Computational Systems Biology
Advanced Technologies in Bioscience 2008-2009
Chalmers Graduate School in Bioscience

Instructor: T. M. Murali

Dates: August 18-22, 2008
Location: MVF 31, Math building, Chalmers

What is Computational Systems Biology?

Cells, tissues, organs and organisms are systems of components whose interactions have been defined, refined, and optimised over hundreds of millions of years of evolution. Computational systems biology is a field that aims at a system-level understanding of biological systems by analysing biological data using computational techniques. Systems biology aims to answer the following key questions by integrating experimental and computational approaches:

  1. What are the basic structures and properties of the biological networks in a living cell?
  2. How does a biological system behave over time under various conditions?
  3. How does a biological system maintain its robustness and stability?
  4. How can we modify or construct biological systems to achieve desired properties?
Answers to these questions require breakthroughs in the fields of biology, chemistry, computer science, engineering, mathematics and other fields. The explosive progress of genome sequencing projects and the massive amounts of data that high-throughput experiments in DNA microarrays, proteomics, and metabolomics yield drive advances in this field. Sophisticated computational ideas process these data sources in an effort to systematically analyse and unravel the complex biological phenomena that take place in a cell.

In this course, we will emphasise a data-driven approach to computational systems biology, focussing on large-scale properties of molecular interaction networks. We will learn techniques from machine learning, data mining, and graph theory and apply them to solve specific biological questions.


Each day of the course will consist of two hours of lectures (10am-12pm) and two hours of exercises (1pm-3pm). Exceptions are the first day, when we will have three hours of lectures; the fourth day, when we have guest lectures by Jasmin Fischer and Andrew Phillips from 1pm-3pm; and the fifth day, when the two-hour lecture on host-pathogen protein interaction networks is also a tutorial at ICSB 2008 from 4:15pm-6:15pm.

Date Topic and papers Lecture
Mon, Aug 18, 2008 Introduction to Computational Systems Biology Lecture
Mon, Aug 18, 2008 Clustering gene expression data Lecture
Mon, Aug 18, 2008 Application to find cancer gene modules Lecture and Exercises
Tue, Aug 19, 2008 Biclustering gene expression data Lecture
Tue, Aug 19, 2008 Application of biclustering to data integration in S. cerevisiae Lecture
Wed, Aug 20, 2008 Response networks Lecture
Wed, Aug 20, 2008 Network legos, building blocks of cellular wiring diagrams Lecture
Thu, Aug 21, 2008 Gene function prediction Lecture
Fri, Aug 22, 2008 Host-pathogen protein interaction networks
Tutorial at ICSB 2008

Papers to be covered

Reading assignments: Papers highlighted with a blue background and with a specific date to their top left are the ones we will discuss in class. Please try to read them before the class. The lists below include other relevant papers. On almost each one of these topics, the literature is too vast to be completely included in these lists.

Introduction to Computational Systems Biology

These articles provide very good introductions to the subject of (computational) systems biology.

Gene Expression Analysis

Functional Annotation

Comparative Systems Biology

Structure of Molecular Interaction Networks

Transcriptional Regulatory Networks

Data Integration

Protein-Protein Interaction (PPI) Networks

Metabolic Networks

Designer Networks

Last modified: Fri Aug 15 12:49:11 EDT 2008