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Best matches for Findeiß S[au]:

Design of Artificial Riboswitches as Biosensors. Findeiß S et al. Sensors (Basel). (2017)

Applicability of a computational design approach for synthetic riboswitches. Domin G et al. Nucleic Acids Res. (2017)

Bioinformatics of prokaryotic RNAs. Backofen R et al. RNA Biol. (2014)

Search results

Items: 28

1.

Evolving methods for rational de novo design of functional RNA molecules.

Hammer S, Günzel C, Mörl M, Findeiß S.

Methods. 2019 May 4. pii: S1046-2023(18)30289-5. doi: 10.1016/j.ymeth.2019.04.022. [Epub ahead of print]

PMID:
31059832
2.

In silico design of ligand triggered RNA switches.

Findeiß S, Hammer S, Wolfinger MT, Kühnl F, Flamm C, Hofacker IL.

Methods. 2018 Jul 1;143:90-101. doi: 10.1016/j.ymeth.2018.04.003. Epub 2018 Apr 13.

PMID:
29660485
3.

Quantitative Characterization of Translational Riboregulators Using an in Vitro Transcription-Translation System.

Senoussi A, Lee Tin Wah J, Shimizu Y, Robert J, Jaramillo A, Findeiss S, Axmann IM, Estevez-Torres A.

ACS Synth Biol. 2018 May 18;7(5):1269-1278. doi: 10.1021/acssynbio.7b00387. Epub 2018 Apr 18.

PMID:
29617125
4.

Design of Artificial Riboswitches as Biosensors.

Findeiß S, Etzel M, Will S, Mörl M, Stadler PF.

Sensors (Basel). 2017 Aug 30;17(9). pii: E1990. doi: 10.3390/s17091990. Review.

5.

RNAblueprint: flexible multiple target nucleic acid sequence design.

Hammer S, Tschiatschek B, Flamm C, Hofacker IL, Findeiß S.

Bioinformatics. 2017 Sep 15;33(18):2850-2858. doi: 10.1093/bioinformatics/btx263.

6.

Applicability of a computational design approach for synthetic riboswitches.

Domin G, Findeiß S, Wachsmuth M, Will S, Stadler PF, Mörl M.

Nucleic Acids Res. 2017 Apr 20;45(7):4108-4119. doi: 10.1093/nar/gkw1267.

7.

Design criteria for synthetic riboswitches acting on transcription.

Wachsmuth M, Domin G, Lorenz R, Serfling R, Findeiß S, Stadler PF, Mörl M.

RNA Biol. 2015;12(2):221-31. doi: 10.1080/15476286.2015.1017235.

8.

Design of transcription regulating riboswitches.

Findeiß S, Wachsmuth M, Mörl M, Stadler PF.

Methods Enzymol. 2015;550:1-22. doi: 10.1016/bs.mie.2014.10.029. Epub 2014 Dec 26.

PMID:
25605378
9.

Bioinformatics of prokaryotic RNAs.

Backofen R, Amman F, Costa F, Findeiß S, Richter AS, Stadler PF.

RNA Biol. 2014;11(5):470-83. Epub 2014 Apr 2. Review.

10.

TSSAR: TSS annotation regime for dRNA-seq data.

Amman F, Wolfinger MT, Lorenz R, Hofacker IL, Stadler PF, Findeiß S.

BMC Bioinformatics. 2014 Mar 27;15:89. doi: 10.1186/1471-2105-15-89.

11.

Mapping the RNA-Seq trash bin: unusual transcripts in prokaryotic transcriptome sequencing data.

Doose G, Alexis M, Kirsch R, Findeiß S, Langenberger D, Machné R, Mörl M, Hoffmann S, Stadler PF.

RNA Biol. 2013 Jul;10(7):1204-10. doi: 10.4161/rna.24972. Epub 2013 May 13.

12.

Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics.

Müller SA, Findeiß S, Pernitzsch SR, Wissenbach DK, Stadler PF, Hofacker IL, von Bergen M, Kalkhof S.

J Proteomics. 2013 Jun 28;86:27-42. doi: 10.1016/j.jprot.2013.04.036. Epub 2013 May 9.

PMID:
23665149
13.

De novo design of a synthetic riboswitch that regulates transcription termination.

Wachsmuth M, Findeiß S, Weissheimer N, Stadler PF, Mörl M.

Nucleic Acids Res. 2013 Feb 1;41(4):2541-51. doi: 10.1093/nar/gks1330. Epub 2012 Dec 28.

