SICS Intelligent Systems Laboratory
Swedish Institute of Computer Science
http://www.sics.se/isl/

Biotechnology

Overview

Biotechnology affects the quality of life of most people via drug design, finding genetic risk factors, genetic modification of crops and animals, etc. It is also one of the major growth areas in science and technology. Providing computer-based methods for coping with and interpreting the genomic data that are being uncovered in large volumes presents one of the grand challenges of our times.

Our research in this area focuses on two themes:

Biotech Supply. Laboratory instruments for life sciences typically need sophisticated software components, e.g. for scheduling robot arm movements, dispensation orders, assay design, or data analysis. The design of such components requires combinatorial problem solving, and is an excellent application area for the constraint technology supplied by the CPS group.

Bioinformatics and Functional Genomics. We conduct projects addressing specific biological problems, in collaboration with biologists. SICS's responsibility in these projects is typically to provide expertise in the computer science and bioinformatics aspects.

Projects

  • DispGen (2003) - a project to develop a dispensation order generator for Pyrosequencing's sequence analysis instruments, using constraint programming technology. The generator computes an instruction sequence based on an input specification. Funding provided by Pyrosequencing AB, an Uppsala company offering complete solutions for applications including genetics, drug discovery, microbiology, SNP and mutation analysis, forensic identification, pharmacogenomics, and bacterial and viral typing.

  • GENKOMB (2003) - The aim of the GENKOMB project was to find and analyse transcription factor binding sites in the human genome, by correlating expression data for a set of genes with the nucleotide sequences in their upstream regions. Apart from detecting transcription factor binding sites, this project has resulted in programs for matching weight matrices to DNA sequences and multiple alignment of short nucleotide sequences. In collaboration with AstraZeneca AB.

    Main funding provided by VINNOVA.

  • GENFUNK (2001-2002) - This project, carried out in collaboration with Global Genomics AB, studied a novel approach of measuring the global gene expression in a tissue sample. In the method, mRNA is extracted from the sample and transformed into cDNA captured on magnetic beads. This is then acted on by type IIS restriction endonucleases, which recognize certain short DNA sequences and cut the DNA close to those sequences. The resulting fragments are amplified in PCR with selected ligation fragments, and displayed in capillary electrophoresis. Determining the gene expression levels from the peak data is combinatorial optimization problem, which can in principle be solved, to give expression levels of most genes active in sampled cells, with good accuracy.

    Main funding provided by VINNOVA.

Researchers

Publications

Bibliography generated from publications.bib

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For more information on the SICS Intelligent Systems Laboratory please email sverker@sics.se.