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SPP1935 -- Deciphering the mRNP code :
RNA-bound Determinants of Post-transcriptional Gene Regulation

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laboratoriesProf. Dr. Backofen

Rolf Backofen Center
Albert-Ludwigs-Universtität Freiburg Institut für Informatik Lehrstuhl für Bioinformatik

Adress
Georges-Köhler-Allee 106, 79110 Freiburg

Phone
004907612037461


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RNA Bioinformatics, Analysis of CLIP and related HTS data, RNA secondary structure and conservation, Workflow-Management-Systems (Galaxy)

Lab InfoPROJECT INFORMATION :

We are interested in the bioinformatics analysis of CLIP data, where we want to determine high affinity binding sites to train a binding model. Using these binding models, we want to find missing binding sites to make use of publicly available CLIP data. Specifically, we want to make use of the massive amount of CLIP data that will be generated in the next years with the ENCODE project. To make these data sets available, we will 1) determine binding sites and associated affinities from CLIP data sets, 2) model the mutual influence of several binding sites on the same target RNA, and 3) investigate cases of strong cooperativity/competition together with experimental partners. The collected information will also provide a valuable resource for external experimental groups, and we will closely collaborate with them to improve the understanding of the code that determines post-transcriptional regulation.




Lab techsKEY TECHNOLOGIES :

- Bioinformatics
- Machine Learning




PublicationsPUBLICATIONS :

Holmqvist E, Wright PR, Li L, Bischler T, Barquist L, Reinhardt R, Backofen R*, Vogel J.* Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo. EMBO J. 2016 May 2;35(9):991-1011. *joint last author

Murakawa Y, Hinz M, Mothes J, Schuetz A, Uhl M, Wyler E, Yasuda T, Mastrobuoni G, Friedel CC, Dolken L, Kempa S, Schmidt-Supprian M, Bluthgen N, Backofen R, Heinemann U, Wolf J, Scheidereit C, Landthaler M. RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-kappaB pathway. Nat Commun. 2015;6:7367.

Ilik IA, Quinn JJ, Georgiev P, Tavares-Cadete F, Maticzka D, Toscano S, Wan Y, Spitale RC, Luscombe N, Backofen R, Chang HY, Akhtar A. Tandem stem-loops in roX RNAs act together to mediate X chromosome dosage compensation in Drosophila. Mol Cell. 2013 Jul 25;51(2):156-73.

Maticzka D, Lange SJ, Costa F, Backofen R. GraphProt: modeling binding preferences of RNA-binding proteins. Genome Biol. 2014 Jan 22;15(1):R17

Ferrarese R, Harsh GRt, Yadav AK, Bug E, Maticzka D, Reichardt W, Dombrowski SM, Miller TE, Masilamani AP, Dai F, Kim H, Hadler M, Scholtens DM, Yu IL, Beck J, Srinivasasainagendra V, Costa F, Baxan N, Pfeifer D, von Elverfeldt D, Backofen R, Weyerbrock A, Duarte CW, He X, Prinz M, Chandler JP, Vogel H, Chakravarti A, Rich JN, Carro MS, Bredel M. Lineage-specific splicing of a brain-enriched alternative exon promotes glioblastoma progression. J Clin Invest. 2014 Jul;124(7):2861-76.