Bioinformatics

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Department of Biomedical Informatics

Synopsis:

Laboratories around the world produce massive amount of new nucleotide and protein sequences, gene expression profiles, 3-D structures and other data of biological character. To illustrate this fact, the number of known nucleotide sequences grew 100 times in just over five years. The database of 3-D structures expanded by 20 % in the same year and more than 3000 organisms have been or are sequenced at the moment. With an ever-increasing amount of data available, grows even the significance of bioinformatics. Bioinformatics collects, archives and most importantly analyses and attempt to find a meaning and useful information in this explosively growing sea of data. Bioinformatics is one of the most dynamically developing areas of biomedical research and basic knowledge of bioinformatics methods becomes quickly indispensable for anyone with a serious interest in doing biomedical research. The aim of this course is to introduce students with basic, but also modern promising bioinformatics methods. These methods will be shown and explained in lectures and later used in a series of practicals. These „hands-on“ practicals are designed to show how to take an advantage of bioinformatics in every day life in a laboratory. The practicals were tested for a long time and successfully on students of the Uppsala University, Sweden. This course is suitable for the second- or higher year students of biology or chemistry who want to specialize within the biomedical field of research. A basic knowledge of structure of biomacromolecules (nucleic acids, proteins) is an advantage ut it is not required to have it.

Requirements:

It is necessary to go through all the practicals, to write an article about significant bioinformatics paper of the past and to pass the final test (50% of points required). The final test will be written, questions and answers (no test), it will take between 2,5 and 3,5 hours.

Syllabus of lectures:

1. Introduction to molecular biology, introduction to bioinformatics

2. Data - how are they generated? (genomics, X-ray crystallography, microarray technology)

3. Data - where to find them? (databases)

4. Sequence alignment - algorithms, how to use it?

5. Looking for similar sequences - BLAST, PSI-BLAST

6. Structural alignment - algorithms, how to use it?

7. Analysis of protein structures

8. Prediction of 3-D structures of proteins

9. Homology modelling and drug design

10. Prediction of genes, phylogeny

11. Systems biology

12. Microarray data analysis

13. Machine learning methods - neural networks, SVM

Syllabus of tutorials:

1. Sequence databases and analysis

2. Structure databases

3. Protein structure prediction

4. Protein structure analysis

5. Homology modelling

6. Microarray analysis

Study Objective:

The basic aim of this course to introduce dynamically developing area of bioinformatics that is on the border of biology, medicine and information technologies. Students will get to know the most common bioinformatic methods theoretically, but they will also learn to use a number of methods in practical exercises. One f the aims is to practise the interpretation of observed data and the critical evaluation of data. To this end, students will be also confronted with research papers, which should facilitate their basic scientific skills.

Study materials:

[1] Zvelebil, M. & Baum, J. (2007): Undestanding bioinformatics. Garland science; 1 edition, 772 pp.

[2] Lesk, A. (2008): Introduction to bioinformatics. Oxford University Press, USA; 3rd edition, 432 pp .

[3] Bourne, P.E. & Weissig, H. (2003): Structural bioinformatics. Wiley-Liss, 649 pp.

[4] Baxevanis, A.D. & Ouellette B. F. F. (2004): Bioinformatics: Practical guide to the analysis of genes and proteins. Wiley-Interscience; 3 edition, 560 pp.

[5] Jones, N.C. & Pevzner, P.A. (2004): An Introduction to Bioinformatics Algorithms. The MIT Press; 1 edition, 454 pp.

Note:

Further information:

No time-table has been prepared for this course

The course is a part of the following study plans:

• Biomedical Informatics - combined study (compulsory course)