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Molecule Design

3D RNA Structures





Findeiß S, Hammer S, Wolfinger MT, Flamm C and Hofacker IL, In silico design of ligand triggered RNA switches, Methods, 2018,

Senoussi A, Lee Tin Wah J, Shimizu Y, Robert J, Jaramillo A, Findeiß S, Axmann I and Estevez-Torres A, Quantitative characterization of translational riboregulators using an in vitro transcription-translation system, ACS Synth Bio, 2018, doi:10.1021/acssynbio.7b00387


Findeiß S, Etzel M, Will S, Mörl M, Stadler PF, Design of Artificial Riboswitches as Biosensors, Sensor, 2017, doi:10.3390/s17091990.

Hammer S, Tschiatschek B, Flamm C, Hofacker IL and Findeiß S, RNAblueprint: Flexible multiple target nucleic acid sequence design, Bioinformatics, 2017, doi:10.1093/bioinformatics/btx263.


Domin G, Findeiß S, Wachsmuth M, Will S, Stadler PF and Mörl M, Applicability of a computational design approach for synthetic riboswitches, Nucleic Acids Research, 2016, doi:10.1093/nar/gkw1267.


Wachsmuth M, Lorenz R, Serfling R, Findeiß S, Stadler PF and Mörl M, Engineering synthetic riboswitches acting on transcription, RNA Biology, 2015 Feb;12(2):221-31.

Findeiß S, Wachsmuth M, Mörl M and Stadler PF. Design of Transcription Regulating Riboswitches, Methods in Enzymology, 2015, 550:1-22.


Amman F, Wolfinger MT, Lorenz R, Hofacker IL, Stadler PF and Findeiß S. TSSAR: TSS Annotation Regime for dRNA-seq data, BMC Bioinformatics, 2014, 15:89.

Backofen R, Amman F, Costa F, Findeiß S, Richter AS and Stadler PF. Bioinformatics of Prokaryotic RNAs , RNA Biology, 2014 May 1;11(5):470-483.


Doose G, Alexis M, Kirsch R, Findeiß S, Langenberger D, Machne R , Mörl M, Hoffmann S and Stadler PF. Mapping the RNA-Seq trash bin: Unusual transcripts in prokaryotic transcriptome sequencing data, RNA Biol. 2013 May 13;10(7).

Müller SA, Findeiß S, Pernitzsch SR, Wissenbache DK, Stadler PF, Hofacker IL, von Bergen M, Kalkhof S. Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics, J Proteomics. 2013 Jun 28;86:27-42.

Wachsmuth M, Findeiß S, Weissheimer N, Stadler PF, Mörl M. De novo design of a synthetic riboswitch that regulates transcription termination. Nucleic Acids Res. 2013 Feb 1;41(4):2541-51.


Schmidtke C, Findeiß S , Sharma CM, Kuhfuß J, Hoffmann S, Vogel J, Stadler PF, Bonas U. Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions. Nucleic Acids Res. 2012 Mar;40(5):2020-31.


Findeiß S, Engelhardt J, Prohaska SJ, Stadler PF. Protein-coding structured RNAs: A computational survey of conserved RNA secondary structures overlapping coding regions in drosophilids. Biochimie. 2011 Nov;93(11):2019-23.

Washietl S, Findeiß S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N. RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. RNA. 2011 Apr;17(4):578-94.

Lechner M, Findeiß S, Steiner L, Marz M, Stadler PF, Prohaska SJ. Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinformatics. 2011 Apr;28;12:124.

Findeiß S, Langenberger D, Stadler PF and Hoffmann S. Traces of Post-Transcriptional RNA Modifications in Deep Sequencing Data. Biol. Chem., 2011 Apr; 392(4):305-13.


Müller SA, Kohajda T, Findeiß S, Stadler PF, Washietl S, Kellis M, von Bergen M and Kalkhof S. Optimization of Parameters for Coverage of Low Molecular Weight Proteins. Analytical and Bioanalytical Chemistry, 2010 Dec; 398(7-8):2867-81

Schilling D, Findeiß S, Richter AS, Taylor JA, Gerischer U. The small RNA Aar in Acinetobacter baylyi: a putative regulator of amino acid metabolism. Microbiol., 2010 Sep; 192(9):691-702.

Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiß S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature, 2010 Mar; 464(7286): 250-5.

Donath A, Findeiß S, Hertel J, Marz M, Otto W, Schulz C, Stadler PF, Wirth S. Noncoding RNA. In Evolutionary Genomics and Systems Biology. ed Caetano-AnollÚs G, Wiley-Blackwell, Hoboken, (2010); 251-293.

Findeiß S, Schubert C, Stadler PF, Bonas U. A novel family of plasmid-transferred anti-sense ncRNAs. RNA Biol, 2010 Mar 8;7(2).

Gruber AR, Findeiß S, Washietl S, Hofacker IL, Stadler PF. RNAZ 2.0: IMPROVED NONCODING RNA DETECTION. Pac Symp Biocomput, 2010 Jan; 15:69-79.


Sonnleitner E, Sorger-Domenigg T, Madej MJ, Findeiß S, Hackermüller J, Hüttenhofer A, Stadler PF, Bläsi U, Moll I. Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools. Microbiology, 2008 Oct; 154(10): 3175-3187.

Wobus M, Wandel E, Prohaska SJ, Findeiß, Tschöp K, Aust G. Transcriptional regulation of the human CD97 promoter by Sp1/Sp3 in smooth muscle cells. Gene, 2008 Apr; 413(1-2): 67-75.


Rose D, Hackermüller J, Washietl S, Reiche K, Hertel J, Findeiß S, Stadler PF, Prohaska SJ. Computational RNomics of drosophilids. BMC Genomics, 2007 Nov; 8:406.

Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature 2007, Nov; 450(7167) :203-18.


Hertel J, Lindemeyer M, Missal K, Fried C, Tanzer A, Flamm C, Hofacker IL, Stadler PF; Students of Bioinformatics Computer Labs 2004 and 2005. The expansion of the metazoan microRNA repertoire. BMC Genomics, 2006 Feb; 7:25.

Last modified: 2017-07-14 14:00:00 sven