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Items: 1 to 20 of 122

1.

RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates.

Thiel BC, Ochsenreiter R, Gadekar VP, Tanzer A, Hofacker IL.

Genes (Basel). 2018 Aug 1;9(8). pii: E392. doi: 10.3390/genes9080392.

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.

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.

5.

Comparative RNA Genomics.

Backofen R, Gorodkin J, Hofacker IL, Stadler PF.

Methods Mol Biol. 2018;1704:363-400. doi: 10.1007/978-1-4939-7463-4_14.

PMID:
29277874
6.

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.

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.

RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets.

Alkan F, Wenzel A, Palasca O, Kerpedjiev P, Rudebeck AF, Stadler PF, Hofacker IL, Gorodkin J.

Nucleic Acids Res. 2017 May 5;45(8):e60. doi: 10.1093/nar/gkw1325.

9.

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.

10.

RNA folding with hard and soft constraints.

Lorenz R, Hofacker IL, Stadler PF.

Algorithms Mol Biol. 2016 Apr 23;11:8. doi: 10.1186/s13015-016-0070-z. eCollection 2016.

11.

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.

12.

Computational Design of a Circular RNA with Prionlike Behavior.

Badelt S, Flamm C, Hofacker IL.

Artif Life. 2016 Spring;22(2):172-84. doi: 10.1162/ARTL_a_00197. Epub 2016 Mar 2.

PMID:
26934089
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.

RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure.

Theis C, Zirbel CL, Zu Siederdissen CH, Anthon C, Hofacker IL, Nielsen H, Gorodkin J.

PLoS One. 2015 Oct 28;10(10):e0139900. doi: 10.1371/journal.pone.0139900. eCollection 2015.

15.

Pseudoknots in RNA folding landscapes.

Kucharík M, Hofacker IL, Stadler PF, Qin J.

Bioinformatics. 2016 Jan 15;32(2):187-94. doi: 10.1093/bioinformatics/btv572. Epub 2015 Oct 1.

16.

Product Grammars for Alignment and Folding.

Höner Zu Siederdissen C, Hofacker IL, Stadler PF.

IEEE/ACM Trans Comput Biol Bioinform. 2015 May-Jun;12(3):507-19. doi: 10.1109/TCBB.2014.2326155.

PMID:
26357262
17.

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.

18.

Optimizing RNA structures by sequence extensions using RNAcop.

Hecker N, Christensen-Dalsgaard M, Seemann SE, Havgaard JH, Stadler PF, Hofacker IL, Nielsen H, Gorodkin J.

Nucleic Acids Res. 2015 Sep 30;43(17):8135-45. doi: 10.1093/nar/gkv813. Epub 2015 Aug 17.

19.

Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams.

Kerpedjiev P, Hammer S, Hofacker IL.

Bioinformatics. 2015 Oct 15;31(20):3377-9. doi: 10.1093/bioinformatics/btv372. Epub 2015 Jun 22.

20.

Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA.

Lavender CA, Lorenz R, Zhang G, Tamayo R, Hofacker IL, Weeks KM.

PLoS Comput Biol. 2015 May 20;11(5):e1004126. doi: 10.1371/journal.pcbi.1004126. eCollection 2015 May.

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