What we actually do

The main areas of our research are: DNA sequencing and assembling (including design of algorithms for the NGS sequencers); protein structure analysis; RNA structure analysis and prediction (including automatic tertiary structure prediction tool); nanotechnology and DNA computing.

DNA is a molecule, that carries genetic information necessary for functioning and evolution of living organisms. Recently, high-throughput sequencing technologies have enabled to commonly read DNA chains (i.e. Roche - 454, Illumina - Solexa, Applied Biosystems - SOLiD). DNA fragments (also called DNA reads) coming out from the sequencers are much shorter than for the previous sequencing methods: gel-based sequencing (Sanger et al., 1977, Maxam and Gilbert, 1977) or sequencing by hybridization (e.g. Southern, 1988). DNA reads are merged together by assemblers into larger sequences, called contigs. In further steps (including also DNA mapping) contigs are linked up into sequence of the whole genome.

In our bioinformatics group we conduct DNA studies in the following topics:
Sequencing by hybridization (SBH),
- DNA assembling - SR-ASM algorithm, GRASShopPER,
- DNA mapping - Simplified Partial Digest Problem,
CLAIM- intergation of microarray data and protein-protein interaction network for functional protein analysis