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Items: 1 to 50 of 128

1.

3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements.

Thiel BC, Beckmann IK, Kerpedjiev P, Hofacker IL.

Version 2. F1000Res. 2019 Mar 14 [revised 2019 Jan 1];8. pii: ISCB Comm J-287. doi: 10.12688/f1000research.18458.2. eCollection 2019.

2.

MSF: Modulated Sub-graph Finder.

Farman MR, Hofacker IL, Amman F.

Version 3. F1000Res. 2018 Aug 29 [revised 2019 Jan 1];7:1346. doi: 10.12688/f1000research.16005.3. eCollection 2018.

3.

Functional RNA Structures in the 3'UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses.

Ochsenreiter R, Hofacker IL, Wolfinger MT.

Viruses. 2019 Mar 24;11(3). pii: E298. doi: 10.3390/v11030298.

4.

Control of Cognate Sense mRNA Translation by cis-Natural Antisense RNAs.

Deforges J, Reis RS, Jacquet P, Sheppard S, Gadekar VP, Hart-Smith G, Tanzer A, Hofacker IL, Iseli C, Xenarios I, Poirier Y.

Plant Physiol. 2019 May;180(1):305-322. doi: 10.1104/pp.19.00043. Epub 2019 Feb 13.

5.

RNA modifications in structure prediction - Status quo and future challenges.

Tanzer A, Hofacker IL, Lorenz R.

Methods. 2019 Mar 1;156:32-39. doi: 10.1016/j.ymeth.2018.10.019. Epub 2018 Oct 30. Review.

6.

Comparative genomics of Czech vaccine strains of Bordetella pertussis.

Dienstbier A, Pouchnik D, Wildung M, Amman F, Hofacker IL, Parkhill J, Holubova J, Sebo P, Vecerek B.

Pathog Dis. 2018 Oct 1;76(7). doi: 10.1093/femspd/fty071.

PMID:
30184175
7.

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.

8.

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
9.

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
10.

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.

11.

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
12.

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.

13.

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
14.

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.

15.

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.

16.

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.

17.

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.

18.

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
19.

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.

20.

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.

21.

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.

22.

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
23.

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.

24.

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.

25.

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.

26.

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.

27.

Predicting RNA 3D structure using a coarse-grain helix-centered model.

Kerpedjiev P, Höner Zu Siederdissen C, Hofacker IL.

RNA. 2015 Jun;21(6):1110-21. doi: 10.1261/rna.047522.114. Epub 2015 Apr 22.

28.

Thermodynamic and kinetic folding of riboswitches.

Badelt S, Hammer S, Flamm C, Hofacker IL.

Methods Enzymol. 2015;553:193-213. doi: 10.1016/bs.mie.2014.10.060. Epub 2015 Feb 12.

PMID:
25726466
29.

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.

30.

Basin Hopping Graph: a computational framework to characterize RNA folding landscapes.

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

Bioinformatics. 2014 Jul 15;30(14):2009-17. doi: 10.1093/bioinformatics/btu156. Epub 2014 Mar 19.

31.

Energy-directed RNA structure prediction.

Hofacker IL.

Methods Mol Biol. 2014;1097:71-84. doi: 10.1007/978-1-62703-709-9_4. Review.

PMID:
24639155
32.

Concepts and introduction to RNA bioinformatics.

Gorodkin J, Hofacker IL, Ruzzo WL.

Methods Mol Biol. 2014;1097:1-31. doi: 10.1007/978-1-62703-709-9_1. Review.

PMID:
24639152
33.

Challenges in RNA virus bioinformatics.

Marz M, Beerenwinkel N, Drosten C, Fricke M, Frishman D, Hofacker IL, Hoffmann D, Middendorf M, Rattei T, Stadler PF, Töpfer A.

Bioinformatics. 2014 Jul 1;30(13):1793-9. doi: 10.1093/bioinformatics/btu105. Epub 2014 Mar 3. Review.

PMID:
24590443
34.

2D meets 4G: G-quadruplexes in RNA secondary structure prediction.

Lorenz R, Bernhart SH, Qin J, Höner zu Siederdissen C, Tanzer A, Amman F, Hofacker IL, Stadler PF.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Jul-Aug;10(4):832-44. doi: 10.1109/TCBB.2013.7.

PMID:
24334379
35.

Predicting RNA structure: advances and limitations.

Hofacker IL, Lorenz R.

Methods Mol Biol. 2014;1086:1-19. doi: 10.1007/978-1-62703-667-2_1.

PMID:
24136595
36.

Automated identification of RNA 3D modules with discriminative power in RNA structural alignments.

Theis C, Höner Zu Siederdissen C, Hofacker IL, Gorodkin J.

Nucleic Acids Res. 2013 Dec;41(22):9999-10009. doi: 10.1093/nar/gkt795. Epub 2013 Sep 4.

37.

Computational design of RNAs with complex energy landscapes.

Höner zu Siederdissen C, Hammer S, Abfalter I, Hofacker IL, Flamm C, Stadler PF.

Biopolymers. 2013 Dec;99(12):1124-36. doi: 10.1002/bip.22337.

PMID:
23818234
38.

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
39.

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.

40.

The RNAsnp web server: predicting SNP effects on local RNA secondary structure.

Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W475-9. doi: 10.1093/nar/gkt291. Epub 2013 Apr 29.

41.

RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs.

Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J.

Hum Mutat. 2013 Apr;34(4):546-56. doi: 10.1002/humu.22273. Erratum in: Hum Mutat. 2013 Jun;34(6):925.

42.

Folding RNA/DNA hybrid duplexes.

Lorenz R, Hofacker IL, Bernhart SH.

Bioinformatics. 2012 Oct 1;28(19):2530-1. Epub 2012 Jul 24.

PMID:
22829626
43.

LocARNA-P: accurate boundary prediction and improved detection of structural RNAs.

Will S, Joshi T, Hofacker IL, Stadler PF, Backofen R.

RNA. 2012 May;18(5):900-14. doi: 10.1261/rna.029041.111. Epub 2012 Mar 26.

44.

RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction.

Washietl S, Hofacker IL, Stadler PF, Kellis M.

Nucleic Acids Res. 2012 May;40(10):4261-72. doi: 10.1093/nar/gks009. Epub 2012 Jan 28.

45.

ViennaRNA Package 2.0.

Lorenz R, Bernhart SH, Höner Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL.

Algorithms Mol Biol. 2011 Nov 24;6:26. doi: 10.1186/1748-7188-6-26.

46.

Animal snoRNAs and scaRNAs with exceptional structures.

Marz M, Gruber AR, Höner Zu Siederdissen C, Amman F, Badelt S, Bartschat S, Bernhart SH, Beyer W, Kehr S, Lorenz R, Tanzer A, Yusuf D, Tafer H, Hofacker IL, Stadler PF.

RNA Biol. 2011 Nov-Dec;8(6):938-46. doi: 10.4161/rna.8.6.16603. Epub 2011 Nov 1.

47.

From structure prediction to genomic screens for novel non-coding RNAs.

Gorodkin J, Hofacker IL.

PLoS Comput Biol. 2011 Aug;7(8):e1002100. doi: 10.1371/journal.pcbi.1002100. Epub 2011 Aug 4. Review.

48.

A folding algorithm for extended RNA secondary structures.

Höner zu Siederdissen C, Bernhart SH, Stadler PF, Hofacker IL.

Bioinformatics. 2011 Jul 1;27(13):i129-36. doi: 10.1093/bioinformatics/btr220.

49.

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.

50.

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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