MDGE Series of 1 Unit Courses
To satisfy degree requirements (MSc - 6 units) or (PhD - 9 units), students can choose from the MDGE 600- or MDGE 700-series of 1 unit courses listed below.
All students in the Biochemistry & Molecular Biology graduate program are required to take MDGE 721 (1 unit).
Registration for all MDGE 1-unit courses must be done as follows:
*NEW!* Starting Fall 2024, students must submit their requests DIRECTLY TO THE COURSE INSTRUCTORS to enroll into MDGE 600- and 700-level courses. Course Instructors will manage student registrations, NO LONGER the Course Coordinators (Drs. Pinaki Bose and Timothy Shutt).
- To register, students must complete the MDGE Course Request Form and submit it DIRECTLY to the course instructors NOT to the Course Coordinators. These are typically done in batches in August (for Fall), December (for Winter), and April (for Spring).
- The course instructors will check your eligibility.
- Instructors will coordinate with GSE to unblock/enroll students.
- If approved, students will be notified by GSE of the registration block removal via email and are responsible for registering themselves in the course within 24 hours of that notice.
- You will know that you have successfully registered if the course appears in your Student Centre within 24 hours.
- PLEASE NOTE: Failure to register in your course may result in being assessed late registration fees.
If you wish to request course outlines for MDGE courses, please contact gsecourses@ucalgary.ca and indicate the course code and name. If you are requesting a past course outline, please indicate what semester it was offered.
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MDGE 1-Unit courses offer greater flexibility and allow students to tailor their learning needs.
For students in the Bioinformatics specialty program within BMB, please contact Dr. Quan Long (quan.long@ucalgary.ca) for enrolment in MDGE 610, 612 and 614. Both 600- and 700-level courses count the same towards a graduate degree.
It is strongly recommended that students take no more than two courses at the same time.
The enrollment for most of the 1-unit courses is typically limited to 12 students (only MDGE 620 and MDGE 721 have unlimited enrollment). However, this limit can be exceeded with instructor approval.
Courses may NOT run if fewer than 4 students are enrolled.
Enrollment will be prioritized (but not guaranteed) for MDGE and MDSC students who have requested enrollment well in advance. Note: Graduate students from other programs can also request enrollment in MDGE 1-unit courses, but a spot will not be confirmed until two weeks prior to the first class.
As some courses are often fully subscribed, it is recommended that enrollment requests be submitted to instructors as soon as possible and well in advance of the course beginning. Last minute requests may not be granted.
Prior to requesting enrollment, students should discuss their course selection with their supervisor and may also want to consult their thesis supervisory committee.
(1 unit)
Instructor: Dr. Jason de Koning
An exploration of the algorithmic foundations of established and emerging bioinformatics techniques, spanning dynamic programming, stochastic processes, probabilistic modelling, Bayesian inference, machine learning, and other topics from computational statistics. Big versus small data, divergent philosophical perspectives, and recent controversies in genomics are addressed through in-class discussions, current literature, and self-directed workshops.
Prerequisite: Admission to the Bioinformatics specialization of the Biochemistry and Molecular Biology graduate program or consent of the instructor.
Notes: This course assumes some computational background including programming or scripting ability.
(1 unit)
Instructor: Dr. Quan Long
Basic statistical/computational theories and current libraries for machine learning will be introduced. Content may evolve according to the progress of the field but includes: 1. History and current status of machine learning. 2. Linear models and regularization. 3. Support vector machine and kernel methods. 4. Neural networks (including deep learning). The module introduces both theories and implementations, with a focus on applying the techniques to biological and medical big-data. The level of difficulties may be adjusted according to the diverse backgrounds of the attendees.
Prerequisite: Foundations of Bioinformatics or consent of the instructor.
(1 unit)
Coordinator: Dr. Jason de Koning (team taught)
An introduction to how biologists approach the study of the problems of life, with an emphasis on sub-organismal scales (molecular and cell biology, biochemistry, and genetics), model organisms, and evolutionary processes.
Notes: This course is intended for students in the Bioinformatics specialization of the Biochemistry and Molecular Biology graduate program who lack prior significant course work in the life sciences.
