| Year |
Citation |
Score |
| 2023 |
Klapproth C, Zötzsche S, Kühnl F, Fallmann J, Stadler PF, Findeiß S. Tailored machine learning models for functional RNA detection in genome-wide screens. Nar Genomics and Bioinformatics. 5: lqad072. PMID 37608800 DOI: 10.1093/nargab/lqad072 |
0.511 |
|
| 2022 |
Ender A, Stadler PF, Mörl M, Findeiß S. RNA Design Principles for Riboswitches that Regulate RNase P-Mediated tRNA Processing. Methods in Molecular Biology (Clifton, N.J.). 2518: 179-202. PMID 35666446 DOI: 10.1007/978-1-0716-2421-0_11 |
0.586 |
|
| 2022 |
Ender A, Grafl N, Kolberg T, Findeiss S, Stadler PF, Mörl M. Synthetic Riboswitches for the Analysis of tRNA Processing by eukaryotic RNase P Enzymes. Rna (New York, N.Y.). PMID 35022261 DOI: 10.1261/rna.078814.121 |
0.387 |
|
| 2021 |
Klapproth C, Sen R, Stadler PF, Findeiß S, Fallmann J. Common Features in lncRNA Annotation and Classification: A Survey. Non-Coding Rna. 7. PMID 34940758 DOI: 10.3390/ncrna7040077 |
0.591 |
|
| 2021 |
Ender A, Etzel M, Hammer S, Findeiß S, Stadler P, Mörl M. Ligand-dependent tRNA processing by a rationally designed RNase P riboswitch. Nucleic Acids Research. PMID 33469651 DOI: 10.1093/nar/gkaa1282 |
0.527 |
|
| 2020 |
Günzel C, Kühnl F, Arnold K, Findeiß S, Weinberg CE, Stadler PF, Mörl M. Beyond Plug and Pray: Context Sensitivity and Design of Artificial Neomycin Riboswitches. Rna Biology. PMID 32882151 DOI: 10.1080/15476286.2020.1816336 |
0.636 |
|
| 2019 |
Hammer S, Günzel C, Mörl M, Findeiß S. Evolving methods for rational de novo design of functional RNA molecules. Methods (San Diego, Calif.). PMID 31059832 DOI: 10.1016/J.Ymeth.2019.04.022 |
0.427 |
|
| 2018 |
Findeiß S, Hammer S, Wolfinger MT, Kühnl F, Flamm C, Hofacker IL. In silico design of ligand triggered RNA switches. Methods (San Diego, Calif.). PMID 29660485 DOI: 10.1016/J.Ymeth.2018.04.003 |
0.703 |
|
| 2018 |
Senoussi A, Lee Tin Wah J, Shimizu Y, Robert J, Jaramillo A, Findeiss S, Axmann IM, Estevez-Torres A. Quantitative characterization of translational riboregulators using an in vitro transcription-translation system. Acs Synthetic Biology. PMID 29617125 DOI: 10.1021/acssynbio.7b00387 |
0.39 |
|
| 2017 |
Findeiß S, Etzel M, Will S, Mörl M, Stadler PF. Design of Artificial Riboswitches as Biosensors. Sensors (Basel, Switzerland). 17. PMID 28867802 DOI: 10.3390/S17091990 |
0.609 |
|
| 2017 |
Hammer S, Tschiatschek B, Flamm C, Hofacker IL, Findeiß S. RNAblueprint: Flexible multiple target nucleic acid sequence design. Bioinformatics (Oxford, England). PMID 28449031 DOI: 10.1093/Bioinformatics/Btx263 |
0.371 |
|
| 2016 |
Domin G, Findeiß S, Wachsmuth M, Will S, Stadler PF, Mörl M. Applicability of a computational design approach for synthetic riboswitches. Nucleic Acids Research. PMID 27994029 DOI: 10.1093/Nar/Gkw1267 |
0.571 |
|
| 2015 |
Wachsmuth M, Domin G, Lorenz R, Serfling R, Findeiß S, Stadler PF, Mörl M. Design criteria for synthetic riboswitches acting on transcription. Rna Biology. 12: 221-31. PMID 25826571 DOI: 10.1080/15476286.2015.1017235 |
0.504 |
|
| 2015 |
Findeiß S, Wachsmuth M, Mörl M, Stadler PF. Design of transcription regulating riboswitches. Methods in Enzymology. 550: 1-22. PMID 25605378 DOI: 10.1016/Bs.Mie.2014.10.029 |
0.553 |
|
| 2014 |
Backofen R, Amman F, Costa F, Findeiß S, Richter AS, Stadler PF. Bioinformatics of prokaryotic RNAs. Rna Biology. 11: 470-83. PMID 24755880 DOI: 10.4161/Rna.28647 |
0.627 |
|
| 2014 |
Amman F, Wolfinger MT, Lorenz R, Hofacker IL, Stadler PF, Findeiß S. TSSAR: TSS annotation regime for dRNA-seq data. Bmc Bioinformatics. 15: 89. PMID 24674136 DOI: 10.1186/1471-2105-15-89 |
0.746 |
|
| 2014 |
Amman F, Wolfinger MT, Hofacker IL, Stadler PF, Findeiß S. TSSAR: transcription start site annotation regime for dRNA-seq data F1000research. 5. DOI: 10.7490/F1000Research.1097124.1 |
0.7 |
|
| 2013 |
