Introduction to
Computational Systems Biology
Lecturer: Dr. Zhuo Wang, Associate Professor
E-mail: zhuowang AT sjtu.edu.cn
Office: 4-221, 09:00AM -- 16:00 PM
Lecture: Tuesday 10:00-11:40
Aims
This course aims to
introduce the main concepts and methodology of modern computational systems
biology applied to biological systems at different scales, including
transcriptomics, proteomics and metabolomics. Students will learn how to
construct and interpret biological network using graph topology, modularity and
metabolic flux analysis, and how to assess the validity of models given
experimental evidence.
Assessment
•
Attendance 5%
•
Lab work
20%
•
Team project 25%
(five in each group)
• Final
exam
50%
(individual)
Lecture slides
1.
Introduction to
systems biology
2.
Introduction to omics technology
4-1.
Network topology analysis
4-2.
Module and motif
6.
Constraint-based model of
metabolic network
7.
Case Study: Human Metabolic Network
8.
Case Study: Constraint-based modeling for metabolic engineering
9. Integrative network for regulation and metabolism
10.
Network comparison and alignment
Computer Lab
Lab2 Cytoscape
Lab3 Guide to MATLAB
Lab4 COBRA toolbox
Lab5 Case study
Team project
Students will form a 6-7 person team and each team will
have to complete a project. Implement the case-study using modeling software and
write an article-like report (5-10 pages in English), including Introduction, Results, Methods and References; Present their final
results at the end of class.
Recommended textbooks
•
Bernhard
Palsson. Systems Biology: Properties of Reconstructed Networks. Cambridge
University Press, 2006
•
Klipp, Edda: Systems biology standards鈥攖he community speaks.
Nature Biotechnology, 2007
•
A.
Kriete, R. Eils (Eds.): Computational systems biology. Elsevier
Academic Press, 2006
•
M.
Buchanan, G. Caldarelli, P. de los Rios, F. Rao, M. Vendrscolo (Eds.): Networks
in cell biology. Cambridge University Press, 2010