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Items: 15

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.

Automatic Curation of Large Comparative Animal MicroRNA Data Sets.

Yazbeck AM, Stadler PF, Tout K, Fallmann J.

Bioinformatics. 2019 Apr 16. pii: btz271. doi: 10.1093/bioinformatics/btz271. [Epub ahead of print]

PMID:
30993337
3.

Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis.

Kutsche LK, Gysi DM, Fallmann J, Lenk K, Petri R, Swiersy A, Klapper SD, Pircs K, Khattak S, Stadler PF, Jakobsson J, Nowick K, Busskamp V.

Cell Syst. 2018 Oct 24;7(4):438-452.e8. doi: 10.1016/j.cels.2018.08.011. Epub 2018 Oct 3.

4.

In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors.

Sutandy FXR, Ebersberger S, Huang L, Busch A, Bach M, Kang HS, Fallmann J, Maticzka D, Backofen R, Stadler PF, Zarnack K, Sattler M, Legewie S, König J.

Genome Res. 2018 May;28(5):699-713. doi: 10.1101/gr.229757.117. Epub 2018 Apr 11.

5.

Accurate mapping of tRNA reads.

Hoffmann A, Fallmann J, Vilardo E, Mörl M, Stadler PF, Amman F.

Bioinformatics. 2018 Jul 1;34(13):2339. doi: 10.1093/bioinformatics/bty118. No abstract available.

PMID:
29547898
6.

Accurate mapping of tRNA reads.

Hoffmann A, Fallmann J, Vilardo E, Mörl M, Stadler PF, Amman F.

Bioinformatics. 2018 Apr 1;34(7):1116-1124. doi: 10.1093/bioinformatics/btx756. Erratum in: Bioinformatics. 2018 Jul 1;34(13):2339.

PMID:
29228294
7.

Recent advances in RNA folding.

Fallmann J, Will S, Engelhardt J, Grüning B, Backofen R, Stadler PF.

J Biotechnol. 2017 Nov 10;261:97-104. doi: 10.1016/j.jbiotec.2017.07.007. Epub 2017 Jul 8. Review.

8.

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.

9.

RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation.

Backofen R, Engelhardt J, Erxleben A, Fallmann J, Grüning B, Ohler U, Rajewsky N, Stadler PF.

J Biotechnol. 2017 Nov 10;261:76-84. doi: 10.1016/j.jbiotec.2017.05.019. Epub 2017 May 26. Review.

10.

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.

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.

Tristetraprolin binding site atlas in the macrophage transcriptome reveals a switch for inflammation resolution.

Sedlyarov V, Fallmann J, Ebner F, Huemer J, Sneezum L, Ivin M, Kreiner K, Tanzer A, Vogl C, Hofacker I, Kovarik P.

Mol Syst Biol. 2016 May 13;12(5):868. doi: 10.15252/msb.20156628.

13.

AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements.

Fallmann J, Sedlyarov V, Tanzer A, Kovarik P, Hofacker IL.

Nucleic Acids Res. 2016 Jan 4;44(D1):D90-5. doi: 10.1093/nar/gkv1238. Epub 2015 Nov 23.

14.

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.

15.

AREsite: a database for the comprehensive investigation of AU-rich elements.

Gruber AR, Fallmann J, Kratochvill F, Kovarik P, Hofacker IL.

Nucleic Acids Res. 2011 Jan;39(Database issue):D66-9. doi: 10.1093/nar/gkq990. Epub 2010 Nov 11.

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