Items where Author is "Stadler, Peter F."

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Number of items: 39.

Journal Paper

  • 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)

  • 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)

  • RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets
    Alkan, Ferhat and Wenzel, Anne and Palasca, Oana and Kerpedjiev, Peter and Rudebeck, Anders Frost and Stadler, Peter F. and Hofacker, Ivo L. and Gorodkin, Jan e60 ISSN 0305-1048 (2017)

  • Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells
    Hölzer, Martin and Krähling , Verena and Amman, Fabian and Barth, Emanuel and Bernhart, Stephan H. and Carmelo, Victor and Collatz, Maximilian and Doose, Gero and Eggenhofer, Florian and Ewald, Jan and Fallmann, Jörg and Feldhahn, Lasse and Fricke, Markus and Gebauer, Juliane and Gruber, Andreas R and Hufsky, Franziska and Indrischek, Henrike and Kanton, Sabina and Linde, Jörg and Mostajo, Nelly and Ochsenreiter, Roman and Riege, Konstantin and Rivarola-Duarte, Lorena and Sahyoun, Abdullah and Saunders, Sita and Seemann, Stefan E and Tanzer, Andrea and Vorgel, bertram and Wehner, Stefanie and Wolfinger, Michael T. and Backofen, Rolf and Gorodkin, Jan and Grosse, Ivo and Hoffmann, Steve and Hofacker, Ivo L. and Kaleta, Christoph and Stadler, Peter F. and Becker, Stephan and Marz, Manja ISSN 2045-2322 (2016)

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

  • Pseudoknots in RNA folding landscapes
    Kucharik, Marcel and Hofacker, Ivo L. and Stadler, Peter F. and Qin, Jing Bioinformatics, 32. pp. 187-194 ISSN 1367-4803 (2016)

  • Product grammars for alignment and folding.
    Höner zu Siederdissen, Christian and Hofacker, Ivo L. and Stadler, Peter F. pp. 507-519 ISSN 1557-9964 (2015)

  • 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)

  • Processed Small RNAs in Archaea and BHB Elements
    Berkemer, Sarah J. and Höner zu Siederdissen, Christian and Amman, Fabian and Wintsche, Axel and Will, Sebastian and Hofacker, Ivo L. and Prohaska, Sonja J. and Stadler, Peter F. Genomics Comp. Biol., 1. e18 ISSN 2365-7154 (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)

  • Bioinformatics of prokaryotic RNAs
    Backofen, Rolf and Amman, Fabian and Costa, Fabrizio and Findeiß, Sven and Richter, Andreas S. and Stadler, Peter F. RNA Biol, 11 (5). pp. 470-483 ISSN 1547-6286 (2014)

  • Basin Hopping Graph: A computational framework to characterize RNA folding landscapes
    Kucharik, Marcel and Hofacker, Ivo L. and Stadler, Peter F. and Qin, Jing Bioinformatics, 30. pp. 2009-2017 ISSN 1367-4803 (2014)

  • Challenges in RNA Virus Bioinformatics
    Marz, Manja and Beerenwinkel, Niko and Drosten, Christian and Fricke, Markus and Frishman, Dmitrij and Hofacker, Ivo L. and Hoffmann, Dieter and Middendorf, Martin and Rattei, Thomas and Stadler, Peter F. and Töpfer, Armin Bioinformatics, 30. pp. 1793-1799 ISSN 1367-4803 (2014)

  • Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics.
    Müller, Stephan A. and Findeiß, Sven and Pernitzsch, Sandy R. and Wissenbach, Dirk K. and Stadler, Peter F. and Hofacker, Ivo L. and von Bergen, Martin and Kalkhof, Stefan J Proteomics, 86. pp. 27-42 ISSN 1874-3919 (2013)

  • 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)

  • Computational Design of RNAs with Complex Energy Landscapes
    Höner zu Siederdissen, Christian and Hammer, Stefan and Abfalter, Ingrid and Hofacker, Ivo L. and Flamm, Christoph and Stadler, Peter F. Biopolymers, 99. pp. 1124-1136 ISSN 0006-3525 (2013)

  • Mapping the RNA-Seq trash bin: unusual transcripts in prokaryotic transcriptome sequencing data.
    Doose, Gero and Alexis, Maria and Kirsch, Rebecca and Findeiß, Sven and Langenberger, David and Machné, Rainer and Mörl, Mario and Hoffmann, Steve and Stadler, Peter F. RNA biology, 10 (7). pp. 1204-10 ISSN 1547-6286 (2013)

  • The RNAsnp Web Server: Predicting SNP effects on local RNA secondary structure
    Sabarinathan, Radhakrishnan and Tafer, Hakim and Seemann, Stefan and Hofacker, Ivo L. and Stadler, Peter F. and Gorodkin, Jan Nucleic Acids Res., 41. W475-W479 ISSN 0305-1048 (2013)

