Topic Courses

This course will focus on selected topics in Developmental Neurobiology and Mechanisms of Nervous System Disorders. Through discussion of research articles, we will explore molecular and cellular mechanisms that guide nervous system development. We will also read about exciting new concepts that link disruptions to neural wiring to the etiology of neurodevelopmental and psychiatric diseases, and that harness neurodevelopmental processes for new therapeutic strategies.

Outline: Course Syllabus

Instructors: Dr. Julie Lefebvre, Dr. Sabine Cordes

Dates: October 14 – December 9, 2025

• Orientation Oct 14
• No classes Oct 28, Nov 18
• Final assignment due Dec 16 [tentative]

Time & Location: Tuesdays 3:00-5:00 pm (LTRI 1062)

This course will focus on recent advances in the study of bacterial pathogens and the mechanisms by which they cause disease. Specifically, we will examine the virulence factors used by pathogens to infect their host, to subvert host innate and adaptive immune defenses and transmit to new cells and new hosts. The course will consist of presentations and discussion of publications (selected by students). The course grade will be based on presentations, participation in discussions, a written NSERC-style grant proposal.

Outline: Course Syllabus

Instructors: Dr. John Brumell, Dr. Jun Liu

Dates: October 15 – December 4, 2025

Time & Location: Wednesdays 10:00 am-12:00 pm (MaRS 1623)

Given recent studies documenting the wide range of viruses, both bacterial and mammalian, found in the human microbiome, the question arises as to why some viral infections induce pathologies while others do not.  This course will examine the mechanisms underpinning the pathogenesis of a number of viruses, with emphasis on the role played by viral factors and the host response to infection.

Outline: Course Syllabus

Instructors: Dr. Alan Cochrane, Dr. James Rini

Dates: October 20 – December 1, 2025

Time & Location: Wednesdays 1:00-4:00 pm (MSB 4174)

This course will cover topics related to the mechanisms underlying post-transcriptional control of gene expression.

Each week, the instructors will give a ~50 min lecture on that week’s topic.

Following the presentation the class will discuss a paper related to the topic. Students (either volunteers or chosen at random) who were not involved in that week’s presentation will present individual figures from the paper.

Outline: Course Syllabus

Instructors: Dr. Julie Claycomb, Dr. Craig Smibert

Dates: October 27 – December 8, 2025

Time & Location: Mondays 3:00-5:00 pm (MaRS 1522)

Stem cells are capable of self-renewal and differentiation into functionally diverse cell types. As these cells from patients can be phenotyped in comparison to healthy cells, they have been utilized for disease modeling and drug screens. This is an advanced discussion/journal club-oriented course covering both the general concepts and translational aspects of stem cell biology. Students will learn how stem cell biology is applied not only to understand disease mechanisms but also to help develop novel therapies. Students will read and discuss assigned papers; at the end of semester, they will submit a stem cell research plan, and review their proposals in a grant panel format. Course grades will be based on journal club presentations, proposals, and the discussions of both.

Outline: Course Syllabus

Instructors: Dr. James Ellis, Dr. Tae-Hee Kim

Dates: October 16 – November 27, 2025

Time & Location: Thursdays 1:00-3:00 pm (PGCRL 18-9701)

This course will consider recent developments in understanding the importance of extracellular vesicles in virus replication. The first class will comprise an interactive review of virus replication with particular attention to release of progeny virions and entry into the next host cell.  Subsequent classes will consist of student presentations of selected papers from the literature, along with class discussion. Papers for presentation will be distributed a week in advance of the presentation.  Assessment is based on presentation of one or more papers (depending on class size), participation in class discussion and a written assignment (Take-home exam).

This version of the course will focus on an aspect of virology that currently is attracting a lot of interest, specifically, the importance of extracellular vesicles for virus replication in cell culture and in vivo.  Contrary to what the textbooks say, it’s not just that viruses get out of infected cells when the cells disintegrate but it is now recognized that several viruses (both enveloped and non-enveloped) are released in vesicles before the cell disintegrates.  Not only do vesicles deliver progeny viruses to new target cells but they also deliver molecules that can modulate conditions within the target cells, resulting in an intracellular environment that is more, or less, conducive to virus replication.  Even commensal bacteria (part of the microbiome) in vivo produce vesicles that can protect against virus infection in animal models and presumably in us too.  Recent papers will be studied to explore different ways by which vesicles mediate proviral and antiviral effects on virus replication, thereby facilitating localized virus spread and possibly disease, or limiting virus spread, thereby protecting the host from more serious widespread infection that could be fatal.   

