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Abteilung / Zentrum / Institut:
Prof. Dr. Rolf Backofen
Sekretariat: Monika Degen-Hellmuth
Dr. Bérénice Batut
Dr. Florian Eggenhofer
Dr. Anika Erxleben
Dr. Björn Grüning
Dr. Torsten Houwaart
Dr. Martin Mann
Dr. Sita J. Saunders
Dr. Patrick Wright
Omer Salem Alkhnbashi
Mariam Alshaikh
Clemens Blank
Stefan Jankowski
Daniel Maticzka
Stefan Mautner
Milad Miladi
Teresa Müller
Michael Uhl
Pavankumar Videm
Joachim Wolff
BMBF: e:Bio ReelinSys
BMBF: e:Bio RNAsys
Prof. Dr. Wolfgang Hess (University of Freiburg)
Prof. Dr. Jörg Vogel (University of Würzburg)
Prof. Dr. Anita Marchfelder (University of Ulm)
Dr. Asifa Akhtar (MPI Freiburg)
Prof. Dr. Heinrich Spiecker (University of Freiburg)
Prof. Dr. Peter F. Stadler (University of Leipzig)
Prof. Dr. Uwe Ohler (Max-Delbrück-Centrum für Molekulare Medizin
Prof. Dr. Nikolaus Rajewsky (Max-Delbrück-Centrum für Molekulare Medizin
Prof. Gad Landau (University of Haifa)
Prof. Dr. Wilfried Weber (University of Freiburg)
Prof. Dr. Tanja Vogel (University of Freiburg)
Prof. Dr. Klaus Palme (University of Freiburg)
Prof. Dr. Fabian Theis (Helmholtz Zentrum München)
Dr. Thomas Manke (MPI Freiburg)
Dr. J. Andrew Pospisilik (MPI Freiburg)


Prof. Dr. Rolf Backofen - Bioinformatics

Research Profile

The fields of work of our group is broadly spread: development of stand alone bioinformatic algorithms, compilation and preparation of analysis workflows, and data analysis.

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 

  • the search for regulatory RNA molecules
  • identifying the mode of action of RNAs
  • the examination of structural features of RNAs and proteins 


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.    

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.


The Freiburg Galaxy Project

Galaxy is an open source, web-based platform for data intensive biomedical research. It makes computational  bioinformatics applications accessible to users lacking programming experience by enabling them to easily specify parameters for running tools and workflows. Galaxy provides access to a powerful analysis infrastructure through the web, and allows for reproducible and transparent data analysis.      

The Freiburg Galaxy Team offers a framework for scientists on e.g. NGS data analyses (RNA-seq, ChIP-seq, Exome-seq, MethylC-seq), genome annotation analyses for eukaryotic and prokaryotic organisms (from gene prediction to functional description), proteomics and metabolomics analysis, and the ChemicalToolBoX for analysis of small compounds. Furthermore, Galaxy has a huge variety of data visualization tools. Galaxy contains more than 800 different single analysis tools and ready-to-use pipelines for different applications. After registration, all tools and the infrastructure for data analysis are freely available and can be used for creation of your own workflows for your specific projects. 

The Freiburg Galaxy Project is part of the "German Network for Bioinformatics Infrastructure" (Deutsches Netzwerk für Bioinformatik-Infrastruktur, de.NBI) and the Collaborative Research Centre (CRC) 992 for Medical Epigenetics and offers within the RNA Bioinformatic Centre (RBC) a central platform for RNA analysis. The RBC will create infrastructures and services for RNA-protein interactions by analysis of CLIP-seq data, detection of RNA motifs and miRNA binding sites; the study of ribozymes and RNAs as decoys; detection of non-coding RNAs, RNA structure prediction, and RNA conservation. The RBC will also conduct research on guide RNAs, comprising miRNA and ncRNA target prediction, and their detection.