Q: What does your research primarily focus on?
A: My research focuses on understanding alternative splicing and its role in disease. One of the tools that we can use to understand alternative splicing is long read RNA sequencing.
I work in two labs and I have two advisors. Dr. Rolf Renne and Dr. Lauren McIntyre. In Dr. McIntyre’s lab I work more on the method developments like developing computational tools to evaluate long read RNASeq experiments and to understand how best to apply it to understanding alternative splicing. In Dr. Renne’s lab I am applying those tools to understand splicing in the context of Kaposi’s Sarcoma associated Herpesvirus (KSHV) infection. This virus is known to cause cancer in immunosuppressed individuals for example in individuals with HIV-AIDS, and it is most prevalent in sub-Saharan Africa. Infection with this virus can lead to cancer so I am trying to understand how alternative splicing can play a role in the development of cancer in individuals infected with KSHV.
Q: What first interested you in this area of research?
A: In undergrad, I worked in a lab studying malaria and so I became really interested in understanding how the human host and malaria pathogen interact with each other, like how the host can control the pathogen and in turn how the pathogen can attack host cells to facilitate its reproduction. I studied transcriptomics and how the malaria parasite affects the gene expression of the host and vice versa. When I came to UF, I knew that I wanted to continue studying transcriptomics in the context of host pathogen interactions. When I learned about these viruses that could cause cancer, it comprised my interest in transcriptomics of host-pathogen interactions and alternative splicing, while also adding a new interesting layer of cancer.
Q: Where did you do your undergrad?
A: NYU in Abu Dhabi. I went very far!
Q: Have you received any other awards as a genetics and genomics graduate student?
A: I’m going to take a step back. So as I said, I work a bit on tool development. We have a collaborator in Spain (Dr. Ana Conesa) and she originally developed SQANTI3, a tool for evaluating the quality of transcriptomes generated from long read RNASeq data. She is a close collaborator to Dr. Mcintyre. In working with a lot of long read RNASeq data sets, including datasets of Type I diabetes patients, Drosophila (fruit flies), and also KSHV infected cells, I saw a need for a tool to evaluate and compare the quality of multi-sample long read RNASeq experiments. As the long read RNASeq technologies continue to improve, we can generate more reads for the same price. So there's more multi sample experiments and datasets being generated. I had the idea to develop SQANTI-reads, which is based on SQANTI3, that can be applied to multiple samples.
I presented the metrics in SQANTI-reads at the Long Read Sequencing Uppsala Conference (2024), where I gave a three minute Flash talk at a conference in Uppsala, Sweden. I won the Best flash talk award there. Receiving that award was really encouraging, because I didn't know how I was going to be able to present six months’ work in three minutes. The flash talk allows you to give a pitch to the audience and encourages them to come to your poster to find out more. It was really motivating to get feedback from all the conference attendees, because this conference was attended by many of the leaders in long read sequencing and their feedback has helped me to improve the tool for users. I also presented SQANTI-reads as a poster at the UFGI Symposium, and I won the Best Graduate Student Poster Award. It was very rewarding, because while working on a tool like this you sometimes think, is anybody going to care and use this tool? I’m hopeful that SQANTI-reads will become the go-to tool for scientists to evaluate their long read RNASeq experiments.
Q: When do you defend your PhD thesis?
A: Probably Spring or Summer of ’26.
Q: What would you like to do after defending your PhD Thesis?
A: I am mostly undecided. Half of me wants to stay in academia and understand more about the pathogenesis of KSHV and other oncogenic viruses. There are seven known human oncoviruses. It has been shown by other groups that KSHV can infect one endothelial cell type, blood endothelial cells, and cause it to take on a different cell identity, lymphatic endothelial cells, leading to a de-differentiated phenotype. We also know that de-differentiation is a hallmark of cancer and that some other viruses can cause their host cells to de-differentiate. So, I want to spend the next few years of my research career trying to determine if de-differentiation is one of the mechanisms that other oncogenic viruses might use to drive oncogenesis.
The other half of me, wants to go into tool development for biotech. As technologies develop and new experimental approaches emerge, the bioinformatics usually lags behind the actual technology. There is often a gap between the development of the experimental technique and the computational and statistical methods for scientists to make meaningful and accurate interpretations from their data. I think I would really enjoy a career trying to fill that gap.
Q: What do you find rewarding about your research?
A: I really like the fact that I work both on the computational side and the wet lab side. When I first came to UF I started off in Dr McIntyre's lab, and I really enjoyed the computational tool development, but I felt really compelled to generate my own dataset from scratch. It’s making my PhD longer and more complicated by having to do my own experiments. But I find it really rewarding to see the experiment through from beginning to end. And I feel like, by the end of my PhD, I'll come out a well-rounded scientist and even if I become a primarily computational researcher, I will have a good appreciation and understanding of the molecular processes underlying my research questions.