Skills

Bioinformatics

DNA sequence analysis & software design

Statistics

Application and interpretation

Python

Data analytics & machine learning

R

Data cleaning, visualization & statistical analysis

Git and Github

Project management & version control

Command line

large-scale data analysis on remote access servers

Scientific writing

Linux and Unix

DNA Barcoding

Experience

 
 
 
 
 

Postdoctoral Researcher

University of Guelph | Centre for Biodiversity Genomics

May 2019 – Present Guelph, On
Research projects:

  • Design of an alignment-free DNA classifier, alfie. The program uses a neural network to rapidly assign kingdom-level taxonomic classifications with greater than 99.5% accuracy and no sequence alignment.
  • Created coil, an R package for alignment, translation and error evaluation of COI-5P barcode data. Available on CRAN
  • Created debar, an R package for the identification and correction of technical errors in high-throughput DNA sequencer outputs for the DNA barcode, COI-5P. Available on CRAN
 
 
 
 
 

PhD Student

University of Guelph | Department of Integrative Biology

Sep 2014 – Apr 2019 Guelph, On
Research projects:

  • Characterized the genetic basis of important Arctic charr aquaculture traits.
  • Designed a custom 87K SNP genotyping array for Arctic charr.
  • Contributed to the assembly of the Arctic charr reference genome.
  • Constructed a linkage map for the Arctic charr genome.

Recent Posts

R’s tryCatch function is a great tool that helps facilitate robust error handling. It lets you try to run a block of code and if an …

As part of my current postdoctoral research I’ve built the R package coil, which is designed to aid users in DNA barcode data cleaning …

Note: Here you will find the raw RMarkdown file for this post, in case you want to follow along and execute the code yourself! …

Older readers of this post may remember the boot screen from Windows XP. This featured a load bar that was there to essentially give a …

When applying a function to a vector, list or dataframe column, your first instinct may be to iterate across the series of inputs. By …

Research Summary

Summary of my postdoctoral research

Biodiversity is declining across the globe. Global wildlife populations have declined by an estimated average of 60% over the last 40 years and one million species are now threatened with extinction. If we hope to maintain the health of ecosystems and stop the loss of biodiversity, informed conservation and management practices are required. Unfortunately, there is a lack of fundamental information available about existing biodiversity within a large portion of the world’s ecosystems. In fact, we still don’t know exactly how many species there are on the planet, let alone where they can all be found or which are facing the most dire threat of extinction.

The Adamowicz lab and the Centre for Biodiversity Genomics are advancing understanding of the diversity and distribution of organisms through the use of DNA barcoding and metabarcoding. My research was focused on improving the accuracy of biodiversity assessments that utilize DNA barcoding by developing statistical tools that can separate biological variation from errors that commonly arise in the methods used in DNA barcoding.

It is my hope that the software and methods I develop in my research can be utilized in the accurate characterization of biodiversity worldwide, which can in turn help inform the conservation and protection of the world’s ecosystems.

Summary of my PhD research

My PhD research was focused on characterizing the evolutionary changes that have shaped the genome of Arctic charr. Arctic charr are a salmonid, and the salmonid ancestor underwent a whole genome duplication in the relatively recent evolutionary past. In a whole genome duplication, the number of copies of each chromosome doubles (from the usual 2 copies up to 4), leading to individuals with genomes that are twice the size of their predecessors. This is followed by a process called diploidization, where the newly tetraploid genome reverts to a diploid state through chromosome rearrangements, deletion of genes and genes evolving to take on novel functions. My PhD involved the mapping of the Arctic charr genome, the identification of chromosomes that share a common ancestor, and variability in the rate of diploidization across the genome.

I addition to this, I also examined the evolution of the genetic basis of loci associated with important aquaculture traits. This involved rearing several thousand aquaculture Arctic charr over several years and collecting growth data and DNA samples along the way. In order to associate variation in their growth with genetic variation, I first designed a tool for accurately assessing Arctic charr genetic variation with high accuracy. With this I then conducted several genome wide association studies and characterized the genetic basis of body mass, fork length and sexual maturity.

Publications

Characterization of biodiversity from environmental DNA samples and bulk metabarcoding data is hampered by off-target sequences that …

Biological conclusions based on DNA barcoding and metabarcoding analyses can be strongly influenced by the methods utilized for data …

Biologic medications account for the majority of outpatient treatment expenditures for inflammatory bowel disease. The US Food and Drug …

Conference Talks