Biological and Biomedical Engineering: Synthetic Biology (Thesis) (M.Sc.)(45 credits)
Offered by: Biological & Biomedical Engineering
Degree: Master of Science
Program credit weight: 45
Program Description
The M.Sc. in Biological and Biomedical Engineering; Synthetic Biology offers training in the application of engineering principles to designing new biological molecules, devices, and systems, as well as repurposing existing ones for beneficial applications in gene therapies, sustainable materials, and food production. The program offers training in disciplines ranging from biology and computational biology, biotechnology and biomanufacturing, genetics, bioinformatics, ethics, machine learning and mathematical modelling, to pharmacology. The Thesis must focus on synthetic biology.
Required Courses (30 credits)
| Course | Title | Credits |
|---|---|---|
| BBME 600D1 | Seminars in Biological and Biomedical Engineering. | 1.5 |
Seminars in Biological and Biomedical Engineering. Terms offered: Fall 2026 Mandatory attendance at the seminar series at which students present a seminar related to their research | ||
| BBME 600D2 | Seminars in Biological and Biomedical Engineering. | 1.5 |
Seminars in Biological and Biomedical Engineering. Terms offered: Winter 2027 Mandatory attendance at the seminar series at which students present a seminar related to their research. | ||
| BBME 600N1 | Seminars in Biological and Biomedical Engineering. | 1.5 |
Seminars in Biological and Biomedical Engineering. Terms offered: Winter 2027 Mandatory attendance at the seminar series at which students present a seminar related to their research | ||
| BBME 600N2 | Seminars in Biological and Biomedical Engineering. | 1.5 |
Seminars in Biological and Biomedical Engineering. Terms offered: Fall 2026 Mandatory attendance at the seminar series at which students present a seminar related to their research. | ||
| BBME 693 | Thesis Research 1. | 6 |
Thesis Research 1. Terms offered: Summer 2026, Fall 2026, Winter 2027 Independent research work under the direction of the Thesis Supervisor | ||
| BBME 694 | Thesis Research 2. | 6 |
Thesis Research 2. Terms offered: Summer 2026, Fall 2026, Winter 2027 Independent research work under the direction of the Thesis Supervisor | ||
| BBME 695 | Thesis Submission. | 12 |
Thesis Submission. Terms offered: Summer 2026, Fall 2026, Winter 2027 Independent research work under the direction of the Thesis Supervisor. | ||
| BIEN 580 | Synthetic Biology. | 3 |
Synthetic Biology. Terms offered: Winter 2027 Engineering principles in biology, BioBricks and standardization of biological components, parts registries, advanced molecular biology tools for DNA assembly, genome editing, high-throughput genetic manipulation methods, construction of biological pathways, strategies for transcriptional control, examples of engineered systems. | ||
Note: students choose either BBME 600D1/D2 or BBME 600N1/N2.
