Training Program

Program Structure

The QuantOmics training program is anchored in the central theme of technology-enabled drug and vaccine discovery, which serves as the unifying thread for all technical training. HQP do not learn skills in isolation — they understand how their work contributes to a larger, translational goal.

Training is organized across three interconnected streams that form a complete research pipeline:

• Stream 1 (S1): Quantum Probe Design & Fabrication — students from NSE (Physics, ECE) enter here
• Stream 2 (S2): Genomics Signal Integration — students from Computational Biology, Molecular Genetics enter here
• Stream 3 (S3): AI-Powered Therapeutic Design — students from Computer Science, Biomedical Engineering enter here

With the circular and interconnected nature of the streams, HQP start based on their background and take courses in sequence along the flow of streams to capture interdisciplinary knowledge.

(A) Technical Courses & Training

QuantOmics offers five specialized courses designed to provide all trainees with a common language and foundational knowledge base:

Course 1.1 — Biosensor Engineering for Precision Health

18 hours · On-demand online · Instructors: Valente, Ruda, Mahshid

Covers the fundamentals of microfluidics, biochemical capture layers, CMOS/MEMS integration, photonic and electrical read-out, and signal-conditioning electronics. Establishes core design vocabulary for quantum biosensor development.

Mandatory for PhDs. MSc students complete minimum two courses (chosen with supervisor).

Course 1.2 — Quantum Nanotechnology for Life Sciences

18 hours · On-demand online · Instructors: Impellizzeri, Rayan

Dives into NV-center physics, quantum-dot synthesis, spin-based magnetometry, and noise-limited detection. Provides the quantum physics foundation underpinning all Stream 1 research.

Mandatory for PhDs. MSc students complete minimum two courses.

Course 1.3 — AI in Genomics

18 hours · On-demand online · Instructors: Khan, Andrews, Corbeil, Simpson

Covers representation learning for sequence data, multimodal fusion, and trustworthy clinical AI. Topics include CNNs for regulatory genomics, RNNs and Transformers for sequence modeling, and techniques for integrating genomic, transcriptomic, proteomic, and clinical data.

Mandatory for PhDs. MSc students complete minimum two courses.

Bootcamp 1.4 — Multimodal-Omics Data Integration

3 weeks intensive · Hybrid delivery · Instructors: Khan, Trost Mandatory for ALL graduate trainees

A hands-on intensive where trainees build complete analysis pipelines that fuse sensor signals, nanopore reads, methylation maps, and EHR features. Three weeks of focused, immersive learning:

Offered once yearly. All graduate trainees must complete this bootcamp.

Course 1.5 — Responsible Innovation & EDI in Precision Health

Quarterly seminars · Live online · Instructors: Impellizzeri, Khan + guest speakers Mandatory for ALL graduate trainees

Examines regulatory pathways, inclusive design, and Indigenous data sovereignty. Topics include:

• Creating inclusive, unbiased, and explainable clinical AI
• Ethical frameworks for Indigenous data sovereignty and community consent
• Navigating regulatory pathways for equitable access to new therapies
• Bias and fairness in genomic AI models
• Responsible quantum technology development

Quarterly seminars throughout the program. Trainees complete at least two sessions.

(B) Experiential Learning

Bi-Monthly Research Seminars

A central component of QuantOmics training is a bi-monthly seminar series featuring world-renowned experts in quantum sensing, genomics, and AI-driven medicine. Held year-round, these seminars cover foundational theories, cutting-edge research, and case studies. All presentations are recorded and made publicly available.

Graduate trainees are required to attend at least 3 seminars per year.

Triennial QuantOmics Symposiums & Job Fairs

A 3-day national symposium is held in Years 3 and 6, alternating between TMU (Toronto) and Université Laval (Québec City). The event features:

• Keynote speakers from academia, industry, and government
• Trainee research presentations with feedback from expert panels
• A concurrent job fair connecting trainees with potential employers from pharma, biotech, government, and academia
• Networking sessions and stakeholder panels

Co-located Workshops at IEEE Conferences

A half-day QuantOmics workshop is held in Years 2, 4, and 5, co-located with major international IEEE conferences (e.g., IEEE Sensors, IEEE BIBM). This provides a premier venue for trainees to:

• Present peer-reviewed work to global experts
• Gain international visibility and feedback
• Build connections with the broader research community

Annual “Personalized Vaccine Design” Challenge

A biennial team hackathon where trainees form interdisciplinary teams to tackle a real-world vaccine design challenge from end to end — from sensor-based biomarker detection through genomic analysis to AI-guided neoantigen prediction. Teams present their solutions to a panel of industry and academic judges.

Innovation Studio Series

A biennial series of structured design sprints where mixed-discipline trainee teams apply the QuantOmics pipeline to novel biomedical problems. Developed in partnership with industry advisors to mirror real-world R&D environments.

Quarterly Technical Tutorials

Hands-on tutorials delivered by senior PhD students and postdoctoral fellows covering specific laboratory techniques and computational tools — operating advanced sequencing platforms, using specialized bioinformatics pipelines, and implementing novel ML frameworks on HPC clusters.

Optional, but trainees are strongly encouraged to attend.

(C) Professional Skills Development

QuantOmics is committed to developing not just excellent researchers, but future leaders who are career-ready. Our professional skills curriculum is structured around the four key domains identified by the Canadian Association for Graduate Studies (CAGS):

The “Translational Trajectory” Mentorship Trio

Every graduate trainee is supported by a structured trio:

1. Primary Supervisor — deep expertise in the trainee’s home stream
2. Co-supervisor — from a complementary QuantOmics stream at a different institution
3. Industry Advisor — from a partner organization, providing real-world perspective

This trio structure guarantees interdisciplinary training and industry connectivity from day one, preventing the development of intellectual silos.

Workshops on EDI Principles & Professional Skills

Trainees must complete:

• Minimum two EDI workshops — covering topics such as anti-racism, unconscious bias, and inclusive research design
• At least one annual professional skills workshop — covering leadership, communication, project management, and career planning

Resources are drawn from institutional programs across all partner universities, including TMU’s Future Smart, UofT’s GradProSkills, Queen’s SGS workshops, McGill’s SKILLSETS, Université Laval’s EDI Action Plan, and USask’s EDI initiatives.

Trainee Mobility

All MSc and PhD trainees complete a mandatory mobility placement:

Option A — Inter-Lab Academic Exchange: Spend time in the lab of a QuantOmics co-applicant at a different discipline and partner university, placed in a different stream of the research pipeline.

Option B — Industrial R&D Internship: Undertake an internship at one of our supporting partner organizations (C2MI, Epiloid Biotech, Terry Fox Research Institute, Ontario Genomics, Klick Health, Alimentiv, Novavax, and others).

Program Deliverables Summary

For questions about specific courses or program requirements, contact n77khan@torontomu.ca