Outline: Course Syllabus

Instructors: Dr. Martha Brown

Dates: October 31 – December 5, 2025

Time & Location: Fridays 2:00-4:00 pm (location TBD)

Please see the Biochemistry Courses page.

The course will serve as an in depth exploration of mechanisms that program and maintain homeostasis of growth (hypertrophy) and cell division (hyperplasia) in metazoan biology. Different animal cell types, or cells from different animal tissues, display marked differences in cell size. Pancreatic acinar cells, for example, are over four times larger than their neighboring pancreatic beta cells. In proliferating cells, maintenance of cell size reflects a coordination of cell growth with rates of cell division. By contrast, in non-proliferating and terminally differentiated cells, size homeostasis exclusively depends on mechanisms that coordinate biosynthesis with turnover. To add to this complexity, both growth and cell division are exquisitely tuned to the balance of mitogenic (proliferative) signals, energy status and nutrient availability.

What is the nature of the molecular program that coordinates growth, division and turnover to maintain homeostasis? While the answer to this question is not yet realized, many new and exciting mechanistic details pertaining to these processes are continuously reported. Science is a union of observations and story-telling. Driven by curiosity, we seek a narrative that weaves disparate observations into a coherent narrative. 

In this course, will rely on an in-depth exploration of literature to derive novel, experimentally testable, narratives on the subject of growth homeostasis. Particular emphasis will be placed on cell cycle checkpoints, cell size checkpoints and sensing mechanisms that respond to changes in metabolic status and nutrient availability.

Outline: Course Syllabus TBD

Instructors: Dr. Ran Kafri, Dr. Jim Dennis

Dates: TBD

Time & Location: TBD

Comparative genomics is the analysis and comparison of genes and genomes from different species. Comparisons among evolutionarily related species can often help to identify functionally important and evolutionarily conserved genes or regulatory elements. In addition to protein and DNA sequences, comparative analysis can be also extended to gene expression profiles, protein-protein interactions, genetic interactions, and regulatory interactions, which in turn help us understand the origin, evolution, and importance of these important cellular interactions.

In contrast to inter-species comparisons, population genomics compares the gene and genome sequences, gene expression or regulation among individuals within a population of the same species. For example, population genomics allows us to determine the level of genetic heterogeneity (variation) in the human population, and how such genetic variation correlates with both gross and molecular phenotypes.

In this course, we will introduce the concepts, computational and experimental methods, databases, and tools that are used in comparative and population genomics. The course will be a mixture of lectures and student presentations, where classical and contemporary papers will be discussed.

Outline: Course Syllabus

Instructors: Dr. Lincoln Stein, Dr. Zhaolei Zhang

Dates: March 25 – April 29, 2026

Time & Location: Wednesdays 1:00-3:00 pm (location TBD)

This discussion-based course will rely on student presentations of recent papers from the literature related to mechanisms of genome structure and function. We will take examples from model organisms to humans. Topics covered vary every year based on the very recent literature, but generally include DNA replication and repair, chromatin, checkpoint control, genetic instability, fundamental genetic elements (centromeres, telomeres), chromosome structure/function and inheritance during cell division. In teams, students will present and lead discussions on 2 assigned papers during the class, and will also participate in all class discussions.  Students will write a short grant proposal on a topic related to class (but unrelated to their own area of research) and participate in a peer review grant panel providing and receiving constructive feedback to/from peers on their grants.

Outline: Course Syllabus

Instructors: Dr. Bri Lavoie, Dr. Dan Durocher, Dr. Christopher Pearson

Dates: March 25 – May 13, 2026

• No class April 29, May 6 (grant submission deadline May 6)

Time & Location: Wednesdays 1:00-3:00 pm (location TBD)

Protozoans comprise a large and diverse group of eukaryotic microbes. There are dozens of protists that infects humans, which together kill over a million people every year. Protozoan parasites that infect humans include apicomplexians, kintoplastids, amoebas, and giardia. There are few treatments for these pathogens and there is still much to understand about how these protists infect hosts and cause disease. Papers selected for discussion will focus on recent advances in protozoan evolution, invasion and virulence mechanisms, and development of therapeutics. There will be a specific emphasis placed on new technologies that are driving discoveries in these challenging organisms. Student grades will be based on written assignments, presentations, and participation in discussions.

Outline: Course Syllabus

Instructor: Dr. Aaron Reinke

Dates: February 2 - March 9, 2026

Time & Location: Mondays 10:00 am-12:00 pm (MaRS 1622)

• No class will be held on Mon Feb 16 due to Family Day; the course will instead be held on Fri Feb 13 (10:00 am-12:00 pm) in MaRS 1522.

