Fall 2015 - MBB 839 G100
Special Topics in Molecular Biology (3)
Class Number: 8878
Delivery Method: In Person
Overview
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Course Times + Location:
Sep 8 – Dec 7, 2015: Tue, Thu, 2:30–4:20 p.m.
Burnaby
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Instructor:
Frederic Pio
fpio@sfu.ca
Description
CALENDAR DESCRIPTION:
Consideration of recent literature concerning selected contemporary research topics. Can be taken more than once with permission of instructor.
COURSE DETAILS:
From Genome to System
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.
LECTURE TOPICS:
- 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
Grading
- 2 Midterm Exams 40%
- Paper - a written proposal aimed at answering a biological question using the concepts and tools developed in class will be evaluated 30%
- Presentation of a paper from recent literature 20%
- Class participation 10%
REQUIREMENTS:
MBB 331 and MBB 342
Materials
REQUIRED READING:
Systems Biology, Constraint-based Reconstruction and Analysis. Bernhard O. Palsson. 2015. Cambridge University Press.
ISBN: 9781107038851
RECOMMENDED READING:
Systems Biology. Robert A. Meyers (Editor). 2012. Wiley-Blackwell.
ISBN: 978-3527326075
Graduate Studies Notes:
Important dates and deadlines for graduate students are found here: http://www.sfu.ca/dean-gradstudies/current/important_dates/guidelines.html. The deadline to drop a course with a 100% refund is the end of week 2. The deadline to drop with no notation on your transcript is the end of week 3.
Registrar Notes:
SFU’s Academic Integrity web site http://students.sfu.ca/academicintegrity.html is filled with information on what is meant by academic dishonesty, where you can find resources to help with your studies and the consequences of cheating. Check out the site for more information and videos that help explain the issues in plain English.
Each student is responsible for his or her conduct as it affects the University community. Academic dishonesty, in whatever form, is ultimately destructive of the values of the University. Furthermore, it is unfair and discouraging to the majority of students who pursue their studies honestly. Scholarly integrity is required of all members of the University. http://www.sfu.ca/policies/gazette/student/s10-01.html
ACADEMIC INTEGRITY: YOUR WORK, YOUR SUCCESS