John Parkinson

Dr. John Parkinson is a computational biologist and Senior Scientist at the Hospital for Sick Children, with cross-appointments in the Departments of Biochemistry and Molecular Genetics at the University of Toronto. His research integrates computational systems biology and comparative genomics to study parasites, pathogens, and microbiomes, focusing on their evolutionary strategies and host interactions.

• Roles: Research Professor, Computational Biologist, Senior Scientist
• Collaborations: Works with clinicians, parasitologists, immunologists, and bioinformaticians
• Platforms: Utilizes SciNet (University of Toronto's HPC)

His research spans three main areas: (1) computational and experimental analysis of parasite genomes, (2) microbiome dynamics in diseases like cystic fibrosis and IBD, and (3) evolutionary innovations in pathogens. Techniques include metagenomics, network biology, and constraint-based metabolic modeling.

Key trends across his publications include cross-species genomic comparisons, metabolic pathway elucidation in parasites, and functional interrogation of microbiomes through metatranscriptomics. Collaborative work on apicomplexan parasites (Toxoplasma, Plasmodium) highlights evolutionary strategies for host persistence.

Scientific Awards

• CIHR New Investigator (2006-2011)
• Ministry of Research and Innovation - Early Researchers Award (2007-2012)
• NATO Postdoctoral Fellowship (1995-1996)
• Wellcome Trust Mathematical Biology Fellowship (1991-1995)

Trainees in the Parkinson Lab acquire expertise in machine learning, metagenomics, and bioinformatics pipelines, supported by access to high-performance computing and wet-lab facilities for Toxoplasma proteomics. The lab maintains active collaborations with clinicians and international sequencing consortia.