DFG-Projekt: MicroRNA as an integral part of cell communication: regularized target prediction and network preditction

Description of the project:
MicroRNAs, endogenously encoded small RNA molecules, play an integral part in transcriptional and post-transcriptional gene regulation. Recent discoveries indicate that miRNAs do not act independently but cooperatively act with other miRNAs and RNA binding proteins. However, current computational approaches do not not appropriately model these cooperative effects encrypted in the context of the miRNA binding sites. Furthermore, most machine learning approaches predict only interaction between miRNAs and their targets, but do not offer guidelines for mutagenesis based experimental verification. In order to assess contextual information a paradigm shift is needed. Therefore we propose (i) to build a miRNA target prediction pipeline that integrates explicit structural information on the interaction site context, (ii) to develop a combined computational and experimental strategies to assess by mutagenesis the importance of both individual positions and sequence/structural motifs in the context, and (iii) to use previous knowledge with expression data to generate tissue and disease specific interaction networks for evaluating the biological function of miRNA based regulation.

Additional information: http://www.bioinf.uni-freiburg.de
contact person: Prof. Dr. Rolf Backofen
Phone: 0761 203 7461
Email: backofen@informatik.uni-freiburg.de
Start of project: 2012
End of project: 2014
Project Management:
Albert-Ludwigs-University Freiburg
Prof. Dr. Rolf Backofen
Prof. Dr. Rolf Backofen
Georges-Köhler-Allee 106
79110 Freiburg

Phone: +49 (0) 761-203-7461
Fax: +49 (0) 761-203-7462
Email: backofen@informatik.uni-freiburg.de
Actual Research Report
    DFG SPP InKoMBio