A survey of ancient paralog expression patterns in Arabidopsis thaliana root cell-types
TBD
CV
Education
- B.Sc.(Honours) in Genome Biology and Evolutionary Biology, University of Toronto, 2015
- M.Sc. in Genome Science and Technology, University of British Columbia, 2019
Work experience
- 2020-2021: Bioinformatician at Canexia Health
- Helped develop a plasma-based oncogenomic panel targeting low-VAF mutations from cfDNA
- Assisted with longitudinal cancer studies
- Optimized FFPE-based cancer screen
- 2017-2019: Graduate Researcher (Adams Lab)
- Generated lab pipelines forthe analysis of duplicate gene expression
- Developed a pipeline forthe detection and quantitative comparison of alternative splicing events
- Supervised an undergraduate research project with the goal of familiarizing the student with HPC best practices using Compute Canada resources
- Performed the role of lab server administrator
- Completed two projects pertaining to evolutionary plant transcriptomics (see below for more detail)
- 2015: Research Assistant
- University of Toronto, Frederickson Lab
- Overview: Supported a project involving the genomic background of legume-rhizobium mutualisms.
- Supervisor: Dr. Megan Frederickson
- 2014-2015: Research Assistant
- University of Toronto, Gilbert Lab
- Overview: Identified and sorted insect samples to order and family in assistance of project involving the migrationrates and colonization of insects inAsclepias syriacametapopulations
- Supervisor: Dr. Benjamin Gilbert
- 2014: Research Assistant
- University of Toronto, Stinchcombe Lab
- Overview: Assisted with a number of projects examining the ecological genomicsunderlying Medicagorhizobia mutualisms.
- Supervisor: Dr. John Stinchcombe
- 2013-2014: Research Assistant
- University of Toronto, Diamond Lab
- Overview: Sample preparation for and performance of gas chromatography-mass spectrometry.
Skills
- Programming
- R
- Python
- Genomics
- RNA-seq data analysis (NGS, single-cell)
- NGS tools (e.g. samtools, bowtie and STAR, variant detection)
- Bisulfite sequencing analysis
- Phylogenomic methods
- Machine Learning
- Regression
- K-Nearest Neighbors
- Cluster Analyses
- Technical
- HPC best practices
- Bash scripting
- Pipeline development
- Git and Github
- Microsoft Azure
- Server administration
- Biological
- Sequencing library preparation (Illumina)
- General wet-lab techniques (e.g. PCR, vector cloning, RNA and DNA extractions)
- Gas chromatography—mass spectrometry
Projects
- Analysis of multiple Brassica transcriptomes under pathogen stress from Sclerotinia sclerotiorum
- Designed an experiment investigating S.sclerotinia infection of Brassica species and performed RNA-seq to generate transcriptome data
- Performed a priori analyses of synteny on the subgenomes of polyploid Brassica napus and its parental genomes to identify homeolog-ortholog relationships
- Created pipelines to (1) generate gene expression data (2) generate junction-specific alternative splicing data
- Investigated Brassica responses to fungal necrotrophs and how interspecific hybridization mightresult in non-parental transcriptome responses to such stress
- A survery of ancient paralog expression patterns in Arabidosis thaliana root cell-types
- Created pipeline to generation expression and alternative splicing data using publicly available cell-specific RNA-seq data
- Performed analyses exploring the evolution of ancien duplicate gene expression between Arabidopsisthaliana root cells
Publications
Talks
Introduction to RNA-Seq informatics
Tutorial at University of British Columbia, BIOL430, Vancouver, British Columbia
A survey of ancient paralog alternative splicing patterns in Arabidopsis thaliana root cell-types
Lightning talk at University of British Columbia, Department of Botany, Vancouver BC, Canada
Evolution of paralog gene expression patterns among paleopolyploid and cytogenetically polyploid plants
Exit seminar at University of British Columbia, Department of Botany, Vancouver BC, Canada
Transcriptomic response of multiple Brassica species to Sclerotinia sclerotiorum infection
Talk at University of Guelph, Plant Canada Conference, Guelph, ON, Canada
Teaching
Awards
University of British Columbia
- Genome Science and Technology Rotation Award (2016-2018)
- Awarded funding to rotate through several labs and learn a variety of genomic technologies
- Awarded tuition funding for two years
University of Toronto
- Dean’s List (2012-2015)
- University College In-Course Excellence Scholarship (2013)
- University of Toronto Presidents Entrance Scholarship (2011)
Other
- Excellence in Technology Skills (2011)
- Demonstrated technological aptitude at Skills Ontario, placing second in Arcitectural Programming
Service and leadership
- Supervised an undergraduate honours thesis and GSAT MSc rotation projects
- Moderated the Adams lab personal server
- Set up the Adams lab Compute Canada account
- Created and moderated the Adams lab slack