Date of Award
12-15-2016
Degree Type
Dissertation
Degree Name
Doctor of Philosophy (PhD)
Department
Computer Science
First Advisor
Alex Zelikovsky
Second Advisor
Zhipeng Cai
Third Advisor
Robert Harrison
Fourth Advisor
Yury Khudyakov
Abstract
Next-generation sequencing (NGS) and mass spectrometry technologies bring unprecedented throughput, scalability and speed, facilitating the studies of biological systems. These technologies allow to sequence and analyze heterogeneous RNA populations rather than single sequences. In particular, they provide the opportunity to implement massive viral surveillance and transcriptome quantification. However, in order to fully exploit the capabilities of NGS technology we need to develop computational methods able to analyze billions of reads for assembly and characterization of sampled RNA populations.
In this work we present novel computational methods for cost- and time-effective analysis of sequencing data from viral and RNA samples. In particular, we describe: i) computational methods for transcriptome reconstruction and quantification; ii) method for mass spectrometry data analysis; iii) combinatorial pooling method; iv) computational methods for analysis of intra-host viral populations.
DOI
https://doi.org/10.57709/9440255
Recommended Citation
Glebova, Olga, "Computational Methods for Sequencing and Analysis of Heterogeneous RNA Populations." Dissertation, Georgia State University, 2016.
doi: https://doi.org/10.57709/9440255