RNA splicing projects in the Knowles lab

1. My first python package LeafletSC is available on github. LeafletSC is a binomial mixture model designed for the analysis of alternative splicing events in single-cell RNA sequencing data. It relies on splice junction counts to infer meaningful cell populations driven by splicing differences.
2. We released a new R package called Isoviz that allows users to clearly visualize splice junctions across transcript isoforms expressed in their cell line of interest. Several visualizations are available as well as a function to design gRNA sequences to target junctions of interest with CRISPR/Cas13 using our lab’s deep learning model TIGER. The Isoviz R package is available on github. Find the pre-print here.
3. IsovizPY coming soon!

Course projects @ Columbia PhD program

Here are some class projects that I have worked on so far:

Predicting COVID-19 RNA-protein interactions

https://github.com/msthilaire5/ecbm-e4060-covid-interactions

Protein sequence-based pathogen assembly from RNA-seq

https://github.com/karini925/VORF

Lymphoma research

From May 2019 to July 2021, I worked in Dr. Robert Kridel’s lab at UHN, Toronto. There, I contributed to several manuscripts focused primarily on functional genomics research in Lymphoma. For example, I created a shiny based website to visualize a patient risk model that combines the PET-CT scan based Deauville score and other clinical risk factors.