Degree Type


Date of Award


Degree Name

Doctor of Philosophy


Genetics, Development and Cell Biology


Bioinformatics and Computational Biology

First Advisor

Volker Brendel

Second Advisor

Roger Wise


In the wake of advanced DNA sequencing technology, a large number of bacterial, animal, and plant genomes have now been completely sequenced and deposited into public databases. The acceleration of genome (and transcriptome) sequence data accumulation remains unabated and poses considerable challenges for data storage, access, and transfer, with even greater challenges for comprehensive data mining to turn the genome information into knowledge.

In particular, detailed genome annotation with respect to the encoded genes and their regulation is still largely confined to a few model species. Thus, important current research problems revolve around automated genome annotation and the related question of how widely applicable insights from the model species are with respect to novel genomes. For example, what features of genome organization are conserved across species? What differences in gene repertoire correlate with clade-specific traits or related species? To what extent are elements of transcriptional regulation shared?

In this thesis, I discussed comparative genomics approaches to these questions. First, I described genome features of eight recently sequenced plant species, with standards for comparison provided by the well established model species for dicots (Arabidopsis) and monocots (rice). Secondly, I discussed software and statistical models for exploring possible cis-regulatory elements of co-regulated genes, with particular application to mapping gene expression data for a species with incomplete genome data to close model genomes.


Copyright Owner

Hong Lu



Date Available


File Format


File Size

121 pages