Microbes do not operate in isolation but rather form complex communities featuring intricate relationships based on for example, competition or mutualism. Over the past decade there has been increasing recognition that disruptions in these communities, particularly within the human gut, are associated with an ever increasing variety of diseases including inflammatory disorders such as diabetes, inflammatory bowel disease as well as those impacting mental health. To provide more mechanistic insights into how changes in gut communities may contribute to disease, next generation sequencing technologies provide exceptional opportunities to study not only how these communities are structured, but also how they function. To date, most studies have relied on the use of 16S rRNA sequence surveys, where the 16S rDNA gene is used as a marker to define taxa present (i.e. who is there). More recently attention is turning to obtaining functional readouts through the application of shotgun DNA  and RNA sequencing (metagenomics/metatranscriptomics) to define which genes and pathways are present and active (i.e. what can they do/what are they doing). Application to of these technologies to diseases such as IBD, diabetes and malnutrition are starting to dissect the pathways by which changes in the microbiome can impact their host.

In this course we will examine how next generation sequencing technologies as well as systems modelling have been applied to the study of microbiomes. The course will feature a mixture of lectures and student-led journal presentations. A course assignment will focus on a dry-lab tutorial that takes the students through the process of analyzing a next generation sequence dataset generated from complex microbial communities.

Outline: Course Syllabus TBD

Instructor: Dr. John Parkinson

Dates: TBD

Time & Location: TBD

This course is designed to teach experimental biologists the basics and hands-on knowledge of bioinformatics programming. In today’s world, most graduate students in Molecular Genetics will encounter situations where they have to make use of computational tools and deal with datasets that are too large to practically handle manually (or with Excel). The main objective of this class is to give students the power of automation via bioinformatics programming. The class teaches by example and makes students comfortable with doing basic programming in R and adapting existing programs to their needs, as well as how to interface with standard bioinformatics software. We focus on R because it is the most popular data science and bioinformatics language and is easier to learn compared to most other programming languages. However, we will also give a brief introduction to the more general language of Python.

Prerequisite: This course is intended and required for first-year MoGen students (MSc or direct entry PhD) who do not have advanced computational biology training. Graduate students from other departments will be considered on a case-by-case basis if there is capacity. Students with advanced computational biology training (approved on a case-by-case basis by the instructors), will enrol in Foundational Computational Biology I (MMG1344; 0.25 FTE) instead of MMG1004.

Outline: Course Syllabus

Instructors: Dr. Brett Trost, Dr. Shu Wang

Dates: April 6 - May 13, 2026

Time & Location: 

• Mondays 10:00 am-11:15 am in MS 2173 (Medical Sciences Building)
• Wednesdays 10:00 am-11:15 am in NL 6 (David Naylor Building)

The Foundational Computational Biology (FCB) courses, offered through the Molecular Genetics Graduate program, are taught as two 6-meeting topic courses that cover selected foundational concepts and current applications for computational biology and bioinformatics.  The courses are targeted to 1^st year graduate students, with preference given to students in the CBMG track of the Molecular Genetics Graduate Program.  

Assignments will be both pen-and-paper and practical assignments requiring programming (e.g., Python) or statistical environments (e.g., R). 

Enrollment is subject to Instructor approval, and will require:

1) evidence of comfort with computer programming and

2) excellence in two or more quantitative subjects, which may include: calculus, linear algebra, probability/statistics or other mathematics courses.

Outline: Course Syllabus

Instructors: Dr. Jüri Reimand, Dr. Kieran Campbell, Dr. Gary Bader

Dates: March 20 - April 24, 2026

Time & Location: Fridays 2:00-4:00 pm (location TBD)

The Foundational Computational Biology (FCB) courses, offered through the Molecular Genetics Graduate program, are taught as two 6-meeting topic courses that cover selected foundational concepts and current applications for computational biology and bioinformatics.  The courses are targeted to 1^st year graduate students, with preference given to students in the CBMG track of the Molecular Genetics Graduate Program.  

Assignments will be both pen-and-paper and practical assignments requiring programming (e.g., Python) or statistical environments (e.g., R). 

Enrollment is subject to Instructor approval, and will require:

1) evidence of comfort with computer programming and

2) excellence in two or more quantitative subjects, which may include: calculus, linear algebra, probability/statistics or other mathematics courses.

Outline: Course Syllabus

Instructors: Dr. Jüri Reimand, Dr. Kieran Campbell, Dr. Gary Bader

Dates: May 1 - June 5, 2026

Time & Location: Fridays 2:00-4:00 pm (location TBD)

Please see the Biochemistry Courses page.