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

Notices (updated 23.12.2005)
o Project work data and information available
o The list of researchers worth checking in Literature section
  • Send the most relevant question (in your opinion) about the next presentation
    (with email subject: t616080:question[day][month])
  • If you do not have a subject already, make a suggestion for an article you would like to read and present
    (if you do not find any, we will offer something (not encouraged))

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
Registration TKK students: WebTopi, others: send mail to

Introduction [back to top]

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 on 27.9.

Prerequisites [back to top]

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.

Course format [back to top]

Journal club (presentation + questions + project work) (5 cr).

Requirements for passing the course [back to top]

The course is graded as fail/pass/pass with distinction. The exercises are graded as fail/pass (some percentage of the exercises is required with 'pass' to pass the course).

Make a presentation about a subject given in the first session.

Read each article to be presented in advance and make one question about it. The question should be the most relevant one in your opinion and one that should be answered in the presentation. Send your question a day before the presentation to the assistant. The questions are browsed after each presentation to make sure that each of them was relevant and was answered.

Complete the project work and return a written report about it.

Attend the seminar session and the discussion actively.

Signing up for the course [back to top]

HUT students: In Webtopi
Other universities: Send email to the organizers or sign up at the introduction lecture.

Literature/Course material [back to top]

Introductory material (read before 20.9.2005):

  1. Listgarten & Emili: Statistical and Computational Methods for Comparative Proteomic Profiling Using Liquid Chromatography-Tandem Mass Spectrometry, Molecular & Cellular Proteomics, 4:419-434, 2005.
  2. Goodacre et al.: Metabolomics by numbers: acquiring and understanding global metabolite data, TRENDS in Biotechnology, Volume 22, Issue 5, 1 May 2004, Pages 245-252.
  3. Patterson, Aebersold: Proteomics: the first decade and beyond, Nature Genetics, vol 33, pp 311--323, 2003

Researchers and research groups worth checking:

Schedule [back to top]

Time Lecturer Subject and material
13.9. Sami Kaski, Janne Nikkilä
20.9 Mikko Katajamaa
27.9. Matej Oresic
  • Analysis and interpretation of metabolomics and proteomics data
  • Slides,
4.10. Leo Lahti
11.10. Abhishek Paliwal
18.10. Laxman Rao Yetukuri
25.10. Sarish Talikota
NOTE!!!: 3.11. 12.15 in A328 Vibhor Kumar
8.11. Gopal Peddinti
15.11. Jarkko Ylipaavalniemi, Leena Hallivuori
22.11. Jarkko Venna
29.11. Laura Pombo, Ilana Saarikko

Project work [back to top]

In short: borrow the data dvd, copy the data, use MZmine to preprocess it, make an analysis, and write a report. DL is 15.1.2006. For more details, see the separate page.

For more information, please send email to

Sami Kaski, Matej Oresic, Janne Nikkilä

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