Program Requirements
The Ph.D. in Biochemistry; Bioinformatics involves the development of strategies for experimental design, the construction of computer science tools to analyze large datasets, the application of modelling techniques, the integration of biological databases, and the use of algorithms and statistics. Permission of the Graduate Program Director to enroll in this concentration is required to ensure that the proposed research thesis focusses on bioinformatics related to biochemistry.
Thesis
A thesis for the doctoral degree must constitute original scholarship and must be a distinct contribution to knowledge. It must show familiarity with previous work in the field and must demonstrate ability to plan and carry out research, organize results, and defend the approach and conclusions in a scholarly manner. The research presented must meet current standards of the discipline; as well, the thesis must clearly demonstrate how the research advances knowledge in the field. Finally, the thesis must be written in compliance with norms for academic and scholarly expression and for publication in the public domain.
Required Courses (3 credits)
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BIOC 696D1 Seminars in Biochemistry (1.5 credits)
Overview
Biochemistry : Seminars in biochemistry.
Terms: Fall 2024
Instructors: There are no professors associated with this course for the 2024-2025 academic year.
Students must register for both BIOC 696D1 and BIOC 696D2.
No credit will be given for this course unless both BIOC 696D1 and BIOC 696D2 are successfully completed in consecutive terms.
BIOC 696D1 and BIOC 696D2 together are equivalent to BIOC 696
Restriction: Open to M.Sc. and Ph.D. Biochemistry students only.
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BIOC 696D2 Seminars in Biochemistry (1.5 credits)
Overview
Biochemistry : See BIOC 696D1 for course description.
Terms: Winter 2025
Instructors: Pastor, William (Winter)
Prerequisite: BIOC 696D1.
Students must register for both BIOC 696D1 and BIOC 696D2.
No credit will be given for this course unless both BIOC 696D1 and BIOC 696D2 are successfully completed
Restriction: Open to M.Sc. and Ph.D. Biochemistry students only.
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BIOC 696N1 Seminars in Biochemistry (1.5 credits)
Overview
Biochemistry : Seminars in biochemistry.
Terms: Winter 2025
Instructors: There are no professors associated with this course for the 2024-2025 academic year.
Students must also register for BIOC 696N2
No credit will be given for this course unless both BIOC 696N1 and BIOC 696N2 are successfully completed in a twelve month period.
BIOC 696N1 and BIOC 696N2 together are equivalent to BIOC 696
Restriction: Open to M.Sc. and Ph.D. Biochemistry students only.
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BIOC 696N2 Seminars in Biochemistry (1.5 credits)
Overview
Biochemistry : For description see BIOC 696N1.
Terms: Fall 2024
Instructors: There are no professors associated with this course for the 2024-2025 academic year.
Prerequisite: BIOC 696N1
No credit will be given for this course unless both BIOC 696N1 and BIOC 696N2 are successfully completed in a twelve month period.
Restriction: Open to M.Sc. and Ph.D. Biochemistry students only.
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BIOC 701 Research Seminar 1 **
Overview
Biochemistry : Presentation on original current laboratory research carried out by student.
Terms: Fall 2024, Winter 2025
Instructors: There are no professors associated with this course for the 2024-2025 academic year.
Biochemistry graduate students
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BIOC 702 Ph.D. Thesis Proposal **
Overview
Biochemistry : Dissertation presented to Committee.
Terms: Fall 2024, Winter 2025
Instructors: There are no professors associated with this course for the 2024-2025 academic year.
Biochemistry graduate students
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BIOC 703 Ph.D. Seminar **
Overview
Biochemistry : Presentation of the planned thesis including central findings and original contribution to knowledge in the field of research.
Terms: Fall 2024, Winter 2025
Instructors: There are no professors associated with this course for the 2024-2025 academic year.
Restriction: Ph.D. students in Biochemistry
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QLSC 601D1 Quantitative Life Sciences Seminars 1
Overview
QLSC : QLS Monthly Seminar Series and Journal Club.
Terms: Fall 2024
Instructors: There are no professors associated with this course for the 2024-2025 academic year.
Students must register for both QLSC 601D1 and QLSC 601D2
No credit will be given for this course unless both QLSC 601D1 and QLSC 601D2 are successfully completed in consecutive terms
Restriction: Restricted to students enrolled in QLS.
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QLSC 601D2 Quantitative Life Sciences Seminars 1
Overview
QLSC : See QLSC 601D1 for description.
Terms: Winter 2025
Instructors: There are no professors associated with this course for the 2024-2025 academic year.
Prerequisite: QLSC 601D1
No credit will be given for this course unless both QLSC 601D1 and QLSC 601D2 are successfully completed in consecutive terms.
Restriction: Restricted to students enrolled in QLS.
