Note: This is the 2014–2015 edition of the eCalendar. Update the year in your browser's URL bar for the most recent version of this page, or click here to jump to the newest eCalendar.
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 (11 credits)
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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 2014
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 2015
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.
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PHGY 604 Responsible Conduct in Research
Overview
Physiology : This course provides students with information on the following areas: 1) an ethics overview; 2) scientific conduct and misconduct; 3) research authorship and peer review; and 4) research on human and animal subjects.
Terms: Fall 2014
Instructors: White, John H (Fall)
Students having taken this course during the M.Sc. in Physiology will not be obliged to re-take the course if transferring to the Ph.D.
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PHGY 701 Ph.D. Comprehensive Examination
Overview
Physiology : The Ph.D. comprehensive exam will be completed between 12-18 months of commencing the program and is designed to ensure that the student's research encompasses the i) acquisition of a comprehensive knowledge of scientific literature; ii) the development of experimental skills and technical expertise with a deep understanding of the experimental design thus iii) ensuring a high degree of scholarship in the thesis submission.
Terms: Fall 2014, Winter 2015
Instructors: There are no professors associated with this course for the 2014-2015 academic year.
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PHGY 703 Ph.D. Progress Seminar 1 (1 credit)
Overview
Physiology : The Progress Seminar is a "work in progress" seminar on what the student has accomplished to date. Following completion of the comprehensive exam, the seminar should be presented to the student's supervisory committee as a formal presentation of approximately 30 minutes followed by a question and discussion period.
Terms: Fall 2014, Winter 2015
Instructors: There are no professors associated with this course for the 2014-2015 academic year.
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PHGY 704 Ph.D. Progress Seminar 2 (1 credit)
Overview
Physiology : A "work in progress" seminar, intended as a report on student progress following the Thesis Proposal Seminar.
Terms: Fall 2014, Winter 2015
Instructors: There are no professors associated with this course for the 2014-2015 academic year.
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PHGY 720 Ph.D. Seminar Course 1 (1 credit)
Overview
Physiology : Required for Ph.D. students. Coordinated in conjunction with the weekly Departmental seminar series, students will meet for one hour before each seminar to critically discuss papers on the subject of the weekly seminar. Students will take turns introducing the papers and leading discussions on an overview of the research topic, some of the methodologies, results and conclusions.
Terms: Fall 2014, Winter 2015
Instructors: Orlowski, John (Fall)
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PHGY 721 Ph.D. Seminar Course 2 (1 credit)
Overview
Physiology : Required for Ph.D. students. Coordinated in conjunction with the weekly Departmental seminar series, students will meet for one hour before each seminar to critically discuss papers on the subject of the weekly seminar. Students will take turns introducing the papers and leading discussions on an overview of the research topic, some of the methodologies, results and conclusions.
Terms: Fall 2014, Winter 2015
Instructors: Orlowski, John (Fall) Orlowski, John (Winter)
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PHGY 722 Ph.D. Seminar Course 3 (1 credit)
Overview
Physiology : Required for Ph.D. students. Coordinated in conjunction with the weekly Departmental seminar series, students will meet for one hour before each seminar to critically discuss papers on the subject of the weekly seminar. Students will take turns introducing the papers and leading discussions on an overview of the research topic, some of the methodologies, results and conclusions.
Terms: Fall 2014, Winter 2015
Instructors: Orlowski, John (Fall) Orlowski, John (Winter)
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PHGY 723 Ph.D. Seminar Course 4 (1 credit)
Overview
Physiology : Required for Ph.D. students. Coordinated in conjunction with the weekly Departmental seminar series, students will meet for one hour before each seminar to critically discuss papers on the subject of the weekly seminar. Students will take turns introducing the papers and leading discussions on an overview of the research topic, some of the methodologies, results and conclusions.
Terms: Fall 2014, Winter 2015
Instructors: Orlowski, John (Fall) Orlowski, John (Winter)
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PHGY 724 Ph.D. Seminar Course 5 (1 credit)
Overview
Physiology : Required for Ph.D. students. Coordinated in conjunction with the weekly Departmental seminar series, students will meet for one hour before each seminar to critically discuss papers on the subject of the weekly seminar. Students will take turns introducing the papers and leading discussions on an overview of the research topic, some of the methodologies, results and conclusions.
Terms: Fall 2014, Winter 2015
Instructors: Orlowski, John (Fall) Orlowski, John (Winter)
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PHGY 725 Ph.D. Seminar Course 6 (1 credit)
Overview
Physiology : Required for Ph.D. students. Coordinated in conjunction with the weekly Departmental seminar series, students will meet for one hour before each seminar to critically discuss papers on the subject of the weekly seminar. Students will take turns introducing the papers and leading discussions on an overview of the research topic, some of the methodologies, results and conclusions.
Terms: Fall 2014, Winter 2015
Instructors: Orlowski, John (Fall)
Complementary Courses (6 credits)
6 credits to be chosen from the following courses:
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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: Fall 2014
Instructors: Stromvik, Martina (Fall)
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 2014-2015 academic year.
Instructors: There are no professors associated with this course for the 2014-2015 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 2015
Instructors: Salavati, Reza; Rouiller, Isabelle; 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 2015
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.
Faculty of Medicine—2014-2015 (last updated Feb. 18, 2014) (disclaimer)
