Introduction to Systems Biology

Plant Biology 471

Department of Plant Biology

Southern Illinois University

Carbondale, Illinois 62901-6509

COURSE OFFERED

Spring semesters

INSTRUCTOR

Dr. Matt Geisler
Dept of Plant Biology
Life Science II, rm 403 phone: 453-3212

COURSE DESCRIPTION

Systems biology is the emerging science of analyzing large datasets produced by high-throughput molecular biology and biochemistry (i.e. the proteome, interactome, transcriptome, and metabolome). This is the next step in the evolution of post-genome biological science. Instead of looking at the behavior and products of a single gene, we now look at all genes in an organism simultaneously. Systems biology today is an information science, with more on-line databases and resources than journal papers as a means of communicating this science. However, there is no hierarchical structure or framework to this information, there are dozens of sites which repeat, duplicate or even contradict each other. It can be bewildering and impenetrable to those unfamiliar with its “Biotechnobabble” jargon.

This course is designed to help students navigate these chaotic waters, and make use of web resources. This is also the perfect time for students who have not embraced the “information age” of computers and the web to take the plunge and learn some basic computing skills. Lectures and a 2 hour per week computer lab will teach you how look up genes, transcripts and proteins from online genome databases, compare genes from different organisms, understanding gene ontology and protein domains. We will look at gene expression, how to download and read transcriptomes and proteomes, and how to cluster gene expression patterns to identify co-expressed genes. We will look at metabolomics, metabolic pathways, how to read MapMan, Metacyc, and enzyme categories, and how to use this data. Finally we examine protein-protein interactions from BioGrid, and look at signaling pathways and protein complexes.

TEXTBOOKS

Systems Biology: Properties of Reconstructed Networks by Bernhard O. Palsson Cambridge University Press (January 16, 2006)

Bioinformatics: A practical approach by Shui Qing Ye. 2008 CRC Press

COURSE OBJECTIVES

Systems biology is a new field which explores the world of genomes and post-genomic datasets and large databases. The goal of systems biology is to comprehensively understand development, physiology, metabolic and gene regulatory networks, by looking at all genes, proteins and metabolites in an organism simultaneously, rather than focusing on just one or two. We finally have all the components of biology laid out in front of us, the genes, transcripts, and proteins. It is now time to begin to learn how all these pieces interact to create the emergent properties of life.

COMPUTER LAB

There is a self-directed computer lab, which will be supervised by the lecturer (me), but should be pretty straight forward. Assignments will be given weekly, and are available along with any sample data on a DVD handed out at the beginning of the course. Please print out the assignment prior to lab, or fill in the answers online and save your work. I highly encourage all students to purchase a 1GB or larger USB memory stick as their workbook for this class. You can turn in your stick, or printed out pages at the end of the lab. Students are encouraged to discuss the assignment amongst the lab group, and to help each other with the problems. However, the work your turn in for grades must be your own. This is not usually a problem as each student will be given a different gene, different organism or so on.

GRADING

Lecture Exams (2) 200 points
Laboratory assignments 200 points

COURSE POLICIES

Systems biology is a difficult subject and it is easy to get lost quickly, and never catch up. The lectures are an open forum format, and active student participation is encouraged. Please ask questions at any time during the lecture by raising your hand. Additional time will be dedicated to questions at the end of each lecture as well. Do not be afraid to ask anything, there are no such things as stupid questions in systems biology.

READING ASSIGNMENTS

You will be given assignments to read each week. Please keep up with your reading.

Lecture syllabus

Lecture	Topic	Text Reading
1	Introduction	SB: Chapter 1
2	Online databases	BI: Chapter 1
3	Bioinformatics Basics I	BI: Chapter 3
4	Bioinformatics Basics II	BI: Chapter 3
5	Analysis of gene expression	BI: Chapter 5
6	Clustering of expression data	BI: Chapter 5
7	Use of orthologs	Papers
8	Proteomics	BI: Chapter 10
9	Functional annotation, AmiGO	BI: Chapter 11/12
10	Domains, SMART, PFAM	Papers
11	Metabolomics, MAPman, MetaCyc	SB: Chapter 2/3
12	Midterm exam
13	Interactomics	Papers
14	Mining the bibliome	Papers
15	Gene regulatory networks	SB: Chapter 4
16	Signaling networks	SB: Chapter 5
17	Dyanmics and Spatial compartmentalization	Papers
18	Morphogen gradients and auto-regulation	Papers
19	Mathematical models of networks	SB: Chapter 6/7
20	The feed forward and feedback loop	Papers
21	Network topology	Papers
22	Comparison of protein and neural networks	Papers
23	Inputs and decision making circuits	Papers
24	Robustness and redundancy	Papers
25	Reconstruction of networks from data	Papers
26	Systems biology analysis	Papers
27	Review

Laboratory schedule

Week	Topic
1	Gene and Protein data handling
2	Genome Database navigation
3	Alignment and phylogeny
4	Ortholog identification
5	Large scale domain analysis
6	Downloading and manipulating transcriptomes
7	Transcriptome meta-analysis
8	Cis-regulatory element search algorithms
9	Interactome analysis and protein interaction domains
10	Motif searching for key interaction sequences
11	Reconstruction of a network project I
12	Reconstruction of a network project II
13	Reconstruction of a network project III
14	Group presentations
15	Review for exam

There will be a worksheet worth 20 points due in-class for every lab, do not miss your labs.

SIUC / College of Science / Intro to Systems Biology
URL: http://www.science.siu.edu/PLB471/index.html
Last updated: 15-Feb-08 / mg