Spring 2022 - MBB 829 G100
Special Topics in Biochemistry (3)
Class Number: 6030
Delivery Method: In Person
Course Times + Location:
We 8:30 AM – 10:20 AM
SSB 6178, Burnaby
Fr 8:30 AM – 10:20 AM
SSB 6178, Burnaby
1 778 782-5657
Consideration of recent literature concerning selected contemporary research topics. Can be taken more than once with permission of the instructor.
The process of extracting biochemical content from genome annotations and literature sources to computationally catalog and interconnect the metabolic pathways available to the cell (i.e., metabolic reconstruction) is well established and has been carried out for a growing number of organisms on the genome scale. Such network reconstruction has led to the development of modeling approaches that gain a better understanding of the observable phenotypes and coordinated functions of the cell. As a result, these approaches are being used to apply and develop in silico models for biological discovery and engineering applications.
In this course we will cover conceptually some methods that enable the integration of Biochemical, Genetic and Genomic knowledge (BiGG) to reconstruct a genomic scale network that defines the metabolic physiology of an organism. We will also describe through examples computational models that integrate high-throughput data sets for prospective experimentation and validation. Finally, we will show how valuable and relevant these approaches are at making important biological predictions that can be validated experimentally. Applications in the fields of microbial evolution, interaction networks, genetic engineering and drug discovery will be discussed through student presentations
- What is System Biology?
- Network reconstruction from biological data
- Genomic scale reconstruction of prokaryotes
- Genomic scale reconstruction of eukaryotes
- Biochemical networks
- Genome metastructures
- Biochemically, Genomically and Genetically structured database (BiGG)
- Properties of reconstituted networks
- Phenotype potential of reconstituted networks
- Applications in microbial evolution, genetic engineering, drug discovery, environmental science, synthetic biology and biomedicine
Pre-requisite: An undergraduate bioinformatics course or equivalent
- 1 Exam 30%
- Quiz/assignments 10%
- Individual paper presentation (20-30 minutes) 10%
- Mini review paper in group (1 page) 10%
- Term proposal/project paper (3 pages) 30%
- Term proposal/project presentation (20-30 minutes) 10%
A First Course in Systems Biology, 2nd Ed, Everhard Voit, 2017, Garland Science. E-book.
Graduate Studies Notes:
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TEACHING AT SFU IN SPRING 2022
Teaching at SFU in spring 2022 will involve primarily in-person instruction, with safety plans in place. Some courses will still be offered through remote methods, and if so, this will be clearly identified in the schedule of classes. You will also know at enrollment whether remote course components will be “live” (synchronous) or at your own pace (asynchronous).
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