Course Descriptions

*The course is exclusively available to first-year students in the Molecular Genetics program.

(0.5 FCE)

"MMG1001H: Foundational Genetic Approaches I" consists of three Units (Genetics, Genomics, Proteins & Proteomics) that are taught in sequence for five weeks each in the fall. The course is required for all incoming graduate students in the Department's M.Sc./Ph.D. Program in Molecular Genetics. Students who enter in January take the course in September of the same year.The goal of MMG1001 is to provide all incoming students with critical foundational knowledge early in their M.Sc./Ph.D. program, thus enhancing their scientific insight and progress through their degree.

MMG1001 is offered in the fall term and is composed of three five-week core modules held two hours/day on MWF. Each module will have its own assignments and format. Marks achieved in each module will be used to calculate the final grade. 

Genetics Unit: Instructor and Course Coordinator, Dr. Howard Lipshitz 

Genomics Unit Instructor: Dr. Tim Hughes 

Proteins/Proteomics Unit Instructor: Dr. Anne-Claude Gingras

Unit 1: Genetics. The goal of this unit is to provide students with an in-depth understanding of the fundamental concepts and techniques of genetics and genetic screens. Students will study review articles and foundational research papers for each of three model organisms: Drosophila, C. elegans, S. cerevisiae. The course coordinator will lead full-class discussions of these papers complemented by invited expert lectures. In groups, with the assistance of TAs, students will engage in practical problem-solving exercises in genetics and will present these to the entire class.

Unit 2: Genomics. The goal of this unit is to provide students with general working knowledge of genomics and genome-scale functional analyses. Examples from the primary literature will illustrate approaches and thinking, with broader context and overview provided by the instructor. Students will also engage in presenting papers and in TA-guided practical problem-solving exercises that reflect common tasks faced by researchers in genetics and genomics.

Unit 3: Proteins and Proteomics. In this unit, students will be exposed to fundamental and advanced experimental approaches for the study of proteins, with a focus on mass spectrometry-based proteomics. Students will use selected publications to ‘solve’ assigned problems by proposing appropriate experimental design, controls and analysis workflows.

(0.25 FCE)

The Colloquium consists of ~ ten weekly departmental seminars by invited world-class scientists. The seminars are open to the entire department and run from 3-4 pm on Monday afternoons in the winter term. In advance of the seminar, students read a research paper and a review  recommended by the invited seminar speaker. On the preceding Wednesday (4-6pm), students meet in small groups of 10-15 members to discuss the research paper and develop a set of questions to submit to the seminar speaker. After attending the seminar, students meet with the seminar speaker as a class to discuss the research (4-5 pm). This course provides first-year graduate students with the opportunity to develop important skills in evaluating scientific research while learning about a broad range of research areas from experts in each field.

Instructors: Julie Lefebvre (coordinator), Tae-Hee Kim, Sagi Abelson, Julien Muffat, Rafa Montenegro Burke

(0.25 FCE)

"MMG1004H: Basic Computational Biology - A Practical Course in Programming for Biologists" 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), and all of the PhD students admitted under CBMG program, will enrol in MMG1344H: Foundational Computation Biology I (FCB I) and MMG 345H: Foundational Computation Biology I (FCB II).

Instructors: Drs. Philip Kim and Gary Bader.

(0.0 FCE)

MMG1111 is the MSc seminar series. The primary goal of MMG1111 is providing practical experience and guidance so students can concisely communicate their research results to an audience of educated, but not necessarily specialist, peers. This is an essential skill for anyone intending to seek a career in scientific research. Completion of this course is mandatory for all graduate students in the program. A secondary goal is to give each student broad knowledge of all aspects of research undertaken in the department. A tertiary goal is giving students experience in listening to scientific seminars and constructively critiquing others’ research. 

