Date of Award


Document Type

Open Access Dissertation

Degree Name

Doctor of Philosophy in Computational Science and Engineering (PhD)

Administrative Home Department

School of Forest Resources and Environmental Science

Advisor 1

Hairong Wei

Committee Member 1

Laura E Brown

Committee Member 2

Qiuying Sha

Committee Member 3

Victor B Busov


In the era of genetics and genomics, the advent of big data is transforming the field of biology into a data-intensive discipline. Novel computational algorithms and software tools are in demand to address the data analysis challenges in this growing field. This dissertation comprises the development of a novel algorithm, web-based data analysis tools, and a data visualization platform. Triple Gene Mutual Interaction (TGMI) algorithm, presented in Chapter 2 is an innovative approach to identify key regulatory transcription factors (TFs) that govern a particular biological pathway or a process through interaction among three genes in a triple gene block, which consists of a pair of pathway genes and a TF. The identification of key TFs controlling a biological pathway or a process allows biologists to understand the complex regulatory mechanisms in living organisms. TF-Miner, presented in Chapter 3, is a high-throughput gene expression data analysis web application that was developed by integrating two highly efficient algorithms; TF-cluster and TF-Finder. TF-Cluster can be used to obtain collaborative TFs that coordinately control a biological pathway or a process using genome-wide expression data. On the other hand, TF-Finder can identify regulatory TFs involved in or associated with a specific biological pathway or a process using Adaptive Sparse Canonical Correlation Analysis (ASCCA). Chapter 4 presents ExactSearch; a suffix tree based motif search algorithm, implemented in a web-based tool. This tool can identify the locations of a set of motif sequences in a set of target promoter sequences. ExactSearch also provides the functionality to search for a set of motif sequences in flanking regions from 50 plant genomes, which we have incorporated into the web tool. Chapter 5 presents STTM JBrowse; a web-based RNA-Seq data visualization system built using the JBrowse open source platform. STTM JBrowse is a unified repository to share/produce visualizations created from large RNA-Seq datasets generated from a variety of model and crop plants in which miRNAs were destroyed using Short Tandem Target Mimic (STTM) Technology.