Items where Author is "Lorenz, Ronny"

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Number of items: 22.

Journal Paper

  • Phylogenetic and Chemical Probing Information as Soft Constraints in RNA Secondary Structure Prediction
    von Löhneysen, Sarah and Spicher, Thomas and Varenyk, Yuliia and Yao, Hua-Ting and Lorenz, Ronny and Hofacker, Ivo L. and Stadler, Peter F. Journal of Computational Biology, 31 (6). pp. 549-563 ISSN 1066-5277 Mary Ann Liebert (2024)

  • DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model
    Badelt, Stefan and Lorenz, Ronny and Hofacker, Ivo L. Bioinformatics, 39 (1). btad034 ISSN 1367-4803 Oxford University Press (2023)

  • Local RNA folding revisited
    Waldl, Maria and Spicher, Thomas and Lorenz, Ronny and Beckmann, Irene K. and Hofacker, Ivo L. and von Löhneysen, Sarah and Stadler, Peter F. p. 2350016 ISSN 1757-6334 World Scientific (2023)

  • Modified RNAs and predictions with the ViennaRNA Package
    Varenyk, Yuliia and Spicher, Thomas and Hofacker, Ivo L. and Lorenz, Ronny Bioinformatics, 39 (11). ISSN 1367-4803 Oxford University Press (2023)

  • Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package
    Yao, Hua-Ting and Lorenz, Ronny and Hofacker, Ivo L. and Stadler, Peter F. Algorithms for Molecular Biology, 18 (1). p. 8 ISSN 1748-7188 Springer (2023)

  • Caveats to deep learning approaches to RNA secondary structure prediction
    Flamm, Christoph and Wielach, Julia and Wolfinger, Michael T. and Badelt, Stefan and Lorenz, Ronny and Hofacker, Ivo L. ISSN 0000-0000 Frontiers (2022)

  • RNAxplorer: harnessing the power of guiding potentials to sample RNA landscapes
    Entzian, Gregor and Hofacker, Ivo L. and Ponty, Yann and Lorenz, Ronny and Tanzer, Andrea Bioinformatics, 37. pp. 2126-2133 ISSN 1367-4803 (2021)

  • RNA modifications in structure prediction – Status quo and future challenges
    Tanzer, Andrea and Hofacker, Ivo L. and Lorenz, Ronny Methods. Elsevier (2018)

  • Predicting RNA secondary structures from sequence and probing data
    Lorenz, Ronny and Wolfinger, Michael T. and Tanzer, Andrea and Hofacker, Ivo L. pp. 86-98 ISSN 1046-2023 (2016)

  • RNA folding with hard and soft constraints
    Lorenz, Ronny and Hofacker, Ivo L. and Stadler, Peter F. ISSN 1748-7188 (2016)

  • Design criteria for synthetic riboswitches acting on transcription
    Wachsmuth, Manja and Domin, Gesine and Lorenz, Ronny and Serfling, Robert and Findeiß, Sven and Stadler, Peter F. and Mörl, Mario RNA Biol, 12 (2). pp. 221-231 ISSN 1547-6286 (2015)

  • Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA
    Lavender, Christopher A. and Lorenz, Ronny and Zhang, Ge and Tamayo, Rita and Hofacker, Ivo L. and Weeks, Kevin M. PLoS Comput Biol, 11. e1004126 ISSN 1553-734X (2015)

  • SHAPE directed RNA folding
    Luntzer, Dominik and Lorenz, Ronny and Hofacker, Ivo L. and Stadler, Peter F. and Wolfinger, Michael T. Bioinformatics, 32. pp. 145-147 ISSN 1367-4803 (2015)

  • TSSAR: TSS Annotation Regime for dRNA-seq data
    Amman, Fabian and Wolfinger, Michael T and Lorenz, Ronny and Hofacker, Ivo L. and Stadler, Peter F and Findeiß, Sven BMC Bioinformatics, 15. p. 89 ISSN 1471-2105 (2014)

  • 2D meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction
    Lorenz, Ronny and Bernhart, Stephan H. and Qin, Jing and Höner zu Siederdissen, Christian and Tanzer, Andrea and Amman, Fabian and Hofacker, Ivo L. and Stadler, Peter F. IEEE Trans. Comp. Biol. Bioinf., 10. pp. 832-844 ISSN 1557-9964 (2013)

  • Folding RNA/DNA hybrid duplexes
    Lorenz, Ronny and Hofacker, Ivo L. and Bernhart, Stephan H Bioinformatics, 28 (19). pp. 2530-2531 ISSN 1367-4803 (2012)

  • ViennaRNA Package 2.0
    Lorenz, Ronny and Bernhart, Stephan H and Höner zu Siederdissen, Christian and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F. and Hofacker, Ivo L. Algorithms for Molecular Biology, 6 (1). p. 26 Biomed Central (2011)

  • Animal snoRNAs and scaRNAs with Exceptional Structures
    Marz, Manja and Gruber, Andreas R. and Höner zu Siederdissen, Christian and Amman, Fabian and Badelt, Stefan and Bartschat, Sebastian and Bernhart, Stephan H. and Beyer, Stephanie and Lorenz, Ronny and Tanzer, Andrea and Yusuf, Dilmurat and Tafer, Hakim and Hofacker, Ivo L. and Stadler, Peter F. RNA Biology, 8 (6). ISSN 1547-6286 Landes Bioscience (2011)

    • Paper in Conference Proceedings or in Workshop Proceedings

  • Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction
    von Löhneysen, Sarah and Spicher, Thomas and Varenyk, Yuliia and Yao, Hua-Ting and Lorenz, Ronny and Hofacker, Ivo L. and Stadler, Peter F. In: International Symposium on Bioinformatics Research and Applications , October 9–12 , Wrocław, Poland (2023)

  • Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding
    Stadler, Peter F. and Hofacker, Ivo L. and Flamm, Christoph and Lorenz, Ronny In: 13th International Joint Conference on Biomedical Engineering Systems and Technologies , 02.2020 , Valletta, Malta (2020)

    • Book Section/Chapter

  • Predicting RNA Structure: Advances and Limitations
    Hofacker, Ivo L. and Lorenz, Ronny In: RNA Folding. Meth. Mol. Biol., 1086 Humana Press, pp. 1-19 (2014)

  • RNA Folding Algorithms with G-Quadruplexes
    Lorenz, Ronny and Bernhart, Stephan H. and Externbrink, Fabian and Qin, Jing and Höner zu Siederdissen, Christian and Amman, Fabian and Hofacker, Ivo L. and Stadler, Peter F. In: Advances in Bioinformatics and Computational Biology. Lecture Notes in Computer Science , 7409 Springer, pp. 49-60 (2012)

    • This list was generated on Fri May 9 09:24:37 2025 CEST.
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