(1 unit)
DRs. Pinaki Bose and Gareth Williams
This course provides an overview of cancer biology and is primarily intended for students whose research may require an understanding of the disease and but have little prior teaching on this topic. The course will give a broad overview on cancer including its causes and incidence, cellular and tissue phenotypes of cancer, cancer genomics, molecular mechanisms driving cancer formation, growth, and metastasis. The course will also introduce students to cancer treatments; and modern research approaches used to study cancer and improve cancer treatment.
Objectives and Focus
The learning objective here is for students to gain a working knowledge of proteomics and metabolomics as it relates to research and cancer biology. We will focus on the objectives of these disciplines, the technologies, methods and informatics used in biological mass spectrometry as applied to the ‘omics. As much as possible, examples will be drawn from cancer-related disciplines (research or clinical). Assessment will involve the analysis of a protein sample provided to (or by) the student. It will require lab-work in the SAMS Centre for Proteomics, and the generation of an informatics report. Each student will be expected to keep up with assigned readings, and select a paper from the recent literature in either proteomics or metabolomics, for presentation in journal-club style.
Objectives and Focus
The learning objective here is for students to gain a working knowledge of tumor immunobiology and immunotherapy. Fundamental and translational topics will be addressed, including: tumour immunogenicity, tumour immune surveillance and editing, immune escape, active immunotherapy, passive immunotherapy, virotherapy and viral vaccines, therapies targeting immunosuppressive mechanisms, and personalized immunotherapy. A basic understanding of tumour biology and immunology is advantageous but not a prerequisite. Classes will consist of an introductory lecture on the topic, followed by a student presentation (mock PDF presentation) and questions. Other evaluation components include a mock PDF fellowship application and a short final exam.
Objectives and Focus
The learning objectives here are for students to gain an understanding of the links between cancer & aging, the experimental definition of the cell cycle, drivers and regulators of the cell cycle (including oncogenes & tumor suppressors, cyclins, CDKs, etc.). An overview of biological and replicative aging will include human biological lifespan potential, changes in life expectancy and rectangularization of the survival curve, experimental models used in aging research, forms of aging in mammals and the "Hayflick model" of replicative senescence and the impact of telomerase expression on cellular aging. Students will need to keep up with assigned readings and select a recent paper in the areas of biological aging and/or cancer for presentation to the class, and will be responsible for preparing critiques of the presentations by class mates.
Objectives and Focus
The learning objective here is for students to master the fundamentals of eukaryotic chromatin assembly, dynamic chromatin regulation (during differentiation, cell cycle progression and the DNA damage response) and post-translational modifications that comprise the field of epigenetics. We will cover the concepts of DNA methylation, histone acetylation, histone methylation, histone phosphorylation (and other histone PTMs), histone variants, regulatory siRNA, nucleosome remodelling and higher-order chromatin organization. Cancer and aging-associated epigenetic alterations will be discussed in detail. Experimental methodologies for epigenetics, both historical and modern, will be reviewed in detail via publication-focused presentations by lecturers and students.
Objectives and Focus
The learning objective here is for students to gain an understanding of the major DNA repair pathways in eukaryotic cells, highlighting proteins involved in the cellular responses to ionizing radiation or anti-cancer chemotherapy. We will cover the main DNA repair pathways including base excision repair, mismatch repair, nucleotide excision repair, and DNA single strand and double strand break repair. We will stress the mechanisms of non-homologous end joining and homologous recombination repair. The topics of ATM and ATR dependent signaling, H2AX foci and roles of protein phosphorylation and protein ubiquitination, the Fanconi Anemia pathway, and the relationship of replication stress and telomere maintenance to the DNA damage response will be covered.
Objectives and Focus
The learning objective here is for students to gain an understanding of the interaction of the cancer cell with the host stroma. Angiogenesis, cell invasion and metastasis will be discussed from molecular, cell biological and clinical perspectives. Methods of experimental modelling of metastatic behavior and angiogenesis, as well as their respective advantages and limitations will be discussed. There will be lab demonstration of available in vitro and in vivo invasion/metastasis/angiogenesis models. Students will be evaluated on the basis of their literature review and presentation on a topic within this area, a focused research proposal, and written assessments of student presentations.
Objectives and Focus
The learning objective here is for students to gain an understanding of the fundamental principles and regulation of receptor-mediated and intracellular-mediated signaling pathways that have important implications in cancer biology. Lectures will be given covering various topics in signaling including a general introduction on receptor and intracellular signaling mechanisms with focus on receptor tyrosine kinase (RTK) and serine/threonine kinase receptor signaling, regulation and function of the intracellular tyrosine kinase Src and its downstream signaling, and role of phosphatase in signaling. Students will also be presenting journal club presentations on assigned papers in areas that complement the lecture materials where other concepts or pathways in signaling are covered.
