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Note: This is the 20122013 edition of the eCalendar. For the most recent publication, click here.

Doctor of Philosophy (Ph.D.); Computer Science — Bioinformatics

Offered by: Computer Science     Degree: Doctor of Philosophy

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

  • COMP 616D1 Bioinformatics Seminar (1.5 credits)

    Offered by: Computer Science (Faculty of Science)

    Administered by: Graduate Studies

    Overview

    Computer Science (Sci) : Introduction to current trends in Bioinformatics and closely related fields such as genomics and proteomics.

    Terms: Fall 2012

    Instructors: Michael Trevor Hallett (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.
  • COMP 616D2 Bioinformatics Seminar (1.5 credits)

    Offered by: Computer Science (Faculty of Science)

    Administered by: Graduate Studies

    Overview

    Computer Science (Sci) : See COMP 616D1 for description.

    Terms: Winter 2013

    Instructors: Michael Trevor Hallett (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.
  • COMP 700 Ph.D. Comprehensive Examination

    Offered by: Computer Science (Faculty of Science)

    Administered by: Graduate Studies

    Overview

    Computer Science (Sci) : An examination that must be passed by all doctoral candidates in order to continue in the doctoral program.

    Terms: Fall 2012, Winter 2013

    Instructors: Xiao-Wen Chang (Fall) Xiao-Wen Chang (Winter)

  • COMP 701 Thesis Proposal and Area Examination (3 credits)

    Offered by: Computer Science (Faculty of Science)

    Administered by: Graduate Studies

    Overview

    Computer Science (Sci) : Submission of doctorate thesis proposal and examination that assesses the student's breadth of knowledge in the research area.

    Terms: Fall 2012, Winter 2013, Summer 2013

    Instructors: Xiao-Wen Chang (Fall) Xiao-Wen Chang (Winter)

Complementary Courses

Two courses chosen from the following:

  • BINF 621 Bioinformatics: Molecular Biology (3 credits)

    Offered by: Plant Science (Agricultural & Environmental Sciences)

    Administered by: Graduate Studies

    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 2012

    Instructors: Martina Stromvik (Fall)

    • Restriction: Enrolment by students in the Bioinformatics option or by permission from the course coordinators only. Limited to 30 students.
  • BMDE 652 Bioinformatics: Proteomics (3 credits)

    Offered by: Biomedical Engineering (Faculty of Medicine)

    Administered by: Graduate Studies

    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 2012-2013 academic year.

    Instructors: There are no professors associated with this course for the 2012-2013 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.
  • BTEC 555 Structural Bioinformatics (3 credits)

    Offered by: Parasitology (Agricultural & Environmental Sciences)

    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 2013

    Instructors: Reza Salavati (Winter)

    • Winter
    • 1-hr lecture, followed by 2 hrs of computer lab.
    • Prerequisite: Molecular biology or biochemistry, and basic bioinformatics, or permission of instructor.
  • COMP 618 Bioinformatics: Functional Genomics (3 credits)

    Offered by: Computer Science (Faculty of Science)

    Administered by: Graduate Studies

    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 2013

    Instructors: Michael Trevor Hallett (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.
  • PHGY 603 Systems Biology and Biophysics (3 credits)

    Offered by: Physiology (Faculty of Medicine)

    Administered by: Graduate Studies

    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 2012-2013 academic year.

    Instructors: There are no professors associated with this course for the 2012-2013 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.

Additional courses at the 500, 600, or 700 level may be required at the discretion of the candidate's supervisory committee. Students who have completed the M.Sc.-level option in Bioinformatics must complete 6 credits of complementary courses not taken in the master's program.

Faculty of Science—2012-2013 (last updated Dec. 20, 2012) (disclaimer)