Instructors: Drs. Richard Collins, Alan Davidson, Scott Gray-Owen, C.C. Hui, Lucy Osborne, Laurence Pelletier, Daniel Schramek, Ian Scott, Lincoln Stein

Course Time and Dates: Winter Tuesdays 1-2 pm 

(0.0 FCE)

MMG1112 is the Ph.D. seminar series. The primary goal of MMG1112 is providing practical experience and guidance so students can concisely communicate their research results to an audience of educated, but not necessarily specialist, peers. This is an essential skill for anyone intending to seek a career in scientific research. Completion of this course is mandatory for all graduate students in the program. A secondary goal of the series is to give each student broad knowledge of all aspects of research undertaken in the department. A tertiary goal is to give students experience in listening to scientific seminars and constructively critiquing others’ research.

Instructors: Richard Collins, Xi Huang, Ran Kafri, Kenichi Okamato, Miguel Ramalho-Santos

Course Time and Dates: Fall Tuesdays 2-4 pm 

(0.25 FCE)

This course entails a seminar presentation in front of a small group of students (~15) and professors (2). At the first meeting of the series, the course coordinator will give a seminar highlighting some of the specific challenges encountered by the types of data and arguments frequently presented in molecular biology seminars. The coordinator and the students will identify commonly made mistakes and discuss ways to avoid them. 

In subsequent weeks, students will meet in small groups of ~15 students. Attendance at every session is mandatory. Each week, 3 or 4 students will present a 15-minute seminar based on their current graduate research and critique the seminars of others. Two professors will also be in the room to help organize, encourage discussion, and evaluate the presentations. Each presenter will be given a set time, uninterrupted, to present the seminar. After the seminar, a typical critique session consists of the presenter running through their presentation again (slide-by-slide), with comments and constructive suggestions from the evaluators (initially the students, then the faculty) being provided at appropriate places. The group will try to identify what makes a “good” slide “good” and how to revise and improve the less effective slides. It is expected that opinions will vary among evaluators, and it will be helpful for everyone to hear a range of opinions. 

For each seminar, each evaluator will provide written feedback on the form provided. This feedback will be provided anonymously to the presenter to help them revise their seminar for presentation to the department in the second academic term. 

Instructors: Richard Collins, Course will also involve additional MoGen faculty (2 faculty per small group discussions).

Course Time and Dates:  Thursday 10 am – 12 pm; 5 weeks in September-October; specific dates will be announced in the preceding summer.

(0.25 FCE)

MMG1114 is the MSc/Ph.D. second-year student seminar presentation. The primary purpose of MMG1114 is to give students experience in presenting their research to a larger audience of their peers. Students will present their seminars in the 2nd year of their graduate program. The primary goal of the Student Seminar Courses is providing practical experience and guidance so that students can concisely communicate their research results to an audience of educated, but not necessarily specialist, peers. This is an essential skill for anyone intending to seek a career in scientific research. Completion of this course is mandatory for all graduate students in the program. A secondary goal is to give each student a broad knowledge of all aspects of research undertaken in the department. A tertiary goal is to provide students with experience listening to scientific seminars and constructively critiquing others’ research.

Instructors: Richard Collins, Alan Davidson, Scott Gray-Owen, C.C. Hui, Lucy Osborne, Laurence Pelletier, Daniel Schramek, Ian Scott, Lincoln Stein

(0.50 FCE)

MMG1115 is the Ph.D. student seminar presentation. The primary purpose of MMG1115 is to give students additional experience in presenting their research in greater depth to a larger audience of their peers. Students will present a seminar in their 4th or 5th year of the Ph.D. program. The primary goal of the Student Seminar Courses is providing practical experience and guidance so that students can concisely communicate their research results to an audience of educated, but not necessarily specialist, peers. This is an essential skill for anyone intending to seek a career in scientific research. Completion of this course is mandatory for all graduate students in the program. A secondary goal is to give each student a broad knowledge of all aspects of research undertaken in the department. A tertiary goal is to provide students with experience listening to scientific seminars and constructively critiquing others’ research.

Instructors: Richard Collins, Xi Huang, Ran Kafi, Kenichi Okamato, Miguel Ramalho-Santos 

Course Time and Dates: Fall Tuesdays 3-5 pm

(0.25 FCE)

Course Instructors:  Jüri Reimand, Kieran Campbell, and Gary Bader

Course Objectives and Learning Outcomes:  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. 

