eCLASH Towards defining the small RNA interactome

• Applicants: Professor Dr. Rolf Backofen; John Andrew Pospisilik, Ph.D.
• Subject Area: Bioinformatics and Theoretical Biology ; Cell Biology
• Term: from 2015 to 2021
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 286021192

• Final Report Year: 2023

Final Report Abstract

In this project, we developed tools and workflows for the analysis of miRNA interactome data. We also provided options to run our workflows on any stateof-the-art RNA-RNA interactome data that generate chimeric reads. Our visualization framework helps in filtering and understanding of detected interactions. Galaxy-based workflows and easy to follow hands-on training material benefits biologists in their data analysis. The latest revision of IntaRNA with enhancements and new features improves the usability of the tool.

Publications

• IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions. Nucleic Acids Research, 45(W1), W435-W439.
  Mann, Martin; Wright, Patrick R. & Backofen, Rolf
  
• Freiburg RNA tools: a central online resource for RNA-focused research and teaching. Nucleic Acids Research, 46(W1), W25-W29.
  Raden, Martin; Ali, Syed M.; Alkhnbashi, Omer S.; Busch, Anke; Costa, Fabrizio; Davis, Jason A.; Eggenhofer, Florian; Gelhausen, Rick; Georg, Jens; Heyne, Steffen; Hiller, Michael; Kundu, Kousik; Kleinkauf, Robert; Lott, Steffen C.; Mohamed, Mostafa M.; Mattheis, Alexander; Miladi, Milad; Richter, Andreas S.; Will, Sebastian; ... & Backofen, Rolf
  
• Integration of accessibility data from structure probing into RNA–RNA interaction prediction. Bioinformatics, 35(16), 2862-2864.
  Miladi, Milad; Montaseri, Soheila; Backofen, Rolf & Raden, Martin
  
• ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data. GigaScience, 10(2).
  Videm, Pavankumar; Kumar, Anup; Zharkov, Oleg; Grüning, Björn Andreas & Backofen, Rolf