14.

Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions.

Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J, Stadler PF, Bonas U.

Nucleic Acids Res. 2012 Mar;40(5):2020-31. doi: 10.1093/nar/gkr904. Epub 2011 Nov 12.

15.

Protein-coding structured RNAs: A computational survey of conserved RNA secondary structures overlapping coding regions in drosophilids.

Findeiss S, Engelhardt J, Prohaska SJ, Stadler PF.

Biochimie. 2011 Nov;93(11):2019-23. doi: 10.1016/j.biochi.2011.07.023. Epub 2011 Jul 31.

PMID:
21835221
16.

Proteinortho: detection of (co-)orthologs in large-scale analysis.

Lechner M, Findeiss S, Steiner L, Marz M, Stadler PF, Prohaska SJ.

BMC Bioinformatics. 2011 Apr 28;12:124. doi: 10.1186/1471-2105-12-124.

17.

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.

Washietl S, Findeiss S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N.

RNA. 2011 Apr;17(4):578-94. doi: 10.1261/rna.2536111. Epub 2011 Feb 28.

18.

Traces of post-transcriptional RNA modifications in deep sequencing data.

Findeiss S, Langenberger D, Stadler PF, Hoffmann S.

Biol Chem. 2011 Apr;392(4):305-13. doi: 10.1515/BC.2011.043. Epub 2011 Feb 24.

PMID:
21345160
19.

Optimization of parameters for coverage of low molecular weight proteins.

Müller SA, Kohajda T, Findeiss S, Stadler PF, Washietl S, Kellis M, von Bergen M, Kalkhof S.

Anal Bioanal Chem. 2010 Dec;398(7-8):2867-81. doi: 10.1007/s00216-010-4093-x. Epub 2010 Aug 28.

20.

The small RNA Aar in Acinetobacter baylyi: a putative regulator of amino acid metabolism.

Schilling D, Findeiss S, Richter AS, Taylor JA, Gerischer U.

Arch Microbiol. 2010 Sep;192(9):691-702. doi: 10.1007/s00203-010-0592-6. Epub 2010 Jun 18.

PMID:
20559624
21.

A novel family of plasmid-transferred anti-sense ncRNAs.

Findeiss S, Schmidtke C, Stadler PF, Bonas U.

RNA Biol. 2010 Mar-Apr;7(2):120-4. Epub 2010 Mar 8.

PMID:
20220307
22.

The primary transcriptome of the major human pathogen Helicobacter pylori.

Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J.

Nature. 2010 Mar 11;464(7286):250-5. doi: 10.1038/nature08756. Epub 2010 Feb 17.

PMID:
20164839
23.

RNAz 2.0: improved noncoding RNA detection.

Gruber AR, Findeiß S, Washietl S, Hofacker IL, Stadler PF.

Pac Symp Biocomput. 2010:69-79.

24.

Conserved introns reveal novel transcripts in Drosophila melanogaster.

Hiller M, Findeiss S, Lein S, Marz M, Nickel C, Rose D, Schulz C, Backofen R, Prohaska SJ, Reuter G, Stadler PF.

Genome Res. 2009 Jul;19(7):1289-300. doi: 10.1101/gr.090050.108. Epub 2009 May 20.

25.

Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools.

Sonnleitner E, Sorger-Domenigg T, Madej MJ, Findeiss S, Hackermüller J, Hüttenhofer A, Stadler PF, Bläsi U, Moll I.

Microbiology. 2008 Oct;154(Pt 10):3175-87. doi: 10.1099/mic.0.2008/019703-0.

PMID:
18832323
26.

Transcriptional regulation of the human CD97 promoter by Sp1/Sp3 in smooth muscle cells.

Wobus M, Wandel E, Prohaska S, Findeiss S, Tschöp K, Aust G.

Gene. 2008 Apr 30;413(1-2):67-75. doi: 10.1016/j.gene.2008.01.021. Epub 2008 Feb 9.

PMID:
18329191
27.

Computational RNomics of drosophilids.

Rose D, Hackermüller J, Washietl S, Reiche K, Hertel J, Findeiss S, Stadler PF, Prohaska SJ.

BMC Genomics. 2007 Nov 8;8:406.

28.

Evolution of genes and genomes on the Drosophila phylogeny.

Drosophila 12 Genomes Consortium, 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, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I.

Nature. 2007 Nov 8;450(7167):203-18.

PMID:
17994087

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