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
Web	http://www.cis.hut.fi/Opinnot/T-61.6080/
Registration	TKK students: WebTopi, others: send mail to t616080@cis.hut.fi
E-mail	t616080@cis.hut.fi

• Introduction
• Prerequisites for attending
• Course format
• Requirements for passing the course
• Signing up for the course
• Literature
• Schedule
• Project work
• One page summary/brochure

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):

• Joyce, Andrew R. and Palsson, Bernhard O. The model organism as a system: integrating 'omics' data sets. Nat Rev Mol Cell Biol 7(3) pp. 198--210, 2006.
• Rhodes, Daniel R and Chinnaiyan, Arul M Integrative analysis of the cancer transcriptome Nat Genet, 2005.
• Roded Sharan and Trey Ideker Modeling cellular machinery through biological network comparison Nature Biotechnology 24, 427 - 433 (2006)
• Good tutorial for those with no biological background:
  Molecular Biology for Computer Scientists
  L. Hunter in AI and molecular biology
• Web tutorial to bioinformatics in general

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	Gene prioritization through genomic data fusion Aerts et al. Nat Biotech 24(5) pp. 537--544, 2006.
28.9.	Heli Hiisilä Ilkka Huopaniemi	Discovery of biological networks from diverse functional genomic data Myers et al. Genome Biology 6(13) pp. R114, 2005. A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae) Troyanskaya et al. PNAS 100(14) pp. 8348--8353, 2003. Fusing microarray experiments with multivariate regression Gilks et al. Bioinformatics 21(suppl. 2) pp. ii137-143, 2005.
5.10.	Merja Oja Jarkko Miettinen	Fusion of Similarity Data in Clustering T Lange and JM Buhmann, NIPS 2005 A data integration methodology for systems biology D. Hwang et al. PNAS November 29, 2005 vol. 102 no. 48, 17296-17301
12.10.	Sampsa Hautaniemi	Integration of microarray data suggests putative novel target genes in breast cancer
19.10.	Jarkko Ylipaavalniemi	Extraction of correlated gene clusters from multiple genomic data by generalized kernel canonical correlation analysis Yamanishi et al. Bioinformatics 19 (Supplement 1): i323. (2003)

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 t616080@cis.hut.fi.

Welcome,
Janne Nikkilä and Leo Lahti