9/10/23, 7:58 PM Syllabus for MGY428H1 F LEC0101 20239:Functional Genomics

Course Syllabus
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MGY428H1

Functional Genomics

Tuesdays and Thursdays at 1:10 pm - 2:00 pm

Quizzes and Midterms via Quercus (you must be logged in during the class time to take the quizzes and
tests!)

MGY428 Functional Genomics covers many aspects of genomics, which is the discipline of defining and
attributing function to all of the heritable material of an organism on a genome-wide scale. The course
encompasses different components of the enterprise, including sequencing, annotation, forward and
reverse genetics, mapping regulatory sites and mechanisms, and proteomics. It also covers many
different techniques, and several model eukaryotes. The primary and review literature are the basis of
all lectures – there is no textbook.

Course Coordinator:

Prof. Andrew Fraser

Donnelly Centre

Department of Molecular Genetics

University of Toronto

The Donnelly Center for Cellular and Biomolecular Research, Rm 1212

Phone: 416.978.2712

e-mail: [email protected] (mailto:[email protected])

Instructors:

Prof. Philipp Maass

SickKids Research Institute

Genetics & Genome Biology

Peter Gilgan Centre for Research *& Learning, Rm 14.9715

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9/10/23, 7:58 PM Syllabus for MGY428H1 F LEC0101 20239:Functional Genomics

Department of Molecular Genetics

University of Toronto

Phone: 416.813.7654 ext. 302181

Email: [email protected] (mailto:[email protected])

Prof. Ben Blencowe

Donnelly Centre

Department of Molecular Genetics

University of Toronto

The Donnelly Center for Cellular and Biomolecular Research, Rm 1016

Phone: 416.978.3016

e-mail: [email protected] (mailto:[email protected])

TA:

Julia Kitaygorodsky

PhD student, Molecular Genetics

Email: [email protected] (mailto:[email protected])

Mark Breakdown:

Quizzes at beginning of each class 25%

Midterm 1 25%

Midterm 2 25%

Final exam 25%

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The General Format of Each Class

There will be one “essential” paper to read for each class and possibly one or two additional
"recommended" papers that we would also encourage you to read.
These papers will be assigned to you through the Quercus system at least one week before the
relevant lecture.
The lecture will use the assigned reading to illustrate principles, facts, approaches and techniques
that are central to the theme of the lecture.
Students will be responsible for the concepts and basic facts conveyed in the mandatory paper, and
also the material in the lectures.

The Quizzes

Each class will start with a short quiz (usually three straightforward multiple-choice questions) that
test whether you have read the paper and recall the main points of the paper.
There are 21 "content" lectures in which there will be a quiz.
To avoid having to track and evaluate illnesses and occasional justified absences, etc., for dozens of
students – and also issues with internet connectivity - everyone gets 2 free passes (i.e. their 2 worst
quiz marks will be given full value). This is true even if the student was absent that day. These free
passes are intended to compensate for the fact that not everyone can attend every single lecture. If
you find yourself missing more than two lectures, then we will engage more formal mechanisms.

Tests/Exams

The midterm exams will take place during class time on Tuesday, October 10 and Thursday,
November 16. They will be 50 minutes long and will consist of a roughly even mix of multiple choice
questions, short answer questions, and long answer questions. It will cover all the lectures up to the
midterm.
The final exam will be scheduled by A&S and will consist of a roughly even mix of multiple choice,
short answer, and long answer questions. It will cover all of the lectures in the course; however, it will
contain many more questions about the material after the midterm. The proportion of points will be
such that, when the scores from the midterms and the final are combined, each lecture receives
approximately equal weight in the final grade.

Communicating with the Instructors

You can email the professors or TA at any time during the course. Please contact the course coordinator
or the TA for administrative matters, or any of the instructors regarding material specific to their sessions.

We will also check the discussion board on Quercus on a daily basis.

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Logging in to Quercus for MGY428

Like many other courses, MGY428 uses Quercus for its course website. To access the MGY428 website,
go to the UofT portal login page at http://q.utoronto.ca. (http://portal.utoronto.ca/) and log in using your
UTORid and password. You should find links to your courses, including the MGY428 course website.

