Computational Methods of Systems Biology
| Year | Semester | Date | Period | Language | In charge |
|---|---|---|---|---|---|
| 2012 | spring | 16.01-23.02. | 3-3 | English | Leena Salmela |
Lectures
| Time | Room | Lecturer | Date |
|---|---|---|---|
| Mon 12-14 | B222 | Leena Salmela | 16.01.2012-23.02.2012 |
| Thu 10-12 | B119 | Leena Salmela | 16.01.2012-23.02.2012 |
Information for international students
The course is lectured in English.
General
The course explores computational methods for biological networks, including network motif discovery, pathway analysis and reconstruction techniques.
Prerequisite studies: recommended background studies include basics in bioinformatics as well as algorithms.
Course book: B. H. Junker, F. Schreiber: Analysis of Biological Networks, Wiley, 2008
The course is lectured by D.Sc.(Tech) Leena Salmela and M.Sc. Markus Heinonen.
First lecture: Monday 16.1 at 12.15-14 B222
Completing the course
The course consists of the following components:
Lectures
Preliminary schedule:
- Monday 16.1. Introduction (Heinonen)
- Thursday 19.1. Network models (Salmela)
- Monday 23.1. Network clustering (Salmela) Note: This lecture will be given in the exercise slot 10-12!
- Hartuv, E. Shamir, R.: A clustering algorithm based on graph connectivity. Information Processing Letters Volume 76, Issues 4-6, 31 December 2000, Pages 175-181
- (Thursday 26.1. Presentation of group work)
- Monday 30.1. Motif discovery (Salmela)
- FPF algorithm: Schreiber & Schwöbbermeyer: Frequency concepts and Pattern Detection for the Analysis of Motifs in Networks. Transactions on Computational Systems Biology III. Lecture Notes in Computer Science, 2005, Volume 3737/2005, 89-104
- Thursday 2.2. Transcriptional regulation networks I (Salmela)
- Monday 6.2. Transcriptional regulation networks II (Salmela)
- Thursday 9.2. Network inference I (Heinonen) (revised the covariance slides sligthly)
- CLR algorithm: Faith et al: Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles. PLoS Biology (2007) 5(1):e8
- Monday 13.2. Network inference II (Heinonen)
- Thursday 16.2. Support vector machines and diffusion kernel (Heinonen)
- Monday 20.2. Metabolic networks I (Heinonen)
- Thursday 23.2. Metabolic networks II (Heinonen)
Group work
- 10% of the grade
- Completed during the group work session
- Monday 23.1. 12-14: Preparation of a short presentation (ca. 15 min) of a network analysis paper
- Thursday 26.1. Presentations of group work
- Network analysis papers:
- Jian Hou, Chunxiang Li, Roman Sirokov, Marcus Söderholm: Zhang & Zhang: A big world inside small world networks
- Mohammad Islam, Andres Levitski, Anna Kuosmanen, Johannes Ylinen: Ravasz & Barabasi: Hierarchical organization in complex networks
- Himanshu Chedda, Hailin Lei, Shewangizaw Sore, Teemu Summanen: Small et al: Scale-free networks which are highly assortative but not small world
- (Callaway et al: Network robustness and fragility: percolation on random graphs)
- The groups should have about three students. If you have preferences about the group you want to be in, send those to Leena Salmela (Leena.Salmela@cs.helsinki.fi) before Thu 19.1. I will then assign you to groups and assign one paper to each group.
Exercises
- 20% of the grade
- completed at home, returned in writing to Hongyu Su (Hongyu.Su@cs.helsinki.fi) prior to the session (don't return late if you want exercise points!), reviewed in the exercise sessions
- Four exercise sessions:
- Monday 30.1. Exercise Set 1 and Solution1
- Monday 06.2. Exercise Set 2 and Solution2
- Monday 13.2. Exercise Set 3 and Solution3 updated!
- Monday 20.2. Exercise Set 4 and Solution4 updated!
Course exam
70% of the grade
Grading
The course will be graded in the scale 1-5. 50% of the maximum points will give the grade of 1/5, 90% of the maximum will give the grade of 5/5.
Literature and material
Text books:
- U. Alon: Introduction to Systems Biology. Chapman & Hall, 2005
- B. H. Junker, F. Schreiber: Analysis of Biological Networks, Wiley, 2008
- E. Klipp et al. Systems Biology in Practise. Wiley, 2005
- B. Palsson. Systems Biology: properties of reconstructed networks, Barnes and Noble, 2005.
Exercise groups
| Time | Room | Instructor | Date | Observe |
|---|---|---|---|---|
| Mon 10-12 | B222 | Hongyu Su | 23.01.2012-24.02.2012 |
Address: Department of Computer Science, P.O. 68 (Gustaf Hällströmin katu 2b), FI-00014 UNIVERSITY OF HELSINKI, FINLAND
Opening Hours: During spring and autumn semesters Mon - Fri 7.45 - 19.45 (7.45 am - 7.45 pm)
Phone: +358 9 1911 (University switch)
General e-mail: info [at] cs.helsinki.fi
Fax: +358 9 1915 1120