  • RNAsnp: Efficient detection of local RNA secondary structure changes induced by SNPs
    Sabarinathan, Radhakrishnan and Tafer, Hakim and Seemann, Stefan E. and Hofacker, Ivo L. and Stadler, Peter F. and Gorodkin, Jan Human Mutation, 34. 546-556 ISSN 1059-7794 (2013)

  • De novo design of a synthetic riboswitch that regulates transcription termination.
    Wachsmuth, Manja and Findeiß, Sven and Weissheimer, Nadine and Stadler, Peter F. and Mörl, Mario Nucleic Acids Research, upcom (upcom). Oxford University Press (2012)

  • LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs
    Will, Sebastian and Joshi, Tejal and Hofacker, Ivo L. and Stadler, Peter F. and Backofen, Rolf RNA, 18 (5). pp. 900-914 ISSN 1355-8382 (2012)

  • RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction
    Washietl, Stefan and Hofacker, Ivo L. and Stadler, Peter F. and Kellis, Manolis Nucleic Acids Research, 40 (10). pp. 4261-4272 ISSN 0305-1048 (2012)

  • Symmetric Circular Matchings and RNA Folding
    Hofacker, Ivo L. and Reidys, Christian M. and Stadler, Peter F. Discrete Mathematics, 312 (1). 100-112 Elsevier (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)

  • Fast Accessibility-Based Prediction of RNA-RNA Interactions
    Tafer, Hakim and Ammann, Fabian and Eggenhoffer, Florian and Stadler, Peter F. and Hofacker, Ivo L. Bioinformatics, 27 (14). pp. 1924-1940 Oxford University Press (2011)

  • A Folding Algorithm for Extended RNA Secondary Structures
    Höner zu Siederdissen, Christian and Berhart, Stephan H. and Stadler, Peter F. and Hofacker, Ivo L. Bioinformatics, 27 ( ). i129-i136 Oxford University Press (2011)

  • RNAcode: robust prediction of protein coding regions in comparative genomics data
    Washietl, Stefan and Findeiß, Sven and Müller, Stephan and Kalkhof, Stefan and Bergen, Martin von and Hofacker, Ivo L. and Stadler, Peter F. and Goldman, Nick RNA , 17 (4). pp. 578-594 Cold Spring Harbor Laboratory Press (2011)

  • RNApredator: Fast accessibility-Based Prediction of sRNA targets
    Eggenhofer, Florian and Tafer, Hakim and Stadler, Peter F. and Hofacker, Ivo L. Nucleic Acids Research, 39 (S2). W149-W154 Oxford University Press (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)

  • Bi-Alignments as Models of Incongruent Evolution of RNA Sequence and Structure
    Waldl, Maria and Will, Sebastian and Wolfinger, Michael T. and Hofacker, Ivo L. and Stadler, Peter F. In: CIBB 2019: 16th International Conference on Computational Intelligence methods for Bioinformatics and Biostatistics , 4-6 September 2019 , Bergamo. Italy (2019)

  • How to Multiply Dynamic Programming Algorithms
    Höner zu Siederdissen, Christian and Hofacker, Ivo L. and Stadler, Peter F. In: Brazilian Symposium on Bioinformatics 2013 , 3-6 Nov 2013 , Recife, Brazil (2013)

  • The Trouble with Long-Range Base Pairs in RNA Folding
    Amman, Fabian and Bernhart, Stephan H. and Doose, Gero and Hofacker, Ivo L. and Qin, Jing and Stadler, Peter F. and Will, Sebastian In: Brazilian Symposium on Bioinformatics 2013 , 3-6 Nov 2013 , Recife, Brazil (2013)

    • Book

  • Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure
    Waldl, Maria and Will, Sebastian and Wolfinger, Michael T. and Hofacker, Ivo L. and Stadler, Peter F. Lecture Notes in Computer Science, 12313 Springer, Cham, pp. 159-170 ISBN 978-3-030-63061-4 (2020)

    • Book Section/Chapter

  • Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure
    Waldl, Maria and Will, Sebastian and Wolfinger, Michael T. and Hofacker, Ivo L. and Stadler, Peter F. In: Computational Intelligence Methods for Bioinformatics and Biostatistics. Lecture Notes in Computer Science, 12313 Springer, pp. 159-170 (2020)

  • Comparative RNA Genomics
    Backofen, Rolf and Gorodkin, Jan and Hofacker, Ivo L. and Stadler, Peter F. In: Comparative Genomics. Methods in Molecular Biology, 1704 Humana Press, pp. 363-400 ISBN 978-1-4939-7461-0 (2018)

  • Design of transcription regulating riboswitches
    Findeiß, Sven and Wachsmuth, Manja and Mörl, Mario and Stadler, Peter F. In: Riboswitches as Targets and Tools. Methods in Enzymology, pp. 1-22 (2015)

  • 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 Thu Apr 18 17:32:01 2024 CEST.
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