1. PABIO 590B Advanced Topics in Bioinformatics
OK, so I found an interesting gene in the genome of my favorite organism.
What I do want to know next?
When (and where) is the gene product expressed?
Who does it hang out with?
What does it do?
Where did it come from?
Use a Systems Biology approach!

2. What is Systems Biology?
Systems biology is an academic field that seeks to integrate different levels of information to understand how biological systems function. By studying the relationships and interactions between various parts of a biological system (e.g., gene and protein networks involved in cell signaling, metabolic pathways, organelles, cells, physiological systems, organisms etc.), it is hoped that eventually an understandable model of the whole system can be developed. (from Wikipedia)
Use high-throughput methods to quantify changes in RNA and protein in response to perturbation of cell
Build regulatory networks linking genes, RNAs, and proteins
Develop mathematical models to represent the system
Predict how different perturbations will affect the system
Test predictions for validity
Refine models and repeat

3. What is Systems Biology?

4. A New Paradigm for Biology
Differences between traditional and systems approach

5. Systems Biology in action
Musser & DeLeo (2005) Am J Path 167:

6. Why use Systems Biology?
Whole organism view
Identify total physiological capacity
More complete understanding
New drugs/vaccine candidates
Produce resource of data and materials
More efficient
Collaborative

7. What you will learn Week 1 – Microarrays Week 2 - Pathways & Networks
Week 3 – Phylogenetic analysis

8. Course structure Monday Tuesday Thursday 30-45 minutes lecture
Homework assignment
Software training
Tuesday
Work on homework assignment
Get help
Thursday
Homework due (via or Catalyst)

9. Course Web-sites Home page Homework submission Discussion group
Homework submission
Discussion group