Publications per year
Publications per year
- 21 results
Search results
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2024
Phylogenetic and Chemical Probing Information as Soft Constraints in RNA Secondary Structure Prediction
von Löhneysen, S., Spicher, T., Varenyk, Y., Yao, H. T., Lorenz, R., Hofacker, I. & Stadler, P. F., 1 Jun 2024, In: Journal of computational biology : a journal of computational molecular cell biology. 31, 6, p. 549-563 15 p.Publications: Contribution to journal › Article › Peer Reviewed
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2023
DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model
Badelt, S., Lorenz, R. & Hofacker, I. L., 1 Jan 2023, In: Bioinformatics (Oxford, England). 39, 1, btad034.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
Local RNA folding revisited
Waldl, M., Spicher, T., Lorenz, R., Beckmann, I. K., Hofacker, I. L., Von Löhneysen, S. & Stadler, P. F., 1 Aug 2023, In: Journal of Bioinformatics and Computational Biology. 21, 4, 2350016.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
Modified RNAs and predictions with the ViennaRNA Package
Varenyk, Y., Spicher, T., Hofacker, I. L. & Lorenz, R., 1 Nov 2023, In: Bioinformatics. 39, 11, btad696.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package
Yao, H. T., Lorenz, R., Hofacker, I. L. & Stadler, P. F., Dec 2023, In: Algorithms for Molecular Biology. 18, 1, 8.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
2022
Caveats to Deep Learning Approaches to RNA Secondary Structure Prediction
Flamm, C., Wielach, J., Wolfinger, M. T., Badelt, S., Lorenz, R. & Hofacker, I. L., 11 Jul 2022, In: Frontiers in bioinformatics. 2, 7 p., 835422.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
2021
Rna secondary structures with limited base pair span: Exact backtracking and an application
Lorenz, R. & Stadler, P. F., Jan 2021, In: Genes. 12, 1, p. 1-9 9 p., 14.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
RNAxplorer: harnessing the power of guiding potentials to sample RNA landscapes
Entzian, G., Hofacker, I. L., Ponty, Y., Lorenz, R. & Tanzer, A., 1 Aug 2021, In: Bioinformatics. 37, 15, p. 2126-2133 8 p.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
2019
RNA modifications in structure prediction – Status quo and future challenges
Tanzer, A., Hofacker, I. L. & Lorenz, R., 1 Mar 2019, In: Methods. 156, p. 32-39 8 p.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
2016
Predicting RNA secondary structures from sequence and probing data
Lorenz, R., Wolfinger, M. T., Tanzer, A. & Hofacker, I. L., 1 Jul 2016, In: Methods. 103, p. 86-98 13 p.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
RNA folding with hard and soft constraints
Lorenz, R., Hofacker, I. L. & Stadler, P. F., 23 Apr 2016, In: Algorithms for Molecular Biology. 11, 1, 13 p., 8.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
SHAPE directed RNA folding
Lorenz, R., Luntzer, D., Hofacker, I., Stadler, P. & Wolfinger, M., 1 Jan 2016, In: Bioinformatics. 32, 1, p. 145-147 3 p.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
2015
Design criteria for synthetic riboswitches acting on transcription
Wachsmuth, M., Domin, G., Lorenz, R., Serfling, R., Findeiss, S., Stadler, P. F. & Moerl, M., 2015, In: RNA Biology. 12, 2, p. 221-231 11 p.Publications: Contribution to journal › Article › Peer Reviewed
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Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA
Lavender, C. A., Lorenz, R., Zhang, G., Tamayo, R., Hofacker, I. L. & Weeks, K. M., May 2015, In: PLoS Computational Biology. 11, 5, 19 p., e1004126.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
2014
TSSAR: TSS annotation regime for dRNA-seq data
Amman, F., Wolfinger, M. T., Lorenz, R., Hofacker, I. L., Stadler, P. F. & Findeiss, S., 27 Mar 2014, In: BMC Bioinformatics. 15, 1, 11 p., 89.Publications: Contribution to journal › Article › Peer Reviewed
Open Access -
2013
2D Meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction
Lorenz, R., Bernhart, S. H., Qin, J., Siederdissen, C. H. Z., Tanzer, A., Amman, F., Hofacker, I. L. & Stadler, P. F., 2013, In: I E E E - A C M Transactions on Computational Biology and Bioinformatics. 10, 4, p. 832-844 13 p.Publications: Contribution to journal › Article › Peer Reviewed
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2012
Folding RNA/DNA hybrid duplexes
Lorenz, R., Hofacker, I. & Bernhart, S., 2012, In: Bioinformatics. 28, 19, p. 2530-2531 2 p.Publications: Contribution to journal › Article › Peer Reviewed
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2011
Animal snoRNAs and scaRNAs with exceptional structures
Marz, M., Gruber, A., Höner zu Siederdissen, C., Amman, F., Badelt, S., Bartschat, S., Bernhart, S., Kehr, S., Lorenz, R., Tanzer, A., Yusuf, D., Tafer, H., Hofacker, I. & Stadler, P., 2011, In: RNA Biology. 8, 6, p. 938-946 9 p.Publications: Contribution to journal › Article › Peer Reviewed
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ViennaRNA Package 2.0
Lorenz, R., Bernhart, S. H. F., Höner zu Siederdissen, C., Tafer, H., Flamm, C., Stadler, P. & Hofacker, I., 2011, In: Algorithms for Molecular Biology. 6Publications: Contribution to journal › Article › Peer Reviewed
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2010
Nematode sbRNAs: Homologs of vertebrate Y RNAs
Boria, I., Gruber, A., Tanzer, A., Bernhart, S., Lorenz, R., Müller, M., Hofacker, I. & Stadler, P., 2010, In: Journal of Molecular Evolution. 70, 4, p. 346-358 13 p.Publications: Contribution to journal › Article › Peer Reviewed
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2008
The Vienna RNA websuite
Lorenz, R., Bernhart, S., Hofacker, I., Gruber, A. & Neuböck, R., 2008, In: Nucleic Acids Research. 36, suppl 2, p. 70-74 5 p.Publications: Contribution to journal › Article › Peer Reviewed