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Items: 21

1.

TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes.

Waldl M, Thiel BC, Ochsenreiter R, Holzenleiter A, de Araujo Oliveira JV, Walter MEMT, Wolfinger MT, Stadler PF.

Genes (Basel). 2018 Jul 26;9(8). pii: E372. doi: 10.3390/genes9080372.

2.

Efficient computation of co-transcriptional RNA-ligand interaction dynamics.

Wolfinger MT, Flamm C, Hofacker IL.

Methods. 2018 Jul 1;143:70-76. doi: 10.1016/j.ymeth.2018.04.036. Epub 2018 May 4.

PMID:
29730250
3.

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
4.

Interplay between the catabolite repression control protein Crc, Hfq and RNA in Hfq-dependent translational regulation in Pseudomonas aeruginosa.

Sonnleitner E, Wulf A, Campagne S, Pei XY, Wolfinger MT, Forlani G, Prindl K, Abdou L, Resch A, Allain FH, Luisi BF, Urlaub H, Bläsi U.

Nucleic Acids Res. 2018 Feb 16;46(3):1470-1485. doi: 10.1093/nar/gkx1245.

5.

The Anaerobically Induced sRNA PaiI Affects Denitrification in Pseudomonas aeruginosa PA14.

Tata M, Amman F, Pawar V, Wolfinger MT, Weiss S, Häussler S, Bläsi U.

Front Microbiol. 2017 Nov 23;8:2312. doi: 10.3389/fmicb.2017.02312. eCollection 2017.

6.

The SmAP1/2 proteins of the crenarchaeon Sulfolobus solfataricus interact with the exosome and stimulate A-rich tailing of transcripts.

Märtens B, Hou L, Amman F, Wolfinger MT, Evguenieva-Hackenberg E, Bläsi U.

Nucleic Acids Res. 2017 Jul 27;45(13):7938-7949. doi: 10.1093/nar/gkx437.

7.

NMR Structural Profiling of Transcriptional Intermediates Reveals Riboswitch Regulation by Metastable RNA Conformations.

Helmling C, Wacker A, Wolfinger MT, Hofacker IL, Hengesbach M, Fürtig B, Schwalbe H.

J Am Chem Soc. 2017 Feb 22;139(7):2647-2656. doi: 10.1021/jacs.6b10429. Epub 2017 Feb 13.

PMID:
28134517
8.

Corrigendum: Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells.

Hölzer M, Krähling V, Amman F, Barth E, Bernhart SH, Carmelo VA, Collatz M, Doose G, Eggenhofer F, Ewald J, Fallmann J, Feldhahn LM, Fricke M, Gebauer J, Gruber AJ, Hufsky F, Indrischek H, Kanton S, Linde J, Mostajo N, Ochsenreiter R, Riege K, Rivarola-Duarte L, Sahyoun AH, Saunders SJ, Seemann SE, Tanzer A, Vogel B, Wehner S, Wolfinger MT, Backofen R, Gorodkin J, Grosse I, Hofacker I, Hoffmann S, Kaleta C, Stadler PF, Becker S, Marz M.

Sci Rep. 2017 Jan 11;7:39421. doi: 10.1038/srep39421. No abstract available.

9.

Cross-regulation by CrcZ RNA controls anoxic biofilm formation in Pseudomonas aeruginosa.

Pusic P, Tata M, Wolfinger MT, Sonnleitner E, Häussler S, Bläsi U.

Sci Rep. 2016 Dec 21;6:39621. doi: 10.1038/srep39621.

10.

Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity.

Tajaddod M, Tanzer A, Licht K, Wolfinger MT, Badelt S, Huber F, Pusch O, Schopoff S, Janisiw M, Hofacker I, Jantsch MF.

Genome Biol. 2016 Oct 25;17(1):220.

11.

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells.

Hölzer M, Krähling V, Amman F, Barth E, Bernhart SH, Carmelo VA, Collatz M, Doose G, Eggenhofer F, Ewald J, Fallmann J, Feldhahn LM, Fricke M, Gebauer J, Gruber AJ, Hufsky F, Indrischek H, Kanton S, Linde J, Mostajo N, Ochsenreiter R, Riege K, Rivarola-Duarte L, Sahyoun AH, Saunders SJ, Seemann SE, Tanzer A, Vogel B, Wehner S, Wolfinger MT, Backofen R, Gorodkin J, Grosse I, Hofacker I, Hoffmann S, Kaleta C, Stadler PF, Becker S, Marz M.

Sci Rep. 2016 Oct 7;6:34589. doi: 10.1038/srep34589. Erratum in: Sci Rep. 2017 Jan 11;7:39421.

12.

Predicting RNA secondary structures from sequence and probing data.

Lorenz R, Wolfinger MT, Tanzer A, Hofacker IL.

Methods. 2016 Jul 1;103:86-98. doi: 10.1016/j.ymeth.2016.04.004. Epub 2016 Apr 5. Review.

13.

The MazF-regulon: a toolbox for the post-transcriptional stress response in Escherichia coli.

Sauert M, Wolfinger MT, Vesper O, Müller C, Byrgazov K, Moll I.

Nucleic Acids Res. 2016 Aug 19;44(14):6660-75. doi: 10.1093/nar/gkw115. Epub 2016 Feb 22.

14.

RNASeq Based Transcriptional Profiling of Pseudomonas aeruginosa PA14 after Short- and Long-Term Anoxic Cultivation in Synthetic Cystic Fibrosis Sputum Medium.

Tata M, Wolfinger MT, Amman F, Roschanski N, Dötsch A, Sonnleitner E, Häussler S, Bläsi U.

PLoS One. 2016 Jan 28;11(1):e0147811. doi: 10.1371/journal.pone.0147811. eCollection 2016.

15.

SHAPE directed RNA folding.

Lorenz R, Luntzer D, Hofacker IL, Stadler PF, Wolfinger MT.

Bioinformatics. 2016 Jan 1;32(1):145-7. doi: 10.1093/bioinformatics/btv523. Epub 2015 Sep 9.

16.

ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines.

Wolfinger MT, Fallmann J, Eggenhofer F, Amman F.

Version 2. F1000Res. 2015 Feb 20 [revised 2015 Jan 1];4:50. doi: 10.12688/f1000research.6157.2. eCollection 2015.

17.

General and MicroRNA-Mediated mRNA Degradation Occurs on Ribosome Complexes in Drosophila Cells.

Antic S, Wolfinger MT, Skucha A, Hosiner S, Dorner S.

Mol Cell Biol. 2015 Jul;35(13):2309-20. doi: 10.1128/MCB.01346-14. Epub 2015 Apr 27.

18.

Memory-efficient RNA energy landscape exploration.

Mann M, Kucharík M, Flamm C, Wolfinger MT.

Bioinformatics. 2014 Sep 15;30(18):2584-91. doi: 10.1093/bioinformatics/btu337. Epub 2014 May 14.

19.

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.

20.

BarMap: RNA folding on dynamic energy landscapes.

Hofacker IL, Flamm C, Heine C, Wolfinger MT, Scheuermann G, Stadler PF.

RNA. 2010 Jul;16(7):1308-16. doi: 10.1261/rna.2093310. Epub 2010 May 26.

21.

Folding kinetics of large RNAs.

Geis M, Flamm C, Wolfinger MT, Tanzer A, Hofacker IL, Middendorf M, Mandl C, Stadler PF, Thurner C.

J Mol Biol. 2008 May 23;379(1):160-73. doi: 10.1016/j.jmb.2008.02.064. Epub 2008 Mar 6.

PMID:
18440024

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