SGN-6156 Computational Systems Biology II, 5cr

The first exam will be organized on 14.05.2008.
Note: the fourth exercise will be organized on Friday, 02.05.2008, at 14:15-16:00.
Lecture 9 available.
Lecture 8 and Exercise 3 available.
Lecture 7 available.
Lecture 6 and Exercise 2 available.
Lectures 4 and 5 are now available.
Note: exercises on Wednesdays 12:15-13:45, TC407.
Exercise 1 available.
Lecture 3 available.
Lecture notes 1 and 2 added.


Computational systems biology

Time and Place:
Period V, Tuesdays 14:15-16:00, TB222 and Wednesdays 10:15-12:00, TB216
Exercises on Wednesdays 12:15-13:45, TC407.

First meeting:

April 1, 2008

Harri Lähdesmäki
office: TF412

[From the course catalog:] Student is able to use computational and mathematical methods for data analysis and experiment design in systems biology.

Preliminary syllabus:
Sequence analysis: pairwise alignment, hidden Markov models, multiple alignment, sequence motifs, motif discovery, structure
Biological networks: stochastic and deterministic models, simulation, parameter and structure inference, metabolic networks

Participation in the exercises and final examination.

Other (official) details (if any):
From the course catalog.


The course is accepted as a postgraduate course but M.Sc. students can participate as well.

Preliminary list of material:
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids,
Richard Durbin, Sean R. Eddy, Anders Krogh and Graeme Mitchison,
Cambridge University Press, 1999.
Amazon, Google books

Genomic Signal Processing and Statistics
E. R. Dougherty, I. Shmulevich, J. Chen, Z. Jane Wang (Eds.)
EURASIP Book Series on Signal Processing and Communications, Hindawi Publishing Corp., 2005.
Publisher's web page, Amazon

Course covers parts of the books. The books can be borrowed from the course instructor. The material will be supplemented by recent articles.

Additional reading:

Lecture 1 (01.04.2008) [pdf]
Lecture 2 (02.04.2008) [pdf]
Lecture 3 (08.04.2008) [pdf]
Lecture 4 (09.04.2008) [pdf]
Lecture 5 (15.04.2008) [pdf]
Lecture 6 (16.04.2008) [pdf]
Lecture 7 (22.04.2008) [pdf]
Lecture 8 (23.04.2008) [pdf]
Lecture 9 (29.04.2008) [pdf]
Lecture 10 (30.04.2008) [pdf]
Lecture 11 (06.05.2008) [pdf]
Lecture 12 (07.05.2008) [pdf]

Exercise 1 (09.04.2008) [pdf]
Exercise 2 (16.04.2008) [pdf]
Exercise 3 (23.04.2008) [pdf]
Exercise 4 (02.05.2008) [pdf]