Instructors

Aaron Petkau is a bioinformatician working for the Public Health Agency of Canada’s National Microbiology Laboratory and the current Head of Bioinformatics Pipeline Development within the Bioinformatics unit of the laboratory. His work primarily focuses on the development of bioinformatics software for infectious disease genomics. Some of his projects have included: developing tools for comparative genomics (GView and GView Server), phylogenetic analysis of microbial genomes (SNVPhyl), the management of genomics data (IRIDA), and indexing, querying, and visualization of mutations or genes derived from collections of microbial genomes (Genomics Data Index). He is currently focused on the development and integration of a diverse set of bioinformatics pipelines into a larger system for routine use within the Public Health Agency of Canada.

Alexandre Reynaud obtained a PhD in Neurosciences from Aix-Marseille Université (France) and a MSc in Computer Sciences from Université de Nice Sophia-Antipolis (France). His research focuses on human visual perception and particularly binocular vision. To study those, he develops computer-based psychophysics, behavioral experiments. His research also focuses on a more clinical/translational aspect: the study of amblyopia, a neurodevelopmental condition which emerges during childhood and results in deficit of binocular vision. He tries to understand and develop treatments for this condition based on digital technologies and digital therapies. 

Her research is focused on understanding intratumoral heterogeneity, tumor evolution, and the tumor microenvironment at single cell resolution. She uses computational approaches to analyze, integrate, and interpret large-scale genomic data, with an emphasis on single-cell RNA-sequencing data. She completed a PhD in Genetics in the laboratory of George Church at Harvard Medical School, and a postdoctoral fellowship in Systems Biology with David Botstein at Princeton University. She was Research Faculty under the mentorship of Tim Ley at Washington University and the McDonnell Genome Institute.

Alysha Cooper is a current PhD candidate in Applied Statistics at the University of Guelph, with her research focusing on optimization of multivariate count outcome models for gut microbiome analyses. Before pursuing her doctoral studies, she gained valuable experience as a data analyst at the Homewood Research Institute in Guelph, ON. Alysha continues to work within the field of mental health and addictions as a part-time data analyst at the Peter Boris Center for Addictions Research in Hamilton, ON.

Amin is a bioinformatician and a PhD student in Dr. Mitchell’s lab in the Department of Cell and Systems Biology at the University of Toronto, focusing on enhancer logic, chromatin accessibility, and 3D genome organization. He uses Python and R to develop computational frameworks that integrate single-cell and bulk epigenomic data, aiming to uncover how genome architecture regulates gene expression. His research is focused on analyzing enhancer-promoter interactions and their role in controlling cell identity during development and disease.

I conduct interdisciplinary research that integrates techniques and methods from machine learning, human computer interaction, and data visualization. I analyze data, build tools, and conduct evaluative studies. My research focuses on the intersection of Data Science and Data Visualization. I am especially interested in the way humans can collaboratively work together with ML/AI systems through visual interfaces. I completed my PhD in Computer Science at the University of British Columbia, where I was jointly advised by Tamara Munzner and Jennifer Gardy. Prior to my PhD, I was a research scientist at the British Columbia Centre for Disease Control and Decipher Biosciences, where I conducted research machine learning and data visualization research toward applications in infectious disease and cancer genomics.  My research has appeared in publications of the ACM (CHI), IEEE (TVCG, CG&A), Oxford Bioinformatics, and Nature.

Andres is a Software Engineer and holds an MSc in Business Information Technologies. He is currently a PhD candidate in Medical Biophysics at the University of Toronto, where his research focuses on leveraging Large Language Models and Knowledge Graphs for advanced healthcare data structuring and analysis. Andres has prior experience as a professor and programming course coordinator at Universidad de Los Andes, Colombia, and as an instructor at the Humber Polytechnic, Toronto.

Dr. McArthur is a Professor and David Braley Chair in Computational Biology at McMaster University and has had a career in the United States and Canada, including NIH-funded positions at the Marine Biological Laboratory and Brown University, where he led the genome assembly of the diarrheal pathogen Giardia intestinalis, plus 10 years of experience in the private sector. Dr. McArthur’s research team focuses on building tools, databases, and algorithms for the genomic surveillance of infectious pathogens. He and his team developed the Comprehensive Antibiotic Resistance Database (card.mcmaster.ca) and the SARS-CoV-2 Illumina GeNome Assembly Line software platform.

Andrew McPherson is an Assistant Laboratory Member at the Memorial Sloan Kettering Cancer Center in the Department of Epidemiology and Biostatistics under the supervision of Dr. Sohrab Shah. Andrew completed a PhD in computing science at Simon Fraser University under the supervision of Dr. Cenk Sahinalp and Dr. Sohrab Shah, focusing on methods for sequencing analysis, including detection and characterization of genome rearrangements, and inference of clonal phylogenies. During his post-doctoral research at University of British Columbia with Dr. Sohrab Shah, Andrew focused on the development of computational methods and infrastructure for a novel single cell sequencing plaform, Direct Library Preparation. Andrew moved to MSKCC in May of 2019 and plans to build on his post-doctoral work in single cell genomics to understand genomic instability, mutational processes, clonal evolution and the role of the microenvironment in cancer development and progression.