since tracing out in vivo conformations is currently impossible. This thesis contributes two computational projects to these efforts. The first project is a set of online and offline calculators of conformational statistics using a variety of published and unpublished methods, addressing the current lack of DNA model-building tools intended for general use. The second project is a reconstructive analysis that could enable in vivo mapping of DNA conformation at high resolution with current experimental technology.