Objectives and Focus
The primary learning objective of this course is to gain an understanding of the fundamental biological concepts and methods in translational cancer research for novel therapeutics development. During this course, students are expected to (i) become familiar with the key concepts in new agents discovery studies and early phase clinical trials, (ii) understand the role of targeted agents and immunotherapeutic approaches in current cancer treatments, and (iii) learn about the experimental approaches for the identification of effective novel therapeutics and treatment approaches for refractory malignancies in the future.
Objectives and Focus
The learning objective here is for students to gain an understanding of fundamental principles of central nervous system development. The module encompasses the first third of MDSC 619.01, which is a core course for all Neuroscience graduate students. The first third of MDSC619.01 can be taken as a stand-alone module. It will cover basic principles of neural induction and neurogenesis, regionalization of the neural tube, neuronal migration, circuit formation (axons and dendrites), neurodevelopmental disorders, and model organisms. Students will be evaluated in a final exam and in two assignments. The first assignment will be to write a News and Views article on a recent publication in neural development, and the second will be a Presentation of new animal models for neurological diseases.
Objectives and Focus
The primary objective of this course is to provide trainees a comprehensive understanding of how cancer can be triggered by our environment. By the end of this course, students will be able to:
(1) understand the scale of global environmentally-induced cancer problem, (2) understand the molecular mechanisms underlying the common causes of cancer, including viruses, environmental toxins, radiation and genetic vulnerability, (3) describe the major human cellular mechanisms of defence against chemical, radiation or viral carcinogen exposure, and (4) appreciate modifiers of environmental cancer risk in terms of behaviour, location, demographics and genetics.
Objectives and Focus
This core module covers landmark discoveries in biochemistry and molecular biology (BMB), summarizes new and evolving BMB technologies, and how these can be implemented into modern research programs. Students will learn how to apply the scientific method at an advanced graduate level, technical and ethical considerations surrounding data analysis, and essential skills for communicating scientific discoveries in the realm of peer-reviewed publication, presentation and grant application contexts.
Objectives and Focus
This module encompasses a graduate-level understanding of how nucleotides are synthesized, utilized and degraded in cells. Students will gain an understanding of structure-function relationships for nucleic acids, advanced knowledge of the enzymatic basis of DNA replication, how genes are read, how the transcribed RNA is processed, and how genes are regulated through a coordinated collaboration between proteins and nucleic acid sequences. Emerging technologies in the study of nucleic acids and RNA at a molecular level will be reviewed.
Objectives and Focus
This module encompasses a graduate-level understanding of how proteins are synthesized, modified and degraded in cells. Students will gain an understanding of structure-function relationships for amino acids, knowledge of the enzymatic basis of protein translation, how ribosomes are synthesized and regulated, how proteins are folded and may be modified post-translationally by enzymatic and non-enzymatic means. Emerging technologies in the study of proteins and post-translational modifications at a molecular level will be reviewed.
Objectives and Focus
This module introduces key bioinformatics concepts and practices, as well as the basic knowledge of how to access resources for graduate-level biologists who are not bioinformatics specialists. Students will become conversant in essential bioinformatics terminologies, and discussions will encompass how to use bioinformatics to infer information about an organism from its genome. Students will gain practical experience with bioinformatics tools and develop basic skills in the collection and presentation of bioinformatics data.
Objectives and Focus
This module introduces high throughput DNA sequencing technologies and genome-wide association genetics that are rapidly changing the landscape of various fields of biological and medical research. Students will gain an overview of the available genomics technologies and their applications for high throughput discovery in biology (model organisms) and medicine (cancer and Mendelian disease genomics). Discussions will also encompass research ethics considerations for collecting, storing and using human genomic data.
Objectives and Focus
Students will learn how to describe structures of biological macromolecules and explain, at a graduate level, the most commonly occurring methods for determination and analysis of the three-dimensional structure of biomolecules. Instructors will provide an overview of biophysical and structural methods used to study the regulation and function of biomolecules, tutorials on commonly available structural visualization software and resources and how structure-guided drug design is being used for pre-clinical drug discovery.