Course Description and Format: The course will consist of lectures as well as hands on assignments. Assignments will be both pen-and-paper and practical assignments requiring programming (e.g., Python) or statistical environments (e.g., R).   

Course Time and Dates:  TBD (Currently held over 6 weeks typically in April and May).

Prerequisite:  This course is targeted to 1^st year graduate students with substantial computational biology experience. For example, students with computational biology experience which is too advanced for MMG1004 (A Practical Course in Programming for Biologists) will be encouraged to take this course. Priority will be given to first-year Molecular Genetics Department admitted graduate students. On a case-by-case basis, the instructors will also admit Molecular Genetics Department students in year 2 or later as well as students from other UofT Departments.

(0.25 FCE)

Course Instructor:  Jüri Reimand, Kieran Campbell, and Gary Bader

Course Objectives and Learning Outcomes:  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. 

Course Description and Format: The course will consist of lectures as well as hands on assignments. Assignments will be both pen-and-paper and practical assignments requiring programming (e.g., Python) or statistical environments (e.g., R).  

Course Time and Dates: TBD (Currently held over 6 weeks, typically in May and June).

Prerequisite:  Foundational Computational Biology I or approval from the instructor. This course is targeted to 1^st year graduate students with substantial computational biology experience. For example, students with computational biology experience which is too advanced for MMG1004 (A Practical Course in Programming for Biologists) will be encouraged to first take Foundational Computational Biology I prior to taking Foundational Computational Biology II. Priority will be given to first-year Molecular Genetics Department admitted graduate students who have already taken Foundational Computational Biology I. On a case-by-case basis, the instructors will also admit Molecular Genetics Department students in year 2 or later as well as students from other UofT Departments.

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.  

(0.5 FCE)

This course is offered during the Fall term. Students who enter the program in September will take this course first, followed by MMG1002 in the Winter term, while students who enter in January will complete MMG1002 (Winter term) first, then complete MMG1001 in the Fall term of their first year. MMG1001 is composed of three five-week core modules held two hours/day on MWF: 1.

Genetics Unit: Instructor and Course Coordinator, Dr. Howard Lipshitz 

Genomics Unit Instructor: Dr. Tim Hughes 

Proteins/Proteomics Unit Instructor: Dr. Anne-Claude Gingras 

Each module will have its own assignments and format. Marks achieved in each module will be used to calculate the final grade. 

(0.5 FCE)

This course is offered during the Winter term. MMG1002 entails two parts, Colloquium and one Computational module. 

Course Coordinator: Dr. Philip Kim

1. Departmental Colloquium (formerly MMG1010)

The Colloquium consists of ~ ten weekly departmental seminars that invited world-class scientists will present. The seminars are open to the entire department and run from 3-4 pm every Monday afternoon. Before each seminar, students read a set of 2-3 designated papers/reviews recommended by the invited seminar speaker to familiarize them with the topic at hand. Students will also meet in small groups of about 10-15 members before each seminar to discuss the research papers and develop a set of questions to submit to the seminar speaker before the seminar. After attending the seminar, students meet with the seminar speaker as a class to discuss the research (4-5 pm). This course provides first-year graduate students with the opportunity to develop important skills in evaluating scientific research while learning about a broad range of research areas from experts in each field.

Instructors: Drs. Tae-Hee Kim, Julie Lefebvre, Philipp Maas, Julien Muffat, Sagi Abelson

2. Introduction to Programming 

This course is for students with an introductory level or no previous programming knowledge.

Instructors: Drs. Philip Kim and Gary Bader.

or

3. Advanced Computational Biology I

This course is for CBMG students and other students with advanced computational experience.
In their first year, CBMG Students are also required to complete:

Instructors: Drs. Fritz Roth and Kieran Campbell. 

4. Advanced Computational Biology II (0.25 FCE)

This course fulfills one of two Modules required for MMG1041 and is required for CBMG students.

