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Items: 11

1.

The RNA workbench 2.0: next generation RNA data analysis.

Fallmann J, Videm P, Bagnacani A, Batut B, Doyle MA, Klingstrom T, Eggenhofer F, Stadler PF, Backofen R, Grüning B.

Nucleic Acids Res. 2019 Jul 2;47(W1):W511-W515. doi: 10.1093/nar/gkz353.

2.

Freiburg RNA tools: a central online resource for RNA-focused research and teaching.

Raden M, Ali SM, Alkhnbashi OS, Busch A, Costa F, Davis JA, Eggenhofer F, Gelhausen R, Georg J, Heyne S, Hiller M, Kundu K, Kleinkauf R, Lott SC, Mohamed MM, Mattheis A, Miladi M, Richter AS, Will S, Wolff J, Wright PR, Backofen R.

Nucleic Acids Res. 2018 Jul 2;46(W1):W25-W29. doi: 10.1093/nar/gky329.

3.

CMV: visualization for RNA and protein family models and their comparisons.

Eggenhofer F, Hofacker IL, Backofen R, Höner Zu Siederdissen C.

Bioinformatics. 2018 Aug 1;34(15):2676-2678. doi: 10.1093/bioinformatics/bty158.

4.

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.

Grüning BA, Fallmann J, Yusuf D, Will S, Erxleben A, Eggenhofer F, Houwaart T, Batut B, Videm P, Bagnacani A, Wolfien M, Lott SC, Hoogstrate Y, Hess WR, Wolkenhauer O, Hoffmann S, Akalin A, Ohler U, Stadler PF, Backofen R.

Nucleic Acids Res. 2017 Jul 3;45(W1):W560-W566. doi: 10.1093/nar/gkx409.

5.

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.

6.

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.

7.

RNAlien - Unsupervised RNA family model construction.

Eggenhofer F, Hofacker IL, Höner Zu Siederdissen C.

Nucleic Acids Res. 2016 Sep 30;44(17):8433-41. doi: 10.1093/nar/gkw558. Epub 2016 Jun 21.

8.

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.

9.

CMCompare webserver: comparing RNA families via covariance models.

Eggenhofer F, Hofacker IL, Höner Zu Siederdissen C.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W499-503. doi: 10.1093/nar/gkt329. Epub 2013 May 2.

10.

RNApredator: fast accessibility-based prediction of sRNA targets.

Eggenhofer F, Tafer H, Stadler PF, Hofacker IL.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W149-54. doi: 10.1093/nar/gkr467. Epub 2011 Jun 14.

11.

Fast accessibility-based prediction of RNA-RNA interactions.

Tafer H, Amman F, Eggenhofer F, Stadler PF, Hofacker IL.

Bioinformatics. 2011 Jul 15;27(14):1934-40. doi: 10.1093/bioinformatics/btr281. Epub 2011 May 18.

PMID:
21593134

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