Complementary Courses (15 credits)
3 credits from the following quantitative core courses:
| Course | Title | Credits |
|---|---|---|
| BIEN 550 | Biomolecular Devices. | 3 |
Biomolecular Devices. Terms offered: this course is not currently offered. Fundamentals of motor proteins in neuronal transport, force generation e.g. in muscles, cell motility and division. A survey of recent advances in using motor proteins to power nano fabricated devices. Principles of design and operation; hands-on-experience in building a simple device. | ||
| BIEN 585 | Metabolic Engineering. | 3 |
Metabolic Engineering. Terms offered: Fall 2026 Metabolic engineering role in transition from fossil resources to a bio-based society. Design-build-test-learn cycle of metabolic engineering. Design, genetic engineering and optimization of microbial biocatalysts. Metabolic network analysis, constraint-based modelling of metabolism, microbial production of valuable chemicals. General biochemical engineering practices. Recombinant DNA technology, enzyme function, kinetics and regulation. Cell chemistry, structure and function. Growth models, fermentation, strain development. Case studies. | ||
| BIEN 590 | Cell Culture Engineering. | 3 |
Cell Culture Engineering. Terms offered: Fall 2026, Winter 2027 Basic principles of cell culture engineering, cell line development and cell culture products; genomics, proteomics and post-translational modifications; elements of cell physiology for medium design and bioprocessing; bioreactor design, scale-up for animal cell culture and single use equipment; challenges in downstream processing of cell-culture derived products; process intensification: fed-batch, feeding strategies and continuous manufacturing; scale-down and process modeling; Process Analytical technologies and Quality by Design (QbD) concept. | ||
| BIEN 595 | Advanced Biomolecular Systems Modelling. | 3 |
Advanced Biomolecular Systems Modelling. Terms offered: Fall 2026 Advanced methods for modelling complex biomolecular systems,with a focus on state-of-the-art, data-driven and integrative methods for modelling protein structures and networks. Modelling of protein structures: protein structure prediction, modelling protein dynamics, use of evolutionary information. Modelling of protein networks: reconstruction, analysis, evolution. Combined protein structure and network modelling. | ||
| BMDE 521 | Computational Methods Single-Cell Analytics. | 3 |
Computational Methods Single-Cell Analytics. Terms offered: Fall 2026 Computational methods (particularly machine learning methods) for various single-cell data analysis, modelling, and visualization tasks that could drive novel biomedical discoveries, focusing on “real-world” biomedical applications. | ||
3 credits from the following core courses:
| Course | Title | Credits |
|---|---|---|
| BIEN 540 | Biocomputation and Biosimulation. | 3 |
Biocomputation and Biosimulation. Terms offered: this course is not currently offered. Biocomputation; DNA computing, biocomputation with networks, membrane computing. Biosimulation; traffic simulation with motile agents. Information storage in biological systems; DNA and cells, abiotic applications, biologically inspired algorithms. | ||
| BMDE 504 | Biomaterials and Bioperformance. | 3 |
Biomaterials and Bioperformance. Terms offered: Winter 2027 Biological and synthetic biomaterials, medical devices, and the issues related to their bioperformance. The physicochemical characteristics of biomaterials in relation to their biocompatibility and sterilization. | ||
| BMDE 505 | Cell and Tissue Engineering. | 3 |
Cell and Tissue Engineering. Terms offered: this course is not currently offered. Application of the principles of engineering, physical, and biological sciences to modify and create cells and tissues for therapeutic applications will be discussed, as well as the industrial perspective and related ethical issues. | ||
| BMDE 507 | Formulation and Delivery of Biotherapeutics. | 3 |
Formulation and Delivery of Biotherapeutics. Terms offered: Fall 2026 Introduction to technologies for formulation and delivery of biotherapeutics. Emphasis is placed on the fundamental principles of formulation, delivery systems, manufacturing, analytical techniques, and biomedical applications. Translational aspects are considered for formulated biotherapeutic products. | ||
| BMDE 508 | Introduction to Micro and Nano-Bioengineering. | 3 |
Introduction to Micro and Nano-Bioengineering. Terms offered: Fall 2026 The micro and nanotechnologies that drive and support the miniaturization and parallelization of techniques for life sciences research, including different inventions, designs and engineering approaches that lead to new tools and methods for the life sciences - while transforming them - and help advance our knowledge of life. | ||
