Ph.D. Final Oral Exam: Fathi Mubaraki

Fathi Mubaraki
Friday, November 20, 2020 - 2:15pm
Event Type: 

Location: Zoom

PhyloVirus: Inferring virus reassortment and a visualization tool for phylogenetic networks (Development and Usability Study).

Objective: Traditional virus evolution studies rely on single-gene phylogenetic trees that do not account for all these processes. Phylogenetic network algorithms can do so but are hampered by computational limitations. We introduce an efficient software package with a graphical user interface called PhyloVirus that can assist in identifying novel Virus Reassortment such as influenza A viruses. Involving people in the early stage of the system development will direct to more usable and beneficial applications. Our objective of conducting the usability study is to advance our perception of the current usability issues on software usage based on unique reference points.

Methods: After finishing developing the software called “PhyloVirus: Inferring virus reassortment, and a visualization tool for phylogenetic trees and networks.”, we invited molecular biologist people, bioinformaticians, and geneticists in the usability study for our software. The study aims to evaluate the software and investigate the usability issues. This research work examines how PhyloVirus is applied to achieve a series of tasks. All participants have received the same procedure: training protocols and a series of quantitative tasks followed by a subjective satisfaction questionnaire.

Results: PhyloVirus can assist in identifying novel Virus Reassortment such as influenza A viruses. By applying the User Experience method, we found that participants can generate (compute and visualize) phylogenetic trees/networks using PhyloVirus software. Participants can detect and visualize recombination, lateral gene transfer, and novel reassortment events.

Conclusion: We developed software for inferring and visualizing evolutionary trees and networks, and applied it to IAV H3N2; we recapitulated known reassortment events, detected novel events. Researchers such as molecular biologists, bioinformaticians, and geneticists may benefit from a deeper understanding of the virus’s evolutionary using PhyloVirus. Furthermore, there is an expected advantage to the participants, who may use the system in future research.

Committee: Oliver Eulenstein (major professor), Phillip Gauger, Leslie Miller, Tavis Anderson, and Xiaoqiu Huang