Laboratory of Computer and Information Science / Neural Networks Research Centre CIS Lab Helsinki University of Technology

T-61.6080 Special course in bioinformatics II:
Analysis of proteomic and metabolic data V P, 5 cr

Lecturers Prof. Sami Kaski, Laboratory of Computer and Information Science,
Doc. Matej Oresic, VTT Systems Biology and Bioinformatics
Assistant M.Sc. Janne Nikkilä, Laboratory of Computer and Information Science
Credits (ECTS) 5
Semester Autumn 2005 (during periods I and II)
Seminar sessions On Tuesdays at 14-16 in lecture hall T4 in computer science building,
Konemiehentie 2, Otaniemi, Espoo. The first session on 13.9.2005.
Language English
Format Seminar (presentation + exercises/project work) (5 cr).
Registration TKK students: WebTopi, others: send mail to The number of participants is limited to about 25. Major students at the arranging laboratories have precedence, and the others are accepted in the order of registration time.


So far the most visible research effort in bioinformatics has been targeted on gene sequences and gene expression measurements (treated on the course T-61.5050). However, the key players controlling the cellular signalling and regulatory pathways are the proteins, products of gene expression. Another important class of molecules are the metabolites that are produced in most of the chemical reactions in the cell, and are key players in controlling the dynamics of the cell and intercellular communication. The measurement techniques to obtain data about these molecules in the cell are developing at an increasing pace, and the analysis of the data obtained is becoming more and more challenging, while also offering new opportunities for bioinformatics research.

This course is designed to introduce computational and statistical concepts and tools necessary to analyse data sets from various proteomic and metabolic data sources, in order to use them for life science and biomedical research.

The course participants have a possibility to visit Biotechnology laboratory in VTT in Otaniemi. The timetable will be fixed in the first session.


This course is intended mainly for graduate students of computer science, statistics, and applied mathematics, but students from other fields are welcome as well. In particular mathematically oriented biology, bioinformatics, and medical students should benefit from the course.

Basic knowledge of probability, statistics, vector algebra, and calculus is assumed (the basic mathematics courses in HUT). A "Basic course in bioinformatics", such as S-114.2510 Computational Systems Biology or equivalent background is assumed as well.

Sami Kaski, Matej Oresic, Janne Nikkilä

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