Summary

• Degrees offered: Doctorate in Philosophy (PhD)
• Registration status option: Full-time
• Language of instruction: English
• Program option (expected duration of the program):
  • with thesis (12 full-time terms; 48 consecutive months)
• Academic units: Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology.

Program Description

The programs refine critical and scholarly skills in fields and areas of specialization and prepare students for a variety of careers in teaching and research both within and outside of academia, including in a governmental, clinical, or industrial setting. Graduates are expected to have acquired autonomy in conducting research, in preparing scholarly publications, through a training that includes course work, research seminars, and independent research leading to a thesis.

The Department is a participating unit in the following collaborative programs: the Bioinformatics program (at the master’s level) and the Pathology and Experimental Medicine program (at the master's and doctoral levels).

The doctoral program participates in the Combined MD / PhD Program, which allows students to graduate with both a PhD in Microbiology and Immunology and an MD. For more information please see the website of the Faculty of Medicine.

Main Areas of Research

• Microbiology
• Host Biology

Other Programs Offered Within the Same Discipline or in a Related Area

• Doctorate in Philosophy Microbiology and Immunology (PhD)
• Doctorate in Philosophy Microbiology and Immunology Specialization in Pathology and Experimental Medicine (PhD)

Fees and Funding

Program fees:

• The estimated amount for university fees associated with this program are available under the section Finance your studies.
• International students enrolled in a French-language program of study may be eligible for a differential tuition fee exemption.
• To learn about possibilities for financing your graduate studies, consult the Awards and financial support section.

Notes

• Programs are governed by the general regulations in effect for graduate studies.
• In accordance with the University of Ottawa regulation, students have the right to complete their assignments, examinations, research papers, and theses in French or in English. Research activities can be conducted either in English, French or both, depending on the language used by the professor and the members of his or her research group.
   

Program Contact Information

Graduate Studies Office, Faculty of Medicine

451 Smyth Road, Room RGN 2016

Ottawa, Ontario, Canada

K1N 6N5
 

Tel.: 613-562-5215

Email: grad.med@uottawa.ca

For the most accurate and up to date information on application deadlines, language tests and other admission requirements, please visit the specific requirements webpage.

To be eligible, candidates must:

• Have a master's degree in microbiology or immunology (or equivalent) with a minimum average of B+ (75%).

Note: International candidates must check the admission equivalencies for the diploma they received in their country of origin.

• Demonstrate a good academic performance in previous studies as shown by official transcripts, research reports, abstracts or any other documents demonstrating research skills.
• The requirements outlined above are a minimum. The Admission Committee reserves the right to add any course considered essential in light of the student’s background. The courses BNF 5106 and/or BNF 6100 could be added to the student’s program requirements.
  
   
• Identify at least one professor who is willing to supervise your research and thesis.
  • We recommend that you contact potential thesis supervisors as soon as possible.
  • To register, you need to have been accepted by a thesis supervisor.
  • The thesis director must be a member of the collaborative program.

Language Requirements

Applicants must be able to understand and fluently speak the language of instruction in the program to which they are applying. Proof of linguistic proficiency may be required.

Applicants whose first language is neither French nor English must provide proof of proficiency in the language of instruction.

Note: Candidates are responsible for any fees associated with the language tests.

Notes

• The admission requirements listed above are minimum requirements and do not guarantee admission to the program.
• Admissions are governed by the general regulations in effect for graduate studies.
• Candidates must apply to the primary program and indicate in their application for admission to the PhD program in Microbiology and Immunology that they wish to be accepted into the collaborative-specialization in Bioinformatics. Students are normally informed about their acceptance into the collaborative program at the same time as being informed about their admission into the primary program. To be admitted to the collaborative program, candidates must also be accepted in the primary program.

Fast-Track from Master’s to PhD

Students enrolled in the master’s program in Microbiology and Immunology at the University of Ottawa may be eligible to fast-track directly into the doctoral program without writing a master’s thesis, provided the following conditions are met:

• Successful completion of the seminar and all the core courses required for the master's program.
• Satisfactory progress in the research program.
• Written recommendation by the supervisor and the advisory committee.
• Approval by the graduate studies committee.

Note: The transfer must take place within sixteen months of initial enrollment in the master’s. Please note that the minimal admission average requirements for the doctoral program must also be met. Following transfer, all of the requirements of the doctoral program must be met.