Email Communication with the Course Instructor

At times, MGY428 course Instructors may decide to send out important course information by email. To
that end, all UofT students are required to have a valid UofT email address. You are responsible for
ensuring that your UofT email address is set up AND properly entered in the ROSI system. You
are responsible for checking your UofT email account on a regular basis.

Accessibility Needs

The University of Toronto is committed to accessibility. If you require accommodations for a disability, or
have any accessibility concerns about the course, the classroom or course materials, please contact
Accessibility Services as soon as possible:

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Note regarding lecture materials and recordings of lectures

Lecturers will post their lecture materials (as ppt or pdf) on Quercus, ahead of time if possible. Video
recordings of lectures from past years may be provided after in-class lectures, at the discretion of each
lecturer.

Students should be aware that: (1) Faculty are not required to provide lecture recording postings or
handouts; this is something we do to make the course easier to follow. (2) The lecture itself is the
primary conduit of information. (3) The lecture may not follow the posted materials/handouts exactly, and
the lectures are likely to contain information that cannot be gained from the slides alone or the assigned
reading material. (4) Exams are likely to include information that is not found on handouts and postings.

The individual lecturers can decide whether to allow recordings for in-person classes. Distribution of any
class recordings (e.g. posting online) without permission constitutes an academic offence.

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2023-MGY428 H1 Schedule

Section 1: Introductory Material (Dr. Fraser)

Th Sep 7 – no lecture

Tu Sep 12 - Lectures 1/2. Introduction to course, genomics, and functional genomics; Molecular
biology review, model systems, overview of genomics and proteomics techniques/approaches,
gene classes/ontology

Section 2: The Human Genome and Vertebrate Genomics (Dr. Maass)

Th Sep 14 - Lecture 3. The human genome: sequence, overview, and annotation

Tu Sep 19 - Lecture 4. The human genome: genes, transcripts, and “functional elements”

(J. Kitaygorodsky) Th Sep 21 – Lecture 5. Human genetics - positional cloning to personal

genomics

Tu Sep 26 - Lecture 6. Mouse and other vertebrate model systems; vertebrate comparative
genomics

Th Sep 28 - Lecture 7. Cell culture: "in vitro" human functional genomics

Tu Oct 3 – Lecture 8. Transcription factors, chromatin, and epigenetics: measuring regulatory

sites in vivo and in vitro

Th Oct 5 – Lecture 9. ENCODE and ongoing controversy about functional elements, pervasive
transcription, genome evolution, and roles of mobile DNA

Tu Oct 10 – Midterm 1 (during class time) (25%) – scores returned by Oct 19

Section 3: Invertebrates, Networks, and Comparative Genomics (Dr. Fraser)

Th Oct 12 - Lecture 10. Introduction to Yeast, Worms and Flies as Genomic Model Systems

Tu Oct 17 - Lecture 11. RNAi screening in worm and fly

Th Oct 19 - Lecture 12. High-content assays, cellular phenotyping, and CRISPR

Tu Oct 24 – Lecture 13. High resolution transcriptomics as a phenotyping tool

Th Oct 26 - Lecture 14. Biological networks

Tu Oct 31 - Lecture 15. Genetic interactions: significance and conservation

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Th Nov 2 - Lecture 16. Predicting gene function

November 6-10 – Reading week

Tu Nov 14 - Lecture 17. Population genetics and comparative genomics of invertebrates AND
Other eukaryotes – emerging models and convergent evolution

Th Nov 16 – Midterm 2 (during class time) (25%)

Section 4: Post-Transcriptional Gene Regulation and Sequencing (Dr. Blencowe)

Tu Nov 21 - Lecture 18. RNA-binding proteins and post-transcriptional gene regulation

Th Nov 23 – Lecture 19. Alternative splicing: regulation and evolution

Tu Nov 28 - Lecture 20. Sequencing technologies and scRNA-seq

Th Nov 30 – Lecture 21. CRISPR-Cas genome manipulation and applications

Section 5: Proteomics, Mass Spectrometry and Course Conclusion (J. Kitaygorodsky)

Tu Dec 5 - Lecture 22. Proteomics, metabolomics, and mass spectrometry

DECEMBER 6 – last day of classes

**Final exam (25%) Dec 9 - Dec 20 (Scheduled by A&S)

Course Summary:
Date Details Due

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