Univ.-Prof. Dipl.-Phys. Dr. Ivo Hofacker
Ivo Hofacker
Summer term 2024
270020 PR Bachelor Laboratory Course D - Theoretical Chemistry and Computational Biological Chemistry
500501 SE Doctoral Research Seminar - Data and Knowledge
Summer term 2023
270020 PR Bachelor Laboratory Course D - Theoretical Chemistry and Computational Biological Chemistry
500501 SE Doctoral Research Seminar - Data and Knowledge
101 - 120 out of 181

Flamm, C., Ullrich, A., Mann, M., Högerl, D., Rohrschneider, M., Scheuermann, G., Klemm, K., Hofacker, I., & Stadler, P. (2010). Evolution of metabolic networks: a computational frame-work. Journal of Systems Chemistry. http://www.jsystchem.com/content/1/1/4

Tanzer, A., Riester, M., Hertel, J., Bermudez-Santana, C., Gorodkin, J., Hofacker, I., & Stadler, P. (2010). Evolutionary genomics of microRNAs and their relatives. In G. Caetano-Anolles (Ed.), Evolutionary Genomics and Systems Biology (pp. 295-327). Wiley-Blackwell. http://onlinelibrary.wiley.com/book/10.1002/9780470570418

Mückstein, U., Leparc, G. G., Posekany, A., Hofacker, I., & Kreil, D. P. (2010). Hybridization thermodynamics of NimbleGen Microarrays. BMC Bioinformatics, 11(Art. 35). https://doi.org/10.1186/1471-2105-11-35



Gruber, A., Bernhart, S., & Hofacker, I. (2010). RNALfoldz: Efficient prediction of thermodynamically stable, local secondary structures. In D. Schomburg, & A. Grote (Eds.), German Conference on Bioinformatics 2010 (pp. 12-21). Gesellschaft f. Informatik.

Tafer, H., Kehr, S., Hertel, J., Hofacker, I., & Stadler, P. (2010). RNAsnoop: efficient target prediction for H/ACA snoRNAs. Bioinformatics, 26(5), 610-616.

Gruber, A., Findeiss, S., Washietl, S., Hofacker, I., & Stadler, P. (2010). RNAz 2.0: improved noncoding RNA detection. In Proceedings of the Pacific Symposion on Biocomputing (pp. 69-79). Unknown publisher. Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb10/abstracts/2010_p69.html



Hofacker, I., Kreil, D. P., Bayer, K., Sykacek, P., Tüchler, T., Striedner, G., & Leparc, G. G. (2009). Model-based probe set optimization for high-performance microarrays. Nucleic Acids Research, 37(3).


Lorenz, R., Hofacker, I., & Flamm, C. (2009). 2d projections of RNA folding landscapes. In I. Grosse, S. Neumann, S. Posch, F. Schreiber, & P. F. Stadler (Eds.), German Conference on Bioinformatics 2009 (pp. 11-20). Gesellschaft für Informatik e.V..

Gruber, A., Hofacker, I., Mosig, A., Hennig, W., Kilgus, C., & Stadler, P. F. (2008). Arthropod 7SK RNA. Molecular Biology and Evolution, 25(9), 1923-1930. https://doi.org/10.1093/molbev/msn140


Wolfinger, M., Tanzer, A., Hofacker, I., Mandl, C., Flamm, C., Thurner, C., Geis, M., Middendorf, M., & Stadler, P. F. (2008). Folding kinetics of large RNAs. Journal of Molecular Biology, 379, 160-173.

Hofacker, I., Bernhart, S., Gruber, A., Tafer, H., Stadler, P. F., Mosig, A., Obernosterer, G., Benecke, B-J., & Koper-Emde, D. (2008). Invertebrate 7SK snRNAs. Journal of Molecular Evolution, 66, 107-115.

Gruber, A., Hofacker, I., Bernhart, S., Stadler, P., & Will, S. (2008). RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics, 9(Art. 474).


101 - 120 out of 181

Computational Estimation of Energy Parameters

Thomas Spicher (Speaker), Ronny Lorenz (Contributor) & Ivo Hofacker (Contributor)

12 Feb 2023

Activity: Talks and presentationsTalk or oral contributionScience to Science


Modeling RNA-RNA interaction formation on direct paths

Maria Waldl (Speaker), Ivo Hofacker (Contributor) & Sebastian Will (Contributor)

12 Feb 2023

Activity: Talks and presentationsTalk or oral contributionScience to Science


The effect of modified nucleotides on secondary structure prediction in tRNA

Yuliia Varenyk (Speaker), Ivo Hofacker (Contributor), Ronny Lorenz (Contributor) & Thomas Spicher (Contributor)

12 Feb 2023

Activity: Talks and presentationsTalk or oral contributionScience to Science


Predicting the effect of