The Department may require students to take additional courses, depending on their backgrounds.

Students must meet the following requirements:

Course List

Code	Title	Units
Compulsory Courses: 1
MED 8166	Professionalism and Professional Skills
3 optional course units in microbiology and immunology (MIC) at the graduate level 2		3 Units
3 optional course units in microbiology and immunology (MIC) at the 8000 level 2		3 Units
Seminars:
MIC 8366	PhD Seminar 3	3 Units
BNF 8166	Seminar in Bioinformatics 4	3 Units
Comprehensive Examination:
MIC 9998	Comprehensive Examination
Thesis:
THD 9999	Doctoral Thesis 5, 6

Note(s)

¹

Students in the BNF PhD program who already have taken BNF 5106 will be required to take one of BCH 5101, BCH 8110, BIO 8301, BNF 5107 or CHM8309.

²

The optional course units must be approved by the Department.

³

The seminar course involves the presentation of a seminar and regular attendance at the departmental seminars.

⁴

The seminar course in bioinformatics involves a written report, the presentation of a seminar, and regular attendance at departmental seminars.

⁵

Successful presentation and defense of a thesis based on original research carried out under the direct supervision of a research faculty member in the Department.

⁶

Students are responsible for ensuring they have met all of the thesis requirements.

Research at the University of Ottawa

Located in the heart of Canada’s capital, a few steps away from Parliament Hill, the University of Ottawa ranks among Canada’s top 10 research universities. Our research is founded on excellence, relevance and impact and is conducted in a spirit of equity, diversity and inclusion.

Our research community thrives in four strategic areas:

• Creating a sustainable environment
• Advancing just societies
• Shaping the digital world
• Enabling lifelong health and wellness

From advancing healthcare solutions to tackling global challenges like climate change, the University of Ottawa’s researchers are at the forefront of innovation, making significant contributions to society and beyond.

Research at the Faculty of Medicine

“The Faculty of Medicine has a long history of conducting both basic and clinical research of the highest quality. Many of our high profile research projects are conducted in partnership with affiliated-teaching hospitals and research institutes. These partnerships lead to biomedical discoveries that have a significant impact on health care. In the process they educate the next generation of Canadian scientists. Our research activity also attracts significant investment, which stimulates the Ottawa economy.”

- Dr. Jocelyn Côté, Vice-Dean, Research

Facilities, Research Centres and Institutes at the Faculty of Medicine

• Centre for Neural Dynamics
• University of Ottawa Centre for Neuromuscular Disease
• Centre for Research in Biopharmaceuticals and Biotechnology
• Canadian Partnership for Stroke Recovery
• Kidney Research Centre
• University of Ottawa Skills and Simulation Centre
• Medical Devices Innovation Institute
• Ottawa Institute of Systems Biology
• University of Ottawa Brain and Mind Research Institute

BNF 5106 Bioinformatics (3 units)

Major concepts and methods of bioinformatics. Topics may include, but are not limited to: genetics, statistics & probability theory, alignments, phylogenetics, genomics, data mining, protein structure, cell simulation and computing.
Course Component: Lecture

BNF 5107 Applied Bioinformatics (3 units)
Computational knowledge discovery in and the dynamic nature of cellular networks. Includes, but is not limited to, knowledge representation, large scale data integration, data mining and computational systems biology. This course is equivalent to BIOL 5516 at Carleton University.
Course Component: Lecture

BNF 5506 Bioinformatique (3 crédits)
Concepts et méthodes en bioinformatique. Les sujets abordés peuvent inclure, entre autres, la génétique, les statistiques et les théories des probabilités, les alignements, la phylogénétique, la génomique et la structure de protéines.
Volet : Cours magistral

BNF 6100 MSc Seminar (3 units)
Current topics in bioinformatics presented by program professors and invited speakers. Oral presentation and written report required. Graded S (Satisfactory) / NS (Not satisfactory).
Course Component: Lecture

BNF 6500 Séminaire de maîtrise (3 crédits)
Sujets courants en bioinformatique présentés par des professeurs membres du programme et des conférenciers invités. Présentation orale et rapport écrit requis. Noté S (satisfaisant) ou NS (non satisfaisant).
Volet : Cours magistral

BNF 8166 Seminar in Bioinformatics (3 crédits)
Current research topics in bioinformatics presented by PhD students and invited speakers. Oral presentation required. Graded S (Satisfactory) / NS (Not satisfactory).

