A Flexible and Efficient System for the Detection of RNA Sequence/Structure Motifs

• Applicant: Professor Dr. Rolf Backofen
• Co-Applicant: Professor Gad Landau
• Subject Area: Theoretical Computer Science ; Bioinformatics and Theoretical Biology
• Term: from 2009 to 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 110058642

• Final Report Year: 2021

Final Report Abstract

No abstract available

Publications

• BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles. Bioinformatics, 30(12):i274–i282, 2014
  Pavankumar Videm, Dominic Rose, Fabrizio Costa, and Rolf Backofen
  
• ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs. BMC Bioinformatics, 15(1):6602, 2014
  Christina Otto, Mathias Mohl, Steffen Heyne, Mika Amit, Gad M. Landau, Rolf Backofen, and Sebastian Will
  
• Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures. Algorithms Mol Biol, 9:19, 2014
  Jing Qin, Markus Fricke, Manja Marz, Peter F. Stadler, and Rolf Backofen
  
• Local exact pattern matching for nonfixed RNA structures. IEEE/ACM Trans. Comput. Biology Bioinform., 11(1):219–230, 2014
  Mika Amit, Rolf Backofen, Steffen Heyne, Gad M. Landau, Mathias Möhl, Christina Otto, and Sebastian Will
  
• SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics. Bioinformatics, 31(15):2489–2496, 2015
  Sebastian Will, Christina Otto, Milad Miladi, Mathias Möhl, and Rolf Backofen
  
• RNAscClust: clustering RNA sequences using structure conservation and graph based motifs. Bioinformatics, 33(14):2089–2096, 02 2017
  Milad Miladi, Alexander Junge, Fabrizio Costa, Stefan E Seemann, Jakob Hull Havgaard, Jan Gorodkin, and Rolf Backofen
  
• Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs. In Katharina T. Huber and Dan Gusfield, editors, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019), volume 143 of Leibniz International Proceedings in Informatics (LIPIcs), pages 14:1–14:13, Dagstuhl, Germany, 2019
  Milad Miladi, Martin Raden, Sebastian Will, and Rolf Backofen
  
• GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering. GigaScience, 8(12), 12 2019. giz150
  Milad Miladi, Eteri Sokhoyan, Torsten Houwaart, Steffen Heyne, Fabrizio Costa, Björn Grüning, and Rolf Backofen
  
• Shaker: Rna shape prediction using graph kernel. Bioinformatics, 35(14):i354–i359, 07 2019
  Stefan Mautner, Soheila Montaseri, Milad Miladi, Martin Raden, Fabrizio Costa, and Rolf Backofen
  
• MutaRNA: analysis and visualization of mutation-induced changes in RNA structure. Nucleic Acids Research, 05 2020
  Milad Miladi, Martin Raden, Sven Diederichs, and Rolf Backofen
  
• The locality dilemma of Sankoff-like RNA alignments. Bioinformatics, 36:i242–i250, 2020
  Teresa Müller, Milad Miladi, Frank Hutter, Ivo Hofacker, Sebastian Will, and Rolf Backofen