RESEARCH INTERESTS

Molecule Design

3D RNA Structures

Proteomics

Transcriptomics

PUBLICATIONS

2013

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, Journal of Proteomics [accepted].

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.

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 Res. 2012 Mar;40(5):2020-31.

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. 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.

2010

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-Anollés 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.

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, 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.

2007

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.

2006

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.

2012

Findeiß S, Rational Transcription Regulator Design , 4th Bioinformatics Round Table, Vienna, Austria, 8 November 2012. Talk.

Findeiß S, Rational Transcription Regulator Design , Young Investigator Day, Vienna, Austria, 19 April 2012. Talk.

Findeiß S, Theo Controls Stop and Go, 27th TBI Winterseminar, Bled, Slovenia, 12 - 19 February, 2012. Talk.

2011

Findeiß S, How time consuming is (self) organization?, 9. Herbstseminar, Vysoka Lipa, Czech Republic, 29th September - 4th October, 2011. Talk

Findeiß S, Expanding the repertoire of bacterial (non-)coding RNAs, Defensio Talk, Leipzig, Germany, 7th March, 2011. Talk

2010

Findeiß S, Hoffmann S., Stadler PF, Towards automated Transcription Start Site annotation, SPP1258 Meeting, Kassel, Germany, 30th June - 2th July, 2010. Talk

Findeiß S, How to assess (non)coding potential?!, Mini workshop on Genome exploration, Copenhagen, Denmark, March 23, 2010. Talk.

Findeiß S, Transcript analysis using RNA-seq; What others call transcriptomics?!, 25th TBI Winterseminar, Bled, Slovenia, February 20, 2010. Talk.

Findeiß S, Transcriptomics in Prokaryotes; Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome, Transcriptomics Journal Club, Leipzig, Germany, January 29, 2010. Talk.

2009
Findeiß S, Schubert C, Stadler PF, Bonas U, Jumping Anti-Sense RNA found in Xanthomonas campestris pv. vesicatoria, ProkaGENOMICS 2009, Göttingen, Germany, October 4-7, 2009. Poster.

Gruber AR, Findeiß S, Washietl S, Hofacker IL, Stadler PF RNAz 2.0: improved noncoding RNA detection, German Conference on Bioinformatics, Halle, Germany, September 28-30, 2009. Poster.

Findeiß S, Schubert C, Stadler PF, Bonas U, Jumping Anti-Sense RNA found in Xanthomonas campestris pv. vesicatoria, ProRNA 2009, Berlin, Germany, June 03-06, 2009. Poster.

Findeiß S, YELLOW Sticks, STRUCTURED RNAs and BLACK Spots Small regulatory RNAs in Xanthomonas campestris pv. vesicatoria, BBZ Doktoranden-Kolloquium, Leipzig, Germany, April 1, 2009. Talk.

Findeiß S, Yellow Sticks Listen To Jazz; Anti Sense RNAs Small regulatory RNAs in Xanthomonas campestris pv. vesicatoria, 24th TBI Winterseminar, Bled, Slovenia, February 21, 2009. Talk.

2008
Findeiß S, Schubert C, Stadler PF, Bonas U, Small regulatory RNAs with a function in the virulence of Xanthomonas campestris pv. vesicatoria, Bioinformatics Herbstseminar, Studeny, Czech republic, November 2, 2008. Talk

Findeiß S, Small regulatory RNAs with a function in the virulence of Xanthomonas campestris pv. vesicatoria, Symposium on Gene Regulation in Prokaryotes, Jugendburg, Germany, October 9, 2008. Talk.

Findeiß S, Schubert C, Stadler PF, Bonas U, Small regulatory RNAs with a function in the virulence of Xanthomonas campestris pv. vesicatoria, 5th Meeting of the GBM study section RNA-Biochemistry, Kassel, Germany, September 18-21, 2008. Poster

Findeiß S, Schubert C, Stadler PF, Bonas U, Small regulatory RNAs with a function in the virulence of Xanthomonas campestris pv. vesicatoria, SPP1258 Meeting, Kassel, Germany, September 16-18, 2008. Poster

2007
Findeiß S, Hernandez Rosales M, Stadler PF, BioInformatic approaches to detect and verify ncRNAs, Kickoff meeting SPP1258, Bochum, Germany, September 5-7, 2007, Poster.

Findeiß S, Trip into the Desert Drosophila melanogaster & Co, 22th TBI Winterseminar, Bled, Slovenia, February 19, 2007, Talk.

2006
Findeiß S, Barrier Trees, The (Bio)Informatics View, Seminar 'parallel algorithms and complex systems', Leipzig, Germany, June 23, 2006. Talk.

Findeiß S, Prohaska SJ, The CD97 Promoter - conserved elements. 3rd EGF-TM7 Workshop, Amsterdam, Netherlands. March 23, 2006. Talk.

2005
Prohaska SJ, Findeiß S, Jöris J, The jungle of motif detection Searching for binding sites in CD97 promotor, Bioinformatics Herbstseminar, Chribska, Czech republic, October 2005. Talk.