3 credits from the following Synthetic Biology core courses:
| Course | Title | Credits |
|---|---|---|
| BIEN 602 | Biomanufacturing for RNA Biologics . | 3 |
Biomanufacturing for RNA Biologics . Terms offered: Winter 2027 Fundamental and quantitative overview of RNA biologics. Introduction to RNA biologics associated biomanufacturing unit operations in upstream (design tools and large-scale production systems of DNA templates for in vitro RNA transcription; small-scale and large-scale RNA bioprocessing systems), and downstream approaches for RNA purification (like Tangential flow filtration and RNA-specific chromatography systems) for emerging mRNA therapeutics. Introduction to established and emerging applications of RNA biologics for gene and cell therapy. | ||
| BINF 621 | Bioinformatics: Molecular Biology. | 3 |
Bioinformatics: Molecular Biology. Terms offered: Winter 2027 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). | ||
| CHEM 540 | Advances in Industrial Biotechnology. | 3 |
Advances in Industrial Biotechnology. Terms offered: Winter 2027 Introduction to emerging technologies and research advances in biotechnologies. Topics include semisynthetic production of drugs and drug candidates through large-scale fermentation, next generation synthesis of DNA and whole genes, green toxicology, single-molecule diagnostics, orphan-drug re-purposing, and next- generation genomic analyses in drug development. Translational research, issues of entrepreneurship, sustainability, and ethics are also covered. | ||
| CHEM 542 | Advanced Nucleic Acid Chemistry. | 3 |
Advanced Nucleic Acid Chemistry. Terms offered: Winter 2027 Advanced-level chemical reactivity and metal binding properties, advanced methods for synthesis, purification and characterization of DNA/RNA, non-canonical DNA/RNA structures and functions, self-assembly of functional nucleic acid-based materials, chemical and fluorescence-based methods for probing nucleic acids in vitro and in vivo, in vitro evolution of functional nucleic acids for biotechnology, and diagnostic and therapeutic applications of modified nucleic acids. | ||
| ECSE 556 | Machine Learning in Network Biology. | 4 |
Machine Learning in Network Biology. Terms offered: Winter 2027 Basics of machine learning; basics of molecular biology; network-guided machine learning in systems biology; network-guided bioinformatics analysis; analysis of biological networks; network module identification; global and local network alignment; construction of biological networks. | ||
| HGEN 660 | Genetics and Bioethics. | 3 |
Genetics and Bioethics. Terms offered: Fall 2026 This course will deal with ethical issues in the gathering, dissemination, and use of genetic information for decisions concerning reproduction, health care, and research. | ||
| HGEN 676 | Lab Course in Genomics. | 3 |
Lab Course in Genomics. Terms offered: this course is not currently offered. Introduction to Next Generation Sequencing (NGS) Based Genomics in the form of seminars and laboratory work. Lectures in state of the art sequencing technologies and their applications. Laboratory work in the preparation of high quality libraries for analyzing DNA and large/small RNAs. Hands on experience in setting up next Generation Sequencing using specialized equipment. Tutorials in use of Bio-informatics Analysis tools in experimental design, quality control, and in depth analysis of data. Practicum in using computational tools for personalized data analyses. Technology paper presentation, as well as production of a report on course data generation and analysis. | ||
| PLNT 662 | Advances in Plant Biotechnology. | 3 |
Advances in Plant Biotechnology. Terms offered: Winter 2027 Current techniques used in plant molecular biology. Topics to be covered may include plant biotechnology, recombinant DNA techniques, transgenic plants as well and gene and gene product analysis. Review of current literature on selected topics in plant molecular biology and genetics. | ||
6 credits from the following Synthetic Biology courses:
| Course | Title | Credits |
|---|---|---|
| BIEN 685 | Gene and Cell Therapy Viral Vectors Biomanufacturing. | 3 |
Gene and Cell Therapy Viral Vectors Biomanufacturing. Terms offered: Winter 2027 Basic knowledge in the design and biomanufacturing of viral vectors for gene and cell therapy interventions. Practical examples and case studies highlighting challenges and solutions associated with use of viral vectors such as Adeno-Associated Vectors (AAV), lentivirus vectors and Adenovirus vectors for gene delivery. Fundamental principles of gene and cell therapies through in-vivo and ex-vivo interventions. Design of AAV, Lentivirus and Adenovirus vectors: example of targeted diseases, including CAR-T cell therapy. Technologies and modes of vector manufacturing for clinical use. | ||
