Bioinformatics Research at IBT

Description of the project

The aim of the Bioinformatics group is to understand biological and medical phenomena in structural, mechanical and systems level by applying bioinformatics tools and applications. There are two major research lines.

Analysis of effects of disease-related mutations ranges from collecting information into publicly accessible databases to detailed structural and functional stuides of the effects and consequences of the variations. Currently we maintain around 130 mutation databases (http://bioinf.uta.fi/). These databases contain information mainly for immunodeficiencies and cancers. The effects and consequences of the mutations are investigated at RNA, DNA and protein level. The ultimate goal is to help in developing new therapies to treat patients. We are developing tools for the prediction of numerous effects on protein structure, function, interactions, stability, aggregation and disorder propensity etc. For this purpose we provide Pathogenic-Or-Not -Pipeline (PON-P), that allows easy and fast access to large number of predictors and interpretation of the predictions. We have predicted successfully effects of thousands of mutations.

The other lines is systems biology applied to immunological processes. We have identified genes and proteins essential for human immunity. Evolution of these genes and proteins has been investigated and a database generated for some 900 proteins. Furthermore, the orthologs of metazoan immune system proteins have been identified. These datasets allow system wide analysis of immunity. Another approach to investigating the immune system at system level is by following gene and protein expression during B-cell development by applying microarray and proteomics methods. We have alreade predicted novel immunodeficiency candidate genes and made a novel classification for immunodeficiencies based on the systems biological approaches and data. In the next step the integrated information is used to model and predict the behaviour of immunological sybsystems in health and disease.

Main collaborators

Prof. Tapio Salakoski, Deparment of Information Technology, University of Turku, Finland
Prof. Harri Savilahti, Department of Biology, University of Turku, Finland
Prof. C. I. Edvard Smith, Karolinska Institutet, Stockholm, Sweden
Human Genome Variation Society board members
Immunodeficiency diagnostic and research laboratories, European Bioinformatics Institute.

Funding

Academy of Finland, EU, Medical Research Fund of Tampere University Hospital, Sigrid Juselius Foundation.