Fall 2016 - MBB 440 D100

Selected Topics in Contemporary Molecular Biology (3)

From Genome to System

Class Number: 1437

Delivery Method: In Person


  • Course Times + Location:

    Sep 6 – Dec 5, 2016: Tue, Thu, 2:30–4:20 p.m.

  • Prerequisites:

    will depend upon the nature of the topic offered.



The topics in this course will vary from term to term, depending on faculty availability and student interest.


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      


-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


  • 2 Midterm Exams (2x30%) 60%
  • Paper presentation 20%
  • Assignments, participation 20%


This course can be counted towards a certificate in genomics.


MBB 331 and MBB 342



Systems Biology, Constraint-based Reconstruction and Analysis.  Bernhard O.  Palsson. 2015. Cambridge University Press.
ISBN: 9781107038851


Systems Biology. Robert A. Meyers (Editor). 2012. Wiley-Blackwell.
ISBN: 978-3527326075

Department Undergraduate Notes:

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Registrar Notes:

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