Topic Courses

Course Overview: This course explores advancements in understanding how viruses spread from infected to new target cells. Designed for students with a background in virology, it begins with an interactive review of virus replication focusing on progeny virion release and entry into host cells. Subsequent classes involve student presentations and discussions of selected literature papers. The focus will be on the release of non-enveloped viruses, challenging traditional views by considering evidence of vesicle-mediated release and alternative spread mechanisms like cell-cell junction disruption and nanotube connections. Assessment includes paper presentations, participation, and a written assignment.

Course Instructor: Dr. Martha Brown

Course Dates: October 18 - November 22, 2024

Time: Fridays 2-4pm

Location: TBD

Course outline: Syllabus

The goal of this topics course is to get a thorough understanding of the main techniques used in Developmental Biology and their history in the lab.

• Course Dates: October 16 – November 20, 2024
• Course Time: Wednesdays, 10am-Noon
• Location: PGCRL, Room TBA

Course Instructors: Dr. Sevan Hopyan and Dr. Madeline Hayes.

Access Course Syllabus

Course Overview:
The course provides a survey of current and emerging approaches in functional genomics and proteomics, with a focus on experimental design and data interpretation.

The course consists of a series of presentations and guided discussions by researchers that are developing cutting-edge functional genomics and/or proteomics approaches. The course is designed to be highly interactive — the presentations by invited speakers provide a framework for discussion and students are expected and encouraged to engage as fully as possible. It’s a great opportunity for students to explore cutting-edge genomics methods with great invited speakers and to learn through these discussions.

Topics to be covered this year will include: a) Next Generation nucleic acid sequencing, b) Genetic interactions in model organisms, c) Proteomics and protein interactions, d) High content screening, e) CRISPR technologies, and f) Systematic assay development, g) computational analysis.

Course outline: Syllabus

Course Location: TBD

Course Time and Date:  October 22 - November 26 2024 (Tuesdays 3-5pm)

Course Instructor(s): Charlie Boone and Andy Fraser

Course outline:

This course will cover the fundamentals of membrane proteomics from a structural, biochemical and genetic standpoint.  Among these will be cryo-EM, crystallography, NMR, and EPR methods as well as mammalian membrane two-hybrid screening and mass-spectrometry-based methods.  A number of in vivo approaches to the discovery of drugs that modulate biological systems will also be covered.  Finally, the techniques used for the development of antibodies against membrane proteins with therapeutic potential will be introduced.

The course will be completed in a total of 12 hours in two-hour blocks and will run over two weeks. In-class sessions will include lectures by professors and presentations by students on current literature. Classes will involve discussion of research papers.

Course outline: Syllabus

Course Location: TBD

Course Time and Date:  October 23 - November 27 2024 (time TBD)

Course Instructor(s): Oliver Ernst and Igor Stagljar

The premise the course is that cancer is largely a product of the sequence-to-phenotype continuum: DNA-to-RNA-to-Proteome-to-Phenotype (i.e. cancer). The course comprises a series of lectures delivered by leading proteomics experts and researchers. Students will learn about mass spectrometry-based proteomics including spectral analysis, and tissue proteome profiling as methods to discover cancer drivers and biomarkers, and to define and compare phenotypes such as normal versus cancer; drug responsive versus drug resistant. Innovative high-content proteomics technologies will be introduced that have been developed and applied to systematically interrogate proteomes for protein interactions associated with disease, cell regulation, and drug responsiveness.

Course instructor: Dr. Michael Moran

Course dates: October 23 - November 27 (Wednesdays, 10am-12pm)

Location: PGCRL, room TBD

Course outline: Syllabus

The course will discuss recent advances in our understanding of the structure and function of the cytoskeleton. Discussion will include, but not be limited to cell division (prokaryotic and eukaryotic), cell migration and ciliogenesis.

Delivery: In person

Dates: November 4 - December 13 (Date and time TBD)

Outline

Course Overview

Mitochondria are essential intracellular organelles that contain their own genomes. This course will focus on understanding how mitochondrial genomes are maintained, inherited and expressed, and how their dysfunction contributes to diseases like cancer. Students will learn both fundamental concepts as well as recent advances in the field of mitochondrial genetics.

The structure of the course is as follows. Students will be organized into six groups. Each group will be assigned a topic from endosymbiotic theory to the role mitochondria play in cancer (see below). Groups will then develop and present a 30-minute power point-assisted lecture that would be suitable to teach this topic to a class of first-year graduate students.

Course Instructors: Dr. Thomas Hurd

Course Dates: November 5 - December 10, 2024

Time: Tuesday 1-3 pm

Location: MaRS Rm. 1523

Course outline: Syllabus

Course Overview:

Stem cells are at the heart of development and regeneration in organisms from plants to humans. We will pursue issues of cell fate, cell division, differentiation and self-renewal (see the weekly topics below). This is a reading and discussion course, so everyone will read the papers for each week before coming to class.  This means you should come to the first meeting having read all of the week one papers or don’t bother coming to class.  Each person may be asked to give the synopsis of a paper and/or initiate the discussion by answering the first questions about the papers. For this course, you must be prepared for robust discussion and presentation.  This course will be fun, and everybody will do well if they participate in the class discussion.

