Groups

Laboratory for molecular biology

NeSys - Neural systems and graphics computing laboratory

The neurotransporter group

Laboratory for genome repair and regulation

Molecular and cellular basis of microbial pathogenesis

Cellular and genetic therapy research group

Laboratory for molecular neuroscience

Bioinformatics group

Laboratory of cellular neurophysiology and ion channel function

Synaptic neurochemistry laboratory

Genome dynamics and microbial pathogenesis

Bioinformatics group

Group home page

The Bioinformatics group uses computational methods to analyse genome sequences, amino acid sequences, and gene expression data, both to identify new genes of interest and to determine their structure, function and role in the cell. Advanced statistical and computational tools are both being used and developed. The group is also creating databases and web sites with our tools and generated data. We are involved in many collaborative projects with different research groups.

Challenges

Huge amounts of molecular biology data is being generated from a range of different technologies. New technologies allows extensive sequencing to be carried out to analyse transcription, sequence variation, epigenetics and other phenomena. Complete genome sequences from more than a thousand organisms as well as data from large-scale protein structure determination projects is also publicly available. The main challenge in computational biology is to integrate and make sense of all of this data.

Projects

• Structural bioinformatics: Computational models of the 3D structure of proteins are created and studied in order to understand the molecular mechanisms of enzyme activities. How does mutations affect the structure and function of a protein? Docking and molecular dynamics simulations are also used in our studies.
• Sequence similarity: Tools like PARALIGN for particularly rapid and sensitive sequence database similarity searches have been developed. Parallel computing technology is exploited to get the highest performance. These tools are now being used to build gene homology networks and to cluster orthologous genes into groups.
• Transcription analysis: Custom microarrays have been designed to study transcription in bacteria and humans. Tiling arrays are used to identify novel transcribed regions in intergenic regions of bacterial genomes. Custom arrays have also been designed to identify human oncogenic fusion transcripts. Large scale sequencing are now used to analyse transcriptional patterns.
• Genome analysis: Human and bacterial genome sequences are analysed to identify particular patterns and frequent sequences, as well as variation in the sequences at particular positions.

Recent achievements

Characterized mutations in the PCSK9 gene involved in cholesterol metabolism (J Int Med 2008, Atherosclerosis 2009) and analysed conservation of the gene (FEBS J 2008). Developed methods for design and analysis of custom tiling microarrays (PLoS One 2009) and arrays for detection of oncogenic fusion transcripts (Mol Cancer 2009). Analysed the mutational spectrum in human segmental duplications (BMC Genomics 2009) and sequences in human G-quadruplex motifs (Nucleic Acids Res 2009). Investigated dynamics of the genomes of pathogenic bacteria (Genome Dyn 2009, FEMS Microbiol Rev 2009).

Publications

List of publications

Group leader

Assoc. professor Torbjørn Rognes

Centre for Molecular Biology and Neuroscience
Department of Microbiology
Oslo University Hospital
Rikshospitalet
NO-0027 Oslo
Norway

Mob: +47 90755587
Tel: +47 22844787
Fax: +47 22844782
E-mail: torognes@ifi.uio.no

Structural model of the PCSK9 protein that mediates degradation of the low density lipoprotein (LDL) receptors. The important Ser462 residue that reduces secretion when mutated is indicated. From Cameron et al. (2009).

Latest 3 publications