Department of Pathology, Division of VirologyProject Title: Automated detection and annotation of RNA virus subgenomic RNAs through analysis of public RNA-seq dataFunding: "Early Career Researcher Seed Fund Award" granted by the C2D3 Cambridge Centre for Data-Driven DiscoveryProject Description: Many +ssRNA viruses, such as SARS-CoV-2, Zika virus, Dengue virus, etc., produce one or more shorter transcripts (alongside their main polyprotein), known as sub-genomic RNAs (sgRNAs), from which additional viral proteins are translated. These sgRNAs are essential to the pathogenicity of many viruses, including the coronaviruses and flaviviruses and are important targets in drug and vaccine development.In order to understand and target viral sgRNAs, we first need to be able to identify them, however, current methods are time consuming and expensive. Publicly available RNA-seq transcriptomic datasets offer a way forward. Thus, the main aim is to develop robust computational methods to leverage publicly available high throughput sequencing data to systematically determine the sgRNA landscape of thousands of viral species. To achieve this, this project will involve the development of a computational pipeline, incorporating AI-based classification, to predict the sgRNAs for viruses found in high throughput RNA-sequencing (RNA-seq) datasets.Overall, the development of this pipeline will expand our knowledge of the molecular biology of poorly studied virus groups. It will also improve genome annotations of better known virus groups (such as coronaviruses), leading to a better understanding of the pathogenesis of these viruses and potentially allowing for novel treatment options or vaccine targets. It will also expedite the identification of sgRNAs in newly identified viruses, increasing our preparedness for future viral outbreaks.

Co-founded the Toronto Bioinformatics Hackathon: Toronto's first in-person computational biology hackathon, to be held from September 27-29.Key roles included planning the event's programs and schedule, acting as their undergraduate liaison and successfully garnering sponsorships from several UofT departments and clubs

Transitioned to a full-time summer research assistant position where I led the work on a project co-sponsored by Dr. Artem Babaian's RNAlab and Dr. Marc Meneghini's lab. Project Details:Saccharomyces cerevisiae, also known as Brewer's yeast, was the first eukaryote to have its genome fully sequenced, and is an extremely common model organism for scientific research. Viruses are the ultimate parasite, infecting virtually every single organism in nature. Fungi as well are infected by a plethora of mycoviruses (viruses which infect fungi), however, due to the commonality of Saccharomyces cerevisiae use in the lab, it is imperative to understand the complete virome of these organisms. In this study, I use the datasets generated by the 1000 yeast project—a study aiming to sequence and characterize the complete range of yeast diversity. By characterizing the RNA specific elements, I found 7 new RNA elements, including 5 novel viruses, 1 novel retrotransposon and a completely novel RNA element which we named ‘Osiris’. Through wet-lab characterization and further analysis, this will generate the complete set of RNA-based infectious agents of Saccharomyces cerevisiae

Continued working as a research assistant at the ‘RNAlab’ run by Dr. Artem Babaian, for the entirety of my year at UofT. This position was a part of the Work Study Program offered by UofT. I worked part-time ~15/week at this lab, working mainly on two projects:1. Tightening up some of the datasets and figures that we created for the Toxoplasma gondii associated Virus paper. This included:- Depositing the new viral sequences into genbank- Redoing Figures 1, 2 and 3 to reflect new evidence that was discovered.- Responding to and rewriting the paper after the reviews came back from the journal2. Investigating and creating novel detection algorithms, such as HMM models for the detection of novel Ribozymes in Viroid-like RNA molecules.

During my summer at the RNA-Based Lifeforms Lab, I worked closely with Dr. Artem Babaian and co-authored my first First-Author research paper titled: A Parasite Odyssey: An RNA virus concealed in Toxoplasma gondii. By the end of the summer, with a lot of effort from the entire lab of undergraduates to software engineers, we released our pre-print marking the lab's first publication as well!Project Abstract:There are roughly 10^12 distinct virus species on Earth, making them as abundant as there are stars in the Milky Way. Advancements in computing have ushered us into the “Platinum Age of Virus Discovery”, an era marked by exponential growth in the discovery of viruses. Stemming from this advancement, we aimed to characterize novel RNA viruses infecting neuron-associated tissue. Our hypothesis: neurological diseases of unknown etiology are caused by an infection of uncharacterized, novel RNA viruses. From a global screen for human neuron-associated viruses, we identified a novel narnavirus—Achaeavirus odysseus (Ao)—which likely infects the neurotropic parasite Toxoplasma gondii. In this study, we present in silico evidence that Ao is a plausible pro-inflammatory factor in mouse and human cells infected by T. gondii. T. gondii infects billions of people worldwide, yet prognosis of toxoplasmosis disease is highly variable, and viruses like Ao could function as a hitherto undescribed hypervirulence factor. Moreover, we explored phylogenetically proximal viruses to Ao and discovered 18 new viral species which all fall under a new genus of viruses which this paper is presenting: Achaeavirus. Overall, in this study, we rapidly analyzed millions of datasets from which we distilled a mechanistically, ecologically, and phylogenetically refined hypothesis. We predict this highly diverged Ao RNA virus is biologically a T. gondii infection, and that Ao, and other viruses like it, will modulate this disease which afflicts billions worldwide.

For a large part of my Grade 12 year in high school, I worked as a student researcher in the ‘Laboratory for RNA-Based Lifeforms’ run by Dr. Artem Babaian at the University of Toronto's Terrence Donnelly Centre for Cellular & Biomolecular Research. This lab is based in the intersection of computational biology and virus discovery. As a part of this lab, I analyze the genomes of various unknown RNA based viruses with tools and methodologies commonly used in computational biology.