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

T-61.6080 Special course in bioinformatics II:
Data integration and fusion in bioinformatics V P, 5 cr

Notices (updated 22.9.2006)
o A preprocessed stress data is available for download.

Lecturer D.Sc.(Tech.) Janne Nikkilä, Laboratory of Computer and Information Science
Assistant M.Sc.(Tech.) Leo Lahti, Laboratory of Computer and Information Science
Credits (ECTS) 5
Semester Autumn 2006, period I (and possibly period II)
Seminar sessions On Thursdays at 14.30-16 in lecture hall T5 in computer science building,
Konemiehentie 2, Otaniemi, Espoo. The first session on Thursday 14.9.2005.
Language English
Registration TKK students: WebTopi, others: send mail to

Introduction [back to top]

In any analysis or modeling task it is usually beneficial to take into account all the available information. In bioinformatics this means collecting heterogeneous data from various measurement devices, databases, and information sources. Examples of such information sources include genomic sequence, gene expression, Gene Ontology, known pathways, protein sequence, protein-DNA binding, cell state, and environmental conditions.

This course is designed to introduce computational and statistical concepts and tools used at the moment in data integration and fusion, especially in bioinformatics. The course does not focus on database integration, which a closely related topic. In contrast, the focus is on the various computational techniques tasks that enable better inference based on multiple data sources as opposed to using individual sources separately.

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 (abstract + presentation + project work) (5 cr).

Requirements for passing the course [back to top]

The course is graded as fail/pass/pass with distinction. The abstracts+presentations and the project works are graded as fail/pass/pass with distinction.

Make a presentation about a subject given in the first session. Prepare a one page extended abstract about your subject and send it electronically to the assistant at least 48 hours before your presentation. The assistant will then comment the abstract if needed, and you will send the corrected abstract to the assistant at least 24 hours before your presentation, and the assistant will send it to the other participants of the course.

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]

A collection of articles.

Introductory material (read before 21.9.2005):

Schedule [back to top]

We aim at having to seminar presentations at each meeting. Time reserved for each presentation is 25 min followed by 5 min for discussion.
Time Lecturer Subject and material
14.9. Janne Nikkilä, Leo Lahti
  • Administrative issues
  • Introduction
21.9 Kari Nousiainen
28.9. Heli Hiisilä
Ilkka Huopaniemi
5.10. Merja Oja
Jarkko Miettinen
12.10. Sampsa Hautaniemi
  • Integration of microarray data suggests putative novel target genes in breast cancer
19.10. Jarkko Ylipaavalniemi

Project work [back to top]

Own topic or one of the topics suggested in the last seminar meeting.

Write a short (A4) project plan before 26. October 2006 and send it to the course assistant. Our suggestions and approval will be made before 2nd November.

DL for the project is 8th December, 2006 at 8 p.m. For more details, see the separate page.

For more information, please send email to

Janne Nikkilä and Leo Lahti

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