| BINF 511 | Bioinformatics for Genomics. | 3 |
Bioinformatics for Genomics. Terms offered: Winter 2027 Bioinformatics methods and reasoning in relation to genomics, proteomics and metabolomics strategies with an emphasis on functional genomics data. The course will cover introduction to UNIX, Perl programming, data processing and integration, file parsing, relational database design and implementation, angled towards solutions relevant for genomics. | ||
| BTEC 535 | Functional Genomics in Model Organisms. | 3 |
Functional Genomics in Model Organisms. Terms offered: Winter 2027 An overview of strategies used to understand the function of genes, especially those identified through genome sequencing and bioinformatics. Use of model organisms that have proved particularly valuable for this purpose. | ||
| CHEE 651 | Advanced Biochemical Engineering. | 4 |
Advanced Biochemical Engineering. Terms offered: Fall 2026 The use of chemical engineering and biological principles in the study, design, use and creation of biologically-based processes and products. Topics: biochemical thermodynamics, protein engineering, manipulation of gene expression, transport phenomena and bioreactor design. | ||
| COMP 561 | Computational Biology Methods and Research. | 4 |
Computational Biology Methods and Research. Terms offered: Fall 2026 Application of computer science techniques to problems arising in biology and medicine, techniques for modeling evolution, aligning molecular sequences, predicting structure of a molecule and other problems from computational biology. An in-depth exploration of key research areas. | ||
| COMP 565 | Machine Learning in Genomics and Healthcare. | 4 |
Machine Learning in Genomics and Healthcare. Terms offered: Fall 2026 Linear models in statistical genetics, causal inference, single-cell genomics, multi-omic learning, electronic health record mining. Applications of machine learning techniques: linear regression, latent factor models, variational Bayesian inference, neural networks, model interpretation. | ||
| HGEN 670 | Advances in Human Genetics 1. | 3 |
Advances in Human Genetics 1. Terms offered: Winter 2027 This course will deal with recent progress in human genetics, and its applications to health care, by identifying different fields including different disciplines (e.g. cancer genetics, neurogenetics), different conceptual approaches, or different methodologic approaches. | ||
| HGEN 675 | Stem Cell Biology. | 3 |
Stem Cell Biology. Terms offered: this course is not currently offered. Introduction to the field of stem cell research. Definition of stem cells. Pluripotent stem cells and reprogramming. Adult stem cells, niche and asymmetric division. Clinical applications of stem cells. Cancer stem cells. Ethical issues surrounding stem cell research and clinical treatment. | ||
| HGEN 677 | Statistical Concepts in Genetic and Genomic Analysis. | 3 |
Statistical Concepts in Genetic and Genomic Analysis. Terms offered: Fall 2026 This course will introduce key statistical concepts that motivate and underlie the many statistical analysis methods currently used in analysis of genetic and genomic data. Emphasis will be placed on understanding how these concepts can influence study designs and analysis choices, and when substantial unanticipated biases can occur. Concepts include an understanding of variability and error, bias and its sources, independence, how distributions of variables impact analysis, outliers, covariates, missing data, the goals of data cleaning, multiple testing, and some consideration of clustering and prediction models. | ||
| PHAR 503 | Drug Discovery and Development 1. | 3 |
Drug Discovery and Development 1. Terms offered: Fall 2026 Chemistry, mechanisms of action, and steps in drug discovery and development. | ||
| PHAR 508 | Drug Discovery and Development 3. | 3 |
Drug Discovery and Development 3. Terms offered: Winter 2027 The design of biologically-relevant drug screens for molecular targets in a cell, tissue, and in vivo setting. Explore the use of stem cells and tissue-based disease models for the understanding of disease and for drug discovery. Situate modern pharmacology into broader medical and societal issues such as personalized medicine and the ethics associated with research. | ||
| PHGY 518 | Artificial Cells. | 3 |
Artificial Cells. Terms offered: Fall 2026 Physiology, biotechnology, chemistry and biomedical application of artificial cells, blood substitutes, immobilized enzymes, microorganisms and cells, hemoperfusion, artificial kidneys, and drug delivery systems. PHGY 517 and PHGY 518 when taken together, will give a complete picture of this field. However, the student can select one of these. | ||
Note: These programs are 45 credits, but credits in this program may minimally be exceeded in some cases due to course selection.