Research at the Frederickson lab
Over the past year I've worked at the Frederickson lab at the University of Toronto. The lab focuses on the study of mutualisms, specifically between different species of Duckweed and their microbiome.
I've worked on two projects over the course of my research. The primary project studies the changes in the microbiomes of Duckweed over different timepoints, in different culturing media, and over the rural to urban gradient. I've been responsible for analyzing the 16S sequence data and performing statistical tests to determine the dynamics of the microbial repertoire. The second project focuses on the assembly of a triploid genome for Duckweeds. I'm responsible for the analysis of coverage and synteny of the resulting assemblies. Here is a link to the project GitHub.
Animations and Algorithms
Creating mathematical visualizations and animations is one of my hobbies. I've done visualizations in topics such as computational geometry, fractals, number theory, and probability. Most are implemented using Python and libraries such as Matplotlib. To the left is an example of an algorithm which can draw any image using a set of lines. More of these animations are presented and explained here.
UpKeep
As I'm heading into my final year at UofT I've noticed that as the number of courses I've taken increases it is harder to maintain everything I've learned. I got the idea to create an application called UpKeep which can extract questions from the pdf of a textbook and then give you a random question from any of the textbooks you have stored.
I implemented this idea in Python and tied it to a html interface where users can add and remove textbooks and get a random question from any of the stored textbooks. The application works for certain textbooks but doesn't for others as pdf to text isn't perfect and the application runs off the assumption that questions are denoted by numbers followed by a period.
Here is a link to the project GitHub.
Research at the Princess Margaret Cancer Centre
From 2019 to 2023, I worked at the Princess Margaret Cancer Research Centre on a research project in the Pugh Lab. The project utilizes a novel TCR sequencing method known as CapTCR for non-invasive immune monitoring of solid-tumour patients given adoptive T-cell therapy.
This project has developed my ability to run bioinformatics pipelines on large multi-omics datasets as well as perform visualization and statistical analysis in R, Python, and Excel. In addition, this project has developed my ability to write manuscripts, perform literature reviews, and work with other researchers in a lab environment. The figure to the right is an example of clone tracking, one of the main visualization techniques in the project.
I've had the opportunity to present my research at the Trans-Atlantic Journeys in Cell and Gene Therapy joint meeting between researchers at the University of Toronto and the University of Manchester.
Here is a link to the project GitHub.
Immune 2.0
A part of the Pioneer international competition, my partner Ahmed Moselhi and I developed Immune 2.0. The project used a machine learning alrgorithm to predict T-cell binding. This algorithm would allow for rapid testing of new vaccines and immunotherapies. Immune 2.0 ended up becoming a winning project a part of the April 2019 cohort. We were also interviewed by Laura Deming about the project.Link to video.
CaMS-Vis: Cancer Mutational Signature Visualization
The construction of mutational catalogues are necessary for the analysis for mutational signatures for many genetically-associated diseases but are highly studies in cancer. Visualizations from variant called files are necessary for these analyses. CaMS-Vis is a tool for the visualization of mutational catalogues based on grouping into the 6 mutation classes and 96 mutation types from a binary variant call format (bcf) file.
The GitHub can be accessedhere.
Various Research Proposals
The ability to write a research proposal is an important skill in academia. Over the past few years, I've written a few research proposals in the molecular biology space.
Production of Highly Variable Hemagglutinin Antigens by Lactococcus lactis populations as a basis for an evolving vaccine
The rapid mutation of viral antigens results in the decreased efficacy of vaccines, and the need for consistent boosters and our yearly flu shot. This research proposal revolves around the idea of creating a vaccine which can evolve with viral antigens. The overall idea was to develop a bacteria which can release antigens into the blood stream as a vaccine would do. But this vaccine would carry the ability to continuously mutate the gene coding for the antigen, allowing us to simulate (and follow) the antigenic drift of the viral antigen.
The research proposal can be foundhere.
Surface-Engineered Lentiviral for Targeted Chimeric Antigen Receptor Transduction on T-memory stem cells
During my research at the Princess Margaret Cancer Research Centre, I noticed the selective expansion of rare T-cell clonotypes. What this means is that there are few T-cells which have a high proliferative capacity in vivo. I hypothesized that these clonotypes could have a T-memory stem cell phenotype. This proposal, aims to demonstrate the use of CAR T-cell therapy to target these T-cell with high proliferative capacity in order to increase the efficacy of novel cancer immunotherapies.
The research proposal can be foundhere.
Increasing Somatic Telomerase Expression through Inhibition of the SUV39H1/SUV39H2 Methyltransferases using PEGylated Liposomes
Longevity is an emerging field in molecular biology with large philosophical implications and lots of biological problems. This research proposal aimed to eliminate the shortening of our telomeres (one of the causes of aging) through epigenetic manipulation. Along with my group, I presented this proposal at the University of Toronto Student Society for Stem Cell Research case study competition and was awarded first place.
The research proposal can be foundhere.