Doose G, Alexis M, Kirsch R, Findeiß S, Langenberger D, Machné R, Mörl M, Hoffmann S, Stadler PF. Mapping the RNA-Seq trash bin: unusual transcripts in prokaryotic transcriptome sequencing data. Rna Biology. 10: 1204-10. PMID 23702463 DOI: 10.4161/Rna.24972 |
0.58 |
|
| 2013 |
Müller SA, Findeiß S, Pernitzsch SR, Wissenbach 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. Journal of Proteomics. 86: 27-42. PMID 23665149 DOI: 10.1016/J.Jprot.2013.04.036 |
0.468 |
|
| 2013 |
Wachsmuth M, Findeiß S, Weissheimer N, Stadler PF, Mörl M. De novo design of a synthetic riboswitch that regulates transcription termination. Nucleic Acids Research. 41: 2541-51. PMID 23275562 DOI: 10.1093/Nar/Gks1330 |
0.582 |
|
| 2012 |
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 Research. 40: 2020-31. PMID 22080557 DOI: 10.1093/Nar/Gkr904 |
0.664 |
|
| 2011 |
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. 93: 2019-23. PMID 21835221 DOI: 10.1016/J.Biochi.2011.07.023 |
0.756 |
|
| 2011 |
Lechner M, Findeiss S, Steiner L, Marz M, Stadler PF, Prohaska SJ. Proteinortho: detection of (co-)orthologs in large-scale analysis. Bmc Bioinformatics. 12: 124. PMID 21526987 DOI: 10.1186/1471-2105-12-124 |
0.725 |
|
| 2011 |
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 (New York, N.Y.). 17: 578-94. PMID 21357752 DOI: 10.1261/Rna.2536111 |
0.612 |
|
| 2011 |
Findeiss S, Langenberger D, Stadler PF, Hoffmann S. Traces of post-transcriptional RNA modifications in deep sequencing data. Biological Chemistry. 392: 305-13. PMID 21345160 DOI: 10.1515/Bc.2011.043 |
0.682 |
|
| 2010 |
Müller SA, Kohajda T, Findeiss S, Stadler PF, Washietl S, Kellis M, von Bergen M, Kalkhof S. Optimization of parameters for coverage of low molecular weight proteins. Analytical and Bioanalytical Chemistry. 398: 2867-81. PMID 20803007 DOI: 10.1007/S00216-010-4093-X |
0.415 |
|
| 2010 |
Schilling D, Findeiss S, Richter AS, Taylor JA, Gerischer U. The small RNA Aar in Acinetobacter baylyi: a putative regulator of amino acid metabolism. Archives of Microbiology. 192: 691-702. PMID 20559624 DOI: 10.1007/S00203-010-0592-6 |
0.356 |
|
| 2010 |
Findeiss S, Schmidtke C, Stadler PF, Bonas U. A novel family of plasmid-transferred anti-sense ncRNAs. Rna Biology. 7: 120-4. PMID 20220307 DOI: 10.4161/Rna.7.2.11184 |
0.586 |
|
| 2010 |
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. 464: 250-5. PMID 20164839 DOI: 10.1038/Nature08756 |
0.682 |
|
| 2010 |
Gruber AR, Findeiß S, Washietl S, Hofacker IL, Stadler PF. RNAz 2.0: improved noncoding RNA detection. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 69-79. PMID 19908359 |
0.56 |
|
| 2010 |
Donath A, Findeiß S, Hertel J, Marz M, Otto W, Schulz C, Stadler PF, Wirth S. Noncoding RNA Evolutionary Genomics and Systems Biology. 251-293. DOI: 10.1002/9780470570418.ch14 |
0.673 |
|
| 2009 |
Hiller M, Findeiss S, Lein S, Marz M, Nickel C, Rose D, Schulz C, Backofen R, Prohaska SJ, Reuter G, Stadler PF. Conserved introns reveal novel transcripts in Drosophila melanogaster. Genome Research. 19: 1289-300. PMID 19458021 DOI: 10.1101/Gr.090050.108 |
0.78 |
|
| 2008 |
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 (Reading, England). 154: 3175-87. PMID 18832323 DOI: 10.1099/Mic.0.2008/019703-0 |
0.614 |
|
| 2008 |
Wobus M, Wandel E, Prohaska S, Findeiss S, Tschöp K, Aust G. Transcriptional regulation of the human CD97 promoter by Sp1/Sp3 in smooth muscle cells. Gene. 413: 67-75. PMID 18329191 DOI: 10.1016/J.Gene.2008.01.021 |
0.576 |
|
| 2007 |
Rose D, Hackermüller J, Washietl S, Reiche K, Hertel J, Findeiss S, Stadler PF, Prohaska SJ. Computational RNomics of drosophilids. Bmc Genomics. 8: 406. PMID 17996037 DOI: 10.1186/1471-2164-8-406 |
0.778 |
|
| 2007 |
Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/Nature06341 |
0.694 |
|
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