Instructors: Drs. Fritz Roth and Kieran Campbell

(0.5 FCE)

This requirement is completed only by Ph.D. students and entails two Modules (0.25 FCE each). The final grade is the average of the marks obtained in each course. Discuss with your Supervisor which courses would be best to take before signing up. No waivers are considered.

STUDENT SEMINARS:

In addition to formal classes, students also complete several seminar courses in which they develop their scientific communication skills.

(0.5 FCE)

MMG1011 entails attendance at department-wide student seminars throughout year 1 in the program, plus a small group seminar presentation. Marks are derived from the attendance grade and the presentation. The presentation takes place in September-October after at least ten months in the program and entails a seminar presentation in front of a small group of students (~15) and professors (2). This seminar series provides students with experience in preparing and presenting a research seminar that effectively conveys their science to an audience of their peers. Students will also be expected to give constructive and critical feedback to their fellow student presenters.

Course Coordinator: Dr. Richard Collins 

(0.5 FCE)

MMG1021 entails attendance at department-wide student seminars throughout year 2 in the program, plus a department-wide seminar presentation in the winter term of year 2. Marks are derived from the attendance grade and the presentation. This course is usually broken into two parallel sessions, in which 2-3 students speak each week. Students will also be expected to give constructive and critical feedback to their fellow student presenters.

Course Coordinators: Richard Collins, Alan Davidson, Scott Gray-Owen, C.C. Hui, Lucy Osborne, Laurence Pelletier, Daniel Schramek, Ian Scott, Lincoln Stein

(0.5 FCE)

MMG1031 is required only for Ph.D. students and entails attendance at department-wide student seminars plus a department-wide seminar presentation in year 4. Marks are derived from the attendance grade and the presentation. Students will also be expected to give constructive and critical feedback to their fellow student presenters. Note that no topic course is required to successfully complete MMG1031. Students are enrolled in MMG1031 upon registration in the Ph.D. program. Students admitted directly into the Ph.D. program will begin the requirements of this course only after completing MMG1011, MMG1021 AND passing their qualification exam. Students complete MMG1031 in the year when they present their Ph.D. seminar.

Course Coordinators: Drs. Richard Collins, Xi Huang, Ran Kafri, Kenichi Okamoto, Miguel Ramalho-Santos

This is a mandatory course for all Molecular Genetics M.Sc. and Ph.D. students to be completed during the fall term of the first year of graduate study. The Colloquium consists of ~12 weekly departmental seminars that invited world-class scientists will present. The seminars are open to the entire department and run from 4-5:15 pm every Monday afternoon. Before each seminar, students will read a set of 2-3 designated papers/reviews recommended by the invited seminar speaker to familiarize them with the topic at hand. Students will also meet in small groups of about 10-15 members before each seminar to discuss the research papers and develop a set of questions to submit to the seminar speaker before the seminar. After attending the seminar, students will meet with the seminar speaker to discuss the research. This course provides first-year graduate students with the opportunity to develop important skills in evaluating scientific research while learning about a broad range of research areas from experts in each field. 

Students must take two topics (0.25 FCE each) in order to complete this course. The mark in this course is the average of the two marks obtained in the topics taken. Courses from other departments cannot replace this course.

Students must give two research seminars and attend the weekly student seminars to obtain a grade for this course. The grade in this course is the average of the grades obtained in the two seminar presentations, minus any marks deducted for poor attendance. See the “Student Seminar Courses” (MMG1114, MMG1115) for a detailed course description.

Students must take two topics (0.25 FCE each during the Ph.D. program). The mark in this course is the average of the two marks obtained in the two topics taken. The student may replace this course with a half course offered by a different department or by a course offered through collaborative programs. Courses taken to replace MMG1016H° must be approved by e-mail by the Graduate Coordinator, and a course replacement form must be submitted prior to taking the course.

Students must take one topic (0.25 FCE), deliver one 18 minute research seminar, attend seminars, and evaluate 30 student seminars. The mark in this course is the average of the student seminar mark (minus any letter grade deduction due to poor attendance) and the topic course mark. See Student Seminars and the Graduate Handbook for more information, and Seminar Schedules for the monthly and yearly schedules. Courses from other departments cannot replace this course.