BNF 8766 Séminaire en bioinformatique (3 crédits)
Sujets courants en bioinformatique présentés par des étudiants en PhD et des conférenciers invités. Présentation orale requise. Noté S (satisfaisant) ou NS (non satisfaisant).

MIC 5100 Pathogen Interactions and Host (3 units)
This course will examine current issues in microbiology/immunology. Topics to be chosen to allow discussion across the broad areas of virology, immunology and bacteriology. Within each of the modules, the focus will be on host-pathogen interactions at the molecular level, how microorganisms utilize, modify or disrupt host cell functions, including immune cell functions and immune responses, to establish infection and cause diseases, or on immunological diseases which may have an infectious component.
Course Component: Lecture
Prerequisite: At least one undergraduate course in microbiology and/or immunology and one course in molecular biology.

MIC 5366 MSc Seminar (3 units)
Attendance at two half-day symposia with guest speakers, attendance and participation in the annual BMI Student Symposium and BMI Poster Day, attendance at BMI seminars relevant to Microbiology and Immunology. Students must present at least one poster and one oral presentation during the course of their program. Graded S (Satisfactory) or NS (Not satisfactory).
Course Component: Seminar

MIC 6003 Thesis Research in Microbiology and Immunology III
Volet / Course Component: Cours magistral / Lecture

MIC 8120 ADVANCED TOPICS IN IMMUNOMETABOLISM (3 units)
An advanced study of the recent literature dealing with the field of immunometabolism, with a focus on both immunometabolic pathways and the specialized techniques that allow for understanding chronic inflammatory/metabolic diseases, such as cancer, type 2 diabetes, obesity, atherosclerosis, neurodegeneration, etc.
Course Component: Lecture

MIC 8122 Advanced Topics in Immunology (3 units)
Focus on cellular immunology, including thymocyte maturation, induction and regulation of cellular responses, immune responses to pathogens, immunological memory, tolerance. Student assessments to be conducted by two methods: weekly assessment of student presentations and participation in class discussions; assessment of take-home assignments such as completion of a research grant on a topic covered in the course. To be offered alternate years subject to sufficient demand.
Course Component: Seminar
Prerequisite: MIC 4125.

MIC 8124 Advanced Topics in Cell Death (3 units)
Molecular mechanisms of cell death. Particular attention to be paid to role of aberrant cell death in human disease. Offered in the Fall of odd numbered years.
Course Component: Lecture

MIC 8125 Special Topics in Microbiology and Immunology (3 units)
Discussion of current topics in Microbiology and Immunology. Topics to vary from year to year depending on the interest of faculty members offering the course and students. Student assessments to be conducted by two methods: weekly assessment of student presentations and participation in class discussions; assessment of take-home assignments such as completion of a research grant on a topic covered in the course.
Course Component: Lecture
Prerequisite: Permission of the course coordinator.

MIC 8126 Immunochemistry (3 units)
Focus is on antigen structure of protein and carbohydrate antigens, receptor structure of B cells and T cells, structure of MHC molecules, accessory molecules and cytokine receptors and cell signalling pathways induced by the antigen and cytokine receptors. Student assessments to be conducted by two methods: weekly assessment of student presentations and participation in class discussions; assessment of takehome assignments such as completion of a research grant on a topic covered in the course. To be offered alternate years subject to sufficient demand.
Course Component: Lecture
Prerequisite: MIC 4125.

MIC 8129 Current Topics in Haematopoietic Stem Cells and Immune Development (3 units)
This course will focus on the haematopoietic system that gives rise to the many cell types of the immune system. Topics to be covered include the developmental processes of embryonic stem cell differentiation into mesoderm and then into haematopoietic and non-haematopoietic progenitors; development of adult haematopoietic and immune systems; symmetric and asymmetric division of cells; intrinsic transcription factors and extracellular microenvironment factors regulating cell fate; immunological aspects of stemcell based therapy; new technologies and their use in the field, and experimental design.
Course Component: Lecture
Prerequisite: At least one undergraduate course in immunology or cell biology.

