RNA Biology

E-mail: ivo(at)tbi.univie.ac.at
Phone: 0043 1 4277 52738
Research Group: http://www.tbi.univie.ac.at/~ivo/
Institution: UniWien

Full member of the DoktoratsKolleg (DK) RNA Biology since 2010.
Full member of the Focus Regulatory RNA (SFB RNA-REG) since 2011.

PhD students within/associated to the DK RNA Biology:

Bernhard Thiel
Roman Ochsenreiter
Mariam Farman
Gregor Entzian
Maria Waldl

DK RNA Biology Alumni & their PhD theses:

Stefan Hammer: “Design of context-sensitive, multi-stable RNA molecules”
Stefan Badelt: “Control of RNA function by conformational design”
Florian Eggenhofer: “Conservation and interaction of RNA in regulatory networks”
Joerg Fallmann: “RNA-protein interactions in RNA decay”
Peter Kerpedjiev: “Coarse grained 3D RNA folding”

For complete list of group members please visit the website of the Theoretical Biochemistry (TBI) Group.

Research:

My scientific interests fit mostly under the computational biology umbrella. Much of my work focuses on RNA Bioinformatics, the most visible part perhaps being the Vienna RNA Package for prediction and comparison of RNA secondary structures, which my coworkers and I have developed for over 15 years.
For a description of the individual projects in our group see the TBI Research page, or browse though my list of publications. Our preprint server contains working papers and downloadable preprints for most papers for the really curious.

 

Publications: (since 2011)

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.

Conserved Secondary Structures in Viral mRNAs.
Kiening M, Ochsenreiter R, Hellinger HJ, Rattei T, Hofacker I, Frishman D.
Viruses. 2019 Apr 29;11(5).

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).

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.

RNA modifications in structure prediction – Status quo and future challenges.
Tanzer A, Hofacker IL, Lorenz R.
Methods. 2019 Mar 1;156:32-39.

MSF: Modulated Sub-graph Finder.
Farman MR, Hofacker IL, Amman F.
Version 3. F1000Res. 2018 Aug 29 [revised 2019 Jan 1];7:1346.

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).

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).

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.

Efficient computation of co-transcriptional RNA-ligand interaction dynamics.
Wolfinger MT, Flamm C, Hofacker IL.
Methods. 2018 Jul 1;143:70-76.

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.

Comparative RNA Genomics.
Backofen R, Gorodkin J, Hofacker IL, Stadler PF.
Methods Mol Biol. 2018;1704:363-400.

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.

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.

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.

RNAlien – Unsupervised RNA family model construction.
Eggenhofer F, Hofacker IL, Höner Zu Siederdissen C.
Nucleic Acids Res. 2016 Sep 30;44(17):8433-41.

Predicting RNA secondary structures from sequence and probing data.
Lorenz R, Wolfinger MT, Tanzer A, Hofacker IL.
Methods. 2016 Jul 1;103:86-98.

RNA folding with hard and soft constraints.
Lorenz R, Hofacker IL, Stadler PF.
Algorithms Mol Biol. 2016 Apr 23;11:8.

Computational Design of a Circular RNA with Prionlike Behavior.
Badelt S, Flamm C, Hofacker IL.
Artif Life. 2016 Spring;22(2):172-84.

Pseudoknots in RNA folding landscapes.
Kucharík M, Hofacker IL, Stadler PF, Qin J.
Bioinformatics. 2016 Jan 15;32(2):187-94.

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.

SHAPE directed RNA folding.
Lorenz R, Luntzer D, Hofacker IL, Stadler PF, Wolfinger MT.
Bioinformatics. 2016 Jan 1;32(1):145-7.

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.

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.

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.

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.

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.

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.

Thermodynamic and kinetic folding of riboswitches.
Badelt S, Hammer S, Flamm C, Hofacker IL.
Methods Enzymol. 2015;553:193-213.

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.

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.

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

Energy-directed RNA structure prediction.
Hofacker IL.
Methods Mol Biol. 2014;1097:71-84.

Concepts and introduction to RNA bioinformatics.
Gorodkin J, Hofacker IL, Ruzzo WL.
Methods Mol Biol. 2014;1097:1-31.

Predicting RNA structure: advances and limitations.
Hofacker IL, Lorenz R.
Methods Mol Biol. 2014;1086:1-19.

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.

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.

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.

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.

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

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.

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.

Folding RNA/DNA hybrid duplexes.
Lorenz R, Hofacker IL, Bernhart SH.
Bioinformatics. 2012 Oct 1;28(19):2530-1.

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

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.

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.

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.

From structure prediction to genomic screens for novel non-coding RNAs.
Gorodkin J, Hofacker IL.
PLoS Comput Biol. 2011 Aug;7(8):e1002100.

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.

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.

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.

Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering.
Hackl M, Jakobi T, Blom J, Doppmeier D, Brinkrolf K, Szczepanowski R, Bernhart SH, Höner Zu Siederdissen C, Bort JA, Wieser M, Kunert R, Jeffs S, Hofacker IL, Goesmann A, Pühler A, Borth N, Grillari J.
J Biotechnol. 2011 Apr 20;153(1-2):62-75.

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.
Washietl S, Findeiss S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N.
RNA. 2011 Apr;17(4):578-94.

RNA Accessibility in cubic time.
Bernhart SH, Mückstein U, Hofacker IL.
Algorithms Mol Biol. 2011 Mar 9;6(1):3.

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.