Program Requirements
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 (6 credits)
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BIOC 696 Seminars in Biochemistry (3 credits) *
Overview
Biochemistry : Seminars in biochemistry.
Terms: Fall 2015, Winter 2016
Instructors: Young, Jason (Fall)
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 2015, Winter 2016
Instructors: There are no professors associated with this course for the 2015-2016 academic year.
Biochemistry graduate students
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BIOC 702 Ph.D. Thesis Proposal **
Overview
Biochemistry : Dissertation presented to Committee.
Terms: Fall 2015, Winter 2016
Instructors: There are no professors associated with this course for the 2015-2016 academic year.
Biochemistry graduate students
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BIOC 703 Research Seminar 2 **
Overview
Biochemistry : Presentation of the planned thesis including central findings and original contribution to knowledge in the field of research.
Terms: Fall 2015, Winter 2016
Instructors: There are no professors associated with this course for the 2015-2016 academic year.
Restriction: Ph.D. students in Biochemistry
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COMP 616D1 Bioinformatics Seminar (1.5 credits)
Overview
Computer Science (Sci) : Introduction to current trends in Bioinformatics and closely related fields such as genomics and proteomics.
Terms: Fall 2015
Instructors: Hallett, Michael Trevor; Blanchette, Mathieu (Fall)
Restrictions: This seminar is restricted to graduate students in the Bioinformatics Option. Enrolment is limited to 30 students.
Note: The seminar will meet for 3 hours every second week over Fall and Winter semesters.
Students must register for both COMP 616D1 and COMP 616D2.
No credit will be given for this course unless both COMP 616D1 and COMP 616D2 are successfully completed in consecutive terms.
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COMP 616D2 Bioinformatics Seminar (1.5 credits)
Overview
Computer Science (Sci) : See COMP 616D1 for description.
Terms: Winter 2016
Instructors: Hallett, Michael Trevor (Winter)
Prerequisite: COMP 616D1.
No credit will be given for this course unless both COMP 616D1 and COMP 616D2 are successfully completed in consecutive terms.
* Students promoted directly 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.
** 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 570 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: Winter 2016
Instructors: Kiss, Robert; Nilsson, Tommy (Winter)
Winter
Prerequisite: BIOC 311 or equivalent
Restriction: Open to U3 and graduate students
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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: Fall 2015
Instructors: Duchaine, Thomas; Montpetit, Alexandre; Hallett, Michael Trevor (Fall)
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 2015
Instructors: Muller, William Joseph; Teodoro, Jose Guerreiro; Gallouzi, Imed Eddine (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, computational methods and theoretical approaches to the determination and analysis of macromolecular structures. Theory and practical applications will be covered. Examples will include interpretation of structure as it applies to biological functions. In conjunction with the Universit茅 de Montr茅al.
Terms: Winter 2016
Instructors: Nagar, Bhushan; Schmeing, Thomas Martin; Gehring, Kalle Burgess (Winter)
Winter
Prerequisite: BIOC 450 or equivalent
Lectures in French and English
Offered in the Fall 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 2016
Instructors: Young, Jason; Dejgaard, Kurt; Thomas, David (Winter)
Winter
Prerequisite: BIOC 450 or equivalent, or permission of instructor.
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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 2016
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 2015
Instructors: Beauchemin, Nicole; Miller, Wilson H (Fall)
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
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EXMD 635D2 Experimental/Clinical Oncology (3 credits)
Overview
Experimental Medicine : See EXMD 635D1 for course description.
Terms: Winter 2016
Instructors: Beauchemin, Nicole; Miller, Wilson H (Winter)
Prerequisite: EXMD 635D1
No credit will be given for this course unless both EXMD 635D1 and EXMD 635D2 are successfully completed in consecutive terms
Plus 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 2015-2016 academic year.
Instructors: There are no professors associated with this course for the 2015-2016 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 2015-2016 academic year.
Instructors: There are no professors associated with this course for the 2015-2016 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 2016
Instructors: Salavati, Reza; Sulea, Traian (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: Winter 2016
Instructors: Hallett, Michael Trevor (Winter)
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 2015-2016 academic year.
Instructors: There are no professors associated with this course for the 2015-2016 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.