MIC 8134 Structure and Expression of Eukaryotic and Prokaryotic Genomes (3 units)
Sequencing of eukaryote and prokaryote genomes with emphasis on recent technologies, sequence alignments and databases and assembly of genomes from massively parallel sequencing data. Focus on mapping studies, including linkage disequilibrium-based genome-wide association study (GWAS), to characterize functional variants associated with complex traits. Analysis and structure of microbial metagenomes from environmental and human habitats, including structure-function analysis of microbial communities, microbiota-human disease correlations, and molecular phylogeny. Genome expression, including measures of RNA transcripts and proteins and statistical analysis of data. Combination of various-omics data to understand gene-environment interactions.
Course Component: Lecture

MIC 8236 Advanced Topics in Virology (3 units)
An in-depth presentation of current topics in virological research. Topics will vary from year to year. To be offered every alternate year subject to sufficient demand.
Course Component: Lecture

MIC 8238 Advanced Topics in Bacteriology - Mechanisms of Pathogenesis (3 units)
Recent advances and current topics in selected areas of bacteriology with emphasis on mechanisms of pathogenesis. Students present and discuss journal articles. Offered every alternate year subject to sufficient demand.
Course Component: Lecture

MIC 8241S Seminars II (2 crédits / 2 units)
Every graduate student will be required to attend the weekly departmental seminars. Compulsory for all graduate students.
Volet / Course Component: Cours magistral / Lecture

MIC 8242S Seminars III (2 crédits / 2 units)
Every graduate student will be required to attend the weekly departmental seminars. Compulsory for all graduate students.
Volet / Course Component: Cours magistral / Lecture

MIC 8243S Seminars IV (2 crédits / 2 units)
Every graduate student will be required to attend the weeklydepartmental seminars. Compulsory for all graduate students.
Volet / Course Component: Cours magistral / Lecture

MIC 8244S Seminars V (2 crédits / 2 units)
Every graduate student will be required to attend the weekly departmental seminars. Compulsory for all graduate students.
Volet / Course Component: Cours magistral / Lecture

MIC 8366 PhD Seminar (3 units)
Attendance at two half-day symposia with guest speakers, attendance and participation in the annual BMI Student Symposium and BMI Poster Day, attendance at BMI seminars relevant to Microbiology and Immunology. Students will present a poster in their first and every alternate year, and an oral presentation the second and every alternate year until they have permission to write their thesis. Graded S (Satisfactory) / NS (Not satisfactory).
Course Component: Seminar

MIC 8401 Advanced Topics in Bacterial Genetics (3 units)
Microbial genetic and genomic methods: origin, purpose and functioning. Analysis and use of genomes to study bacterial pathogenesis and host-microbe interactions.
Course Component: Lecture
Prerequisite: MIC 5224 or equivalent.

MIC 8500 Special Topics in Health- Related Environmental Microbiology (3 crédits)
Recent advances and current topics in selected areas of health-related environmental microbiology. Topics reflect student interest. Offered in alternate years subject to sufficient demand.
Volet : Cours magistral
Prerequisite: MIC 5500 or equivalent.

MIC 8534 Structure et expression des génomes procaryotes et eucaryotes (3 crédits)
Le séquençage des génomes eucaryotes et procaryotes, avec un accent particulier sur les technologies récentes, l'alignement des séquences et les bases de données, et l'assemblage des génomes à partir de données générées par séquençage haut débit. Les études de cartographie comparée incluant les études d'associations pangénomiques basées sur le déséquilibre de liaison pour caractériser les variantes fonctionnelles associées aux traits complexes. L'analyse et la structure de métagénomes microbiens issus d'habitats humains et environnementaux incluant l'analyse structurefonction des communautés microbiennes, les corrélations entre les maladies humaines et le microbiome ainsi que la phylogénie moléculaire. L'expression génique incluant les mesures de transcriptomes et de protéomes ainsi que l'analyse statistique des données. La combinaison des différentes données omiques pour comprendre les interactions gène-environnement.
Volet : Cours magistral

MIC 8700 Biology and Pathogenesis of HIV Infection (3 crédits)
Biology and pathogenesis of Human Immunodeficiency Virus (HIV) infection. Genetics, replication, structure, regulation of gene expression, immunopathogenesis, antiviral therapy and vaccine development. Offered in alternate years subject to sufficient demand.
Volet : Séminaire

MIC 9998 Examen de synthèse / Comprehensive Examination
Volet / Course Component: Recherche / Research