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Items: 1 to 50 of 141

1.

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 Feb 13. pii: pp.00043.2019. doi: 10.1104/pp.19.00043. [Epub ahead of print]

2.

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

Tanzer A, Hofacker IL, Lorenz R.

Methods. 2018 Oct 30. pii: S1046-2023(18)30195-6. doi: 10.1016/j.ymeth.2018.10.019. [Epub ahead of print] Review.

3.

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
4.

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.

5.

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
6.

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
7.

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.

8.

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
9.

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.

10.

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
11.

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.

12.

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.

13.

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.

14.

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.

15.

microRNA-122 target sites in the hepatitis C virus RNA NS5B coding region and 3' untranslated region: function in replication and influence of RNA secondary structure.

Gerresheim GK, Dünnes N, Nieder-Röhrmann A, Shalamova LA, Fricke M, Hofacker I, Höner Zu Siederdissen C, Marz M, Niepmann M.

Cell Mol Life Sci. 2017 Feb;74(4):747-760. doi: 10.1007/s00018-016-2377-9. Epub 2016 Sep 27.

PMID:
27677491
16.

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.

17.

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.

18.

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.

19.

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.

20.

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
21.

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.

22.

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.

23.

Practical Guidelines for Incorporating Knowledge-Based and Data-Driven Strategies into the Inference of Gene Regulatory Networks.

Hsiao YT, Lee WP, Yang W, Müller S, Flamm C, Hofacker I, Kügler P.

IEEE/ACM Trans Comput Biol Bioinform. 2016 Jan-Feb;13(1):64-75. doi: 10.1109/TCBB.2015.2465954. Epub 2015 Aug 20.

PMID:
26441429
24.

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.

25.

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
26.

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.

27.

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.

28.

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.

29.

Sequence-controlled RNA self-processing: computational design, biochemical analysis, and visualization by AFM.

Petkovic S, Badelt S, Block S, Flamm C, Delcea M, Hofacker I, Müller S.

RNA. 2015 Jul;21(7):1249-60. doi: 10.1261/rna.047670.114. Epub 2015 May 21.

30.

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.

31.

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.

32.

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
33.

Impact of Hfq on the Bacillus subtilis transcriptome.

Hämmerle H, Amman F, Večerek B, Stülke J, Hofacker I, Bläsi U.

PLoS One. 2014 Jun 16;9(6):e98661. doi: 10.1371/journal.pone.0098661. eCollection 2014.

34.

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.

35.

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.

36.

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
37.

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
38.

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
39.

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
40.

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
41.

Alterations of the transcriptome of Sulfolobus acidocaldarius by exoribonuclease aCPSF2.

Märtens B, Amman F, Manoharadas S, Zeichen L, Orell A, Albers SV, Hofacker I, Bläsi U.

PLoS One. 2013 Oct 7;8(10):e76569. doi: 10.1371/journal.pone.0076569. eCollection 2013.

42.

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.

43.

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
44.

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
45.

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.

46.

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.

47.

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.

48.

Modelling translation initiation under the influence of sRNA.

Amman F, Flamm C, Hofacker I.

Int J Mol Sci. 2012 Nov 30;13(12):16223-40. doi: 10.3390/ijms131216223.

49.

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
50.

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.

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