Course outline: Syllabus

Course Location: Room 1112 – CCBR (11^th Floor, 160 College Street)

Course Time and Date: October 29 – December 3, 2024 (Tuesdays, 2 PM – 4 PM)

Course Instructor(s): Derek van der Kooy and John Dick 

Enrollment: 15

Course Overview: 

In this topics course, we will explore the fascinating world of epigenetic inheritance and chromatin-based gene regulation. 

The format for this course is a little different from other topics courses you may have taken and will require a greater sustained effort but will not involve a lengthy final assignment. We’re aiming for maximal student engagement and will in fact require you to assume much responsibility for the development of the course curriculum as well as marking. Brief weekly written assignments will comprise a significant portion of your grade and will be evaluated by you. The quality of the class you lead (as explained below) will comprise another major area of evaluation. 

Course outline: See syllabus here

Course Location: TBD

Course Time and Date: March 20 – April 24, 2025 (Thursdays, 2-4pm)

Course Instructor(s): Marc Meneghini and Paul Delgado Olguin

Course Overview:

The course will start with an introductory lecture, covering the basic theoretical and practical aspects of human genome analysis, including a historical perspective of current advances in the field. Subsequent sessions will involve class presentations of papers covering topics related to human genome analysis. 

Course Outline: See syllabus here

Course Coordinator: Ryan Yuen and Gregory Costain 

Course Location: Peter Gilgan Centre for Research & Learning (PGCRL), room TBD

Course Time and Date: March 20 – April 24, 2025 (Thursdays, 2-4p)

Course Overview

This course will survey the genetic and biophysical forces that have shaped the evolutionary history of genes and proteins. The first lecture will review basic concepts in molecular evolution and mutational processes, while the latter lectures will discuss recent theoretical and experimental advances. Topics to be covered include: mutational processes; positive and negative selection; neutral theory of protein evolution; predicting deleterious protein mutations; evolution of gene expression and gene regulation; de novo mutations; biophysical models of protein evolution; protein sequence and structure spaces; mutational robustness; evolvability; epistasis and co-evolution of interacting amino acid residues; and examples of using evolutionary information to infer biophysical properties of proteins. Student grades will be based on participation in discussions, a written CIHR grant LOI, and referee reports on two grant proposals submitted by fellow students

Instructor: Zhaolei Zhang

Date: March 19 – April 23, 2025

Time: Wednesdays, 1-3pm

Location: Donnelly Centre - White Seminar Room

Syllabus

This course will focus on recent advances in cancer molecular genetics and application to human disease. Specifically, we will address genetic factors with respect to cancer susceptibility (tumor suppressor and DNA repair genes), tumor-specific genomics and gene expression (tumor suppressor genes and oncogenes), and therapies targeting this knowledge. Within each area, clinical application and relevance will be emphasized. Scientific tools that enable this research will be addressed, such as statistical genetics, expression profiling, genomic screens, and siRNA approaches to targeted therapies. The course will consist of lectures and presentations and discussion by students of selected publications. The course grade will be based on presentations, participation in discussions and a short written paper.

Course Date and Time: February 20 - April 3 (except March 13), Thursdays, 2-4pm

Location: Room 1062 Mt. Sinai Hospital

Course Instructor(s): Irene Andrulis / Daniel Schramek

Course Outline: Click Here

Course Overview

Quantitative high-dimension technologies continue to rapidly revolutionize the study of molecular biology. With increasing parameters, resolution, dimensions, and new modalities, paired computational analysis is necessary to properly utilize these methods. Covering the current standard and state of the art in single cell and spatial transcriptomics, their analysis, and utilization with other ‘omics technologies including proteomics, this course will detail how to use these technologies from experimental workflows through to paired analysis pipelines. Furthermore, we will discuss cutting-edge applications, the limitations of current systems, and a framework to develop new experimental and analysis methods. The course will feature a combination of lectures, discussion of recent publications, guest speakers and student presentations.

Course Time and Date: April 8 - May 13, Tuesdays 2-4pm

Location: Room 1062 Mt. Sinai Hospital

Course Instructor(s): Dr. Hartland Jackson, Dr. Aleksandrina Goeva

Course Outline: Syllabus

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.

Course Instructors: Brett Trost

• Course Dates: April 7 - May 14, 2025
• Time: Mondays & Wednesdays, 10-11:30am 
• Location: 
  • Mondays: MS 2173 (Medical Science Building) 
  • Wednesdays: NL 6 (C David Naylor Building - next to MSB). 

Course Overview

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

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

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

•  Course Dates: March 21st – April 25th
• Time: Fridays, 2-4 pm
• Location: Donnelly Black Room
• Course Syllabus

Enrollment: Subject to Instructor approval (for non-CBMG students) and will require: 

1. Emailing the course coordinator with the following information:
2. Evidence of comfort with computer programming and 
3. Excellence in two or more quantitative subjects, including calculus, linear algebra, probability/statistics, or other mathematics courses. 

Once approval is acquired, email the Graduate Coordinators to confirm enrollment.

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

• Course Dates: May 2nd -June 6^th
• Time: Fridays, 2-4 pm
• Location: Donnelly Black Room
• Course Syllabus

Course Overview

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

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

Enrollment: Subject to Instructor approval (for non-CBMG students) and will require: 

1. Emailing the course coordinator with the following information:
2. Evidence of comfort with computer programming and 
3. Excellence in two or more quantitative subjects, including calculus, linear algebra, probability/statistics, or other mathematics courses. 

Once approval is acquired, email the Graduate Coordinators to confirm enrollment.