Details

Autor(en) / Beteiligte

• Chen, Xintong

Titel

Surveys of Genomic and Transcriptional Landscapes with Sequencing Technology

Ort / Verlag

ProQuest Dissertations & Theses

Erscheinungsjahr

2018

Quelle

ProQuest Dissertations & Theses A&I

Beschreibungen/Notizen

• Next generation sequencing technology has evolved rapidly in the past decade, propelling the reach of modern biomedical research to unprecedented resolution and scale. In this thesis, I investigated genomic and transciptome complexity by developing methods which leverage third generation sequencing to tackle important open biological questions. I first introduced a tool that we developed for detection of one of the most problematic types of genomic sequence variations – transposons. We applied the tool to high coverage PacBio datasets and showed that our tool not only outperforms Next-Generation Sequencing (NGS) short read tools but also retains high accuracy with low coverage data. Next, I considered the transcriptomic complexity of alternative splicing in two cancer cell lines subjected to drug treatment. We performed short read and long read RNA-seq experiments on treated cells, quantified nontrivial long-read derived splicing signals with short-reads through integrative analysis, and proposed a novel annotation procedure.