PABIO 590B Advanced Topics in Bioinformatics

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Presentation transcript:

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!

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

What is Systems Biology?

A New Paradigm for Biology Differences between traditional and systems approach

Systems Biology in action Musser & DeLeo (2005) Am J Path 167:1461-1472

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

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

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

Course Web-sites Home page Homework submission Discussion group http://faculty.washington.edu/mylerpj/PABIO590A/index.shtml Homework submission https://catalysttools.washington.edu/collectit/dropbox/mylerpj/5795 Discussion group https://catalysttools.washington.edu/gopost/board/mylerpj/11122/