*Students choose either BIOC 696D1/D2 or BIOC 696N1/N2. Students fast-tracking from the M.Sc. to the Ph.D. program, and who registered for and passed BIOC 696 at the M.Sc. level, do not register for BIOC 696 at the Ph.D. level. Likewise, students fast-tracking from the M.Sc. to the Ph.D. program, and who registered for and passed QLSC 601 at the M.Sc. level, do not register for QLSC 601 at the Ph.D. level.
**NOTE: Students DO NOT register for these courses until notified by the Student Affairs Officer.
Students must complete BIOC 701 in the third term after admission to the program, BIOC 702 in the fifth or sixth term, and BIOC 703 approximately six months prior to submission of the Ph.D. thesis.
Complementary Courses*** (9 credits)
3 credits from the following:
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BIOC 600 Advanced Strategies in Genetics and Genomics (3 credits)
Overview
Biochemistry : Advanced technologies and methods in genomics research, presented by experts actively pursuing the experimental approaches discussed.
Terms: Winter 2025
Instructors: Duchaine, Thomas; Montpetit, Alexandre; Dejgaard, Kurt; Dostie, Josee; Giguere, Vincent; Najafabadi, Hamed; Yamanaka, Yojiro; Huang, Sidong; Watson, Ian; Kazak, Lawrence (Winter)
Enrolment limited to 15 graduate students.
Prerequisite: BIOC 454 or equivalent
Restriction: Must take part in the Biochemistry graduate program
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BIOC 603 Genomics and Gene Expression (3 credits)
Overview
Biochemistry : Examination of recent developments in analysis of eukaryotic cell genomes and control of gene expression during differentiation and growth control. Molecular genetics; genomics and the bioinformatics of analysis of genomic and functional-genomic data; mechanisms and signal-transduction pathways for regulation of gene expression; applications to human disease with a strong emphasis on cancer.
Terms: Fall 2024
Instructors: McCaffrey, Luke; Muller, William Joseph; Gallouzi, Imed Eddine; Siegel, Peter; Huang, Sidong; Walsh, Logan; Kazak, Lawrence; Pastor, William (Fall)
Fall
Prerequisites: BIOC 454 and permission of instructor.
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BIOC 604 Macromolecular Structure (3 credits)
Overview
Biochemistry : X-Ray crystallography, NMR spectroscopy, Electron Microscopy. Theory and methods used to determine macromolecular structures will be covered. Several practical sessions with hands-on experience for students are included.
Terms: This course is not scheduled for the 2024-2025 academic year.
Instructors: There are no professors associated with this course for the 2024-2025 academic year.
Offered in the Winter term, in even alternate years.
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BIOC 605 Protein Biology and Proteomics (3 credits)
Overview
Biochemistry : Examination of recent developments in protein biology and proteomics analysis. Proteomics, modeling and biophysical approaches to characterize the functional interactions of biological macromolecules; applications to biological problems. Lectures and in-class discussions are supplemented by practical training in proteomics.
Terms: Winter 2025
Instructors: Denis, Maxime; Dejgaard, Kurt (Winter)
Winter
Prerequisite: BIOC 450 or equivalent, or permission of instructor.
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BIOC 670 Biochemistry of Lipoproteins (3 credits)
Overview
Biochemistry : Structure, function and metabolism of lipids and lipoproteins as they relate to lipid storage diseases, obesity, diabetes and heart disease.
Terms: This course is not scheduled for the 2024-2025 academic year.
Instructors: There are no professors associated with this course for the 2024-2025 academic year.
Prerequisite: BIOC 311 or permission of instructor
Restrictions: Open to graduate students only with permission of instructor.
Winter
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EXMD 615 Essentials of Glycobiology (3 credits)
Overview
Experimental Medicine : Examination of the structure, function, and biosynthesis of glycoproteins, glycolipids and glycosaminoglycans, and the biological role of complex carbohydrates. Lectins, methods for elucidating carbohydrate structure, glycomics, and human diseases due to disorders of glycan synthesis.
Terms: Winter 2025
Instructors: Gilfix, Brian (Winter)
Winter
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EXMD 635D1 Experimental/Clinical Oncology (3 credits)
Overview
Experimental Medicine : The course will deal, on a site by site basis, with the incidence of cancer, present treatment, treatment outcome, underlying causes, current research and directions for development of new treatments. Chemotherapy, surgery, radiation therapy and nutrition as therapy and treatment of cancer will be included.
Terms: Fall 2024
Instructors: Nepveu, Alain; Teodoro, Jose Guerreiro; Tanguay, Simon; Gregorieff, Alex; Deblois, Genevieve; Fuks, Abraham; Sebag, Michael; Fiset, Pierre; Ursini-Siegel, Josie; Malag贸n, Tal铆a (Fall)
Prerequisite: Students must request permission from the instructor.
Students must register for both EXMD 635D1 and EXMD 635D2
No credit will be given for this course unless both EXMD 635D1 and EXMD 635D2 are successfully completed in consecutive terms
Previous solid knowledge in biochemistry and molecular biology required. Students will be required to write a long essay and give an oral presentation.
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EXMD 635D2 Experimental/Clinical Oncology (3 credits)
Overview
Experimental Medicine : See EXMD 635D1 for course description.
Terms: Winter 2025
Instructors: Nepveu, Alain; Basik, Mark; Teodoro, Jose Guerreiro; Kassouf, Wassim; Zogopoulos, George; Johnson, Nathalie; Kukolj, George; Laneuville, Pierre; Shenouda, George; Tremblay, Michel (Winter)
Prerequisite: EXMD 635D1 and permission from the instructor.
Students must register for both EXMD 635D1 and EXMD 635D2
No credit will be given for this course unless both EXMD 635D1 and EXMD 635D2 are successfully completed in consecutive terms
Previous solid knowledge in biochemistry and molecular biology required. Students will be required to write a long essay and give an oral presentation.
6 credits from the following:
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BINF 621 Bioinformatics: Molecular Biology (3 credits)
Overview
Bioinformatics : The main problems related to the analysis of biological sequences (sequence comparison, homology, gene annotation, phylogenetic inference, comparative genomics) and the computational approaches (dynamic programming algorithms, Blast heuristics, hidden Markov models, Bayesian statistics).
Terms: This course is not scheduled for the 2024-2025 academic year.
Instructors: There are no professors associated with this course for the 2024-2025 academic year.
Restriction: Enrolment by students in the Bioinformatics option or by permission from the course coordinators only. Limited to 30 students.
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BMDE 652 Bioinformatics: Proteomics (3 credits)
Overview
Biomedical Engineering : Overview of high-throughput proteomic technologies commonly employed to study the localization and function of all proteins in an organism, and the bioinformatic approaches to analyze raw data and deposit them in proteome databases.
Terms: This course is not scheduled for the 2024-2025 academic year.
Instructors: There are no professors associated with this course for the 2024-2025 academic year.
Prerequisite: Enrolment in Bioinformatics option program or permission by coordinators.
Note: The course is inter-disciplinary and is targeted to students with different scientific backgrounds. A substantial portion of marks will be given based on practical assignments.
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BTEC 555 Structural Bioinformatics (3 credits)
Overview
Biotechnology : Fundamentals of protein structure and the application of tools for structure determination, how protein structure allows us to understand the complex biological functions, and how knowledge of protein structure can contribute to drug discovery.
Terms: Winter 2025
Instructors: Salavati, Reza; Sulea, Traian; Mirzavand Borujeni, Poorya (Winter)
Winter
1-hr lecture, followed by 2 hrs of computer lab.
Prerequisite: Molecular biology or biochemistry, and basic bioinformatics, or permission of instructor.
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COMP 618 Bioinformatics: Functional Genomics (3 credits)
Overview
Computer Science (Sci) : Techniques related to microarrays (normalization, differential expression, class prediction, class discovery), the analysis of non-coding sequence data (identification of transcription factor binding sites), single nucleotide polymorphisms, the inference of biological networks, and integrative Bioinformatics approaches.
Terms: This course is not scheduled for the 2024-2025 academic year.
Instructors: There are no professors associated with this course for the 2024-2025 academic year.
Prerequisite: Enrolment in Bioinformatics Option Program or permission of coordinators.
Restrictions: Enrolment by students in the Bioinformatics Option Program or by permission of course coordinators only. Computer Science graduate students not in the Bioinformatics Option Program need additional permission of the M.Sc. or Ph.D. Committee respectively.
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PHGY 603 Systems Biology and Biophysics (3 credits)
Overview
Physiology : Introduction to classical and current topics in biophysics and systems biology in order to model the control of gene expression and intracellular signal transduction, as well as gene spread in populations.
Terms: This course is not scheduled for the 2024-2025 academic year.
Instructors: There are no professors associated with this course for the 2024-2025 academic year.
Prerequisite: Knowledge of differential equations at the MATH 315 level or equivalent.
Notes: Enrolment is limited to 20 students per semester. The course is 1.5 hours of lecture and 1.5 hours of seminar per week. Readings will focus on classic and current journal articles.
*** Complementary courses are chosen in consultation with the Research Director.
The Graduate Advisory Committee may stipulate additional coursework depending on the background of the candidate. BIOC 450 (Protein Structure and Function) and BIOC 454 (Nucleic Acids) are additional requirements for those who have not previously completed equivalent courses in their prior training. These additional courses are not counted towards the credits for this program.
