Institute of Computer Science
University Freiburg


General Research Description

Our team develops computer models for the analysis and prediction of biochemical processes in living cells. Particularly, we examine the influence of regulatory RNA molecules which is one of the most important but yet inadequately studied class of molecules. There are three important kinds of long-chained molecules in living cells: DNA (the genetic information), RNA and Proteins.

RNA functions amongst others as the link in the translation of genetic information (DNA) into Proteins, the latter being necessary for all essential processes. RNA molecules play, however, a more important role as previously assumed. Besides their function as a translation template for Proteins, they are also involved in the regulation of cell processes.

We are particularly interested in

Regulatory RNAs

The regulation of the cell is a complex process whereby a lot of involved elements are not known yet. RNAs influence considerably more processes than previously assumed. Although parts of the genes that are read but not translated into Proteins, the so-called non-coding RNAs, account for 98% of the genetic information, the research focused up to now on parts of the genome that are translated into Proteins which represent only 1% of the DNA.

The determination of the essential parts of the so-called regulatory elements by biochemical procedures is very complex. Since the sequencing of the human genome, however, it is possible to selectively search for those elements with the aid of Bioinformatic approaches. These procedures are assisted by the deciphering of the genetic material of many additional species.

A comparison of the genetic material between related species can now be achieved with the aid of our models. Similarities and differences permit conclusions on regulatory elements. It is not sufficient to search for simple sequence patterns but additional structural properties of the molecules have to be incorporated.

The field of Bioinformatics enables the prediction of RNA structures as their experimental identification is time and resource intensive. The prediction procedures unfortunately have high computational complexity. For this reason, a main part of our work is the optimization of the corresponding procedures.

Regulatory Signals

The determination of regulatory elements provides the first step in uncovering of processes that are being controlled by them. For further analysis, we develop computer models that examine the influence of the regulatory signals in the cell. In this field, we are particularly interested in the effects of the interactions of RNA molecules as well as the cellular selection of the corresponding gene segment.

Main Goals

Regulatory RNAs are engaged in all essential processes of the cell. A faulty RNA regulation can cause serious diseases. Among those are many types of cancer as well as diseases of the nervous system; amongst others Prader-Willi syndrome, autism and Alzheimer's disease. The field of Bioinformatics contributes to the basic understanding of the regulatory mechanisms and permits to establish suitable starting points for treatment.

Main Research Areas

RNA Structure


Simplified Protein Models

Alternative Splicing

Transcriptional Regulation

Promoter structure

Constraint-based Methods for Bioinformatics

Funded Research Projects ( via Research database University of Freiburg )


Detailed information