Fall 2018 - MBB 839 G100

Special Topics in Molecular Biology (3)

From Genome to System

Class Number: 3554

Delivery Method: In Person

Overview

  • Course Times + Location:

    We, Fr 8:30 AM – 10:20 AM
    SSB 6178, Burnaby

Description

CALENDAR DESCRIPTION:

Consideration of recent literature concerning selected contemporary research topics. Can be taken more than once with permission of instructor.

COURSE DETAILS:

DESCRIPTION:  

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 will be explored. Applications of these approaches in the fields of microbial evolution, interaction networks, genetic engineering and drug discovery will be discussed.

COURSE DETAILS:  

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  

Pre-requisite: An undergraduate bioinformatics course or equivalent

Grading

  • 2 Midterm Exams (2 x 30%) 60%
  • Paper presentation and participation - a written proposal aimed at answering a biological question using the concepts and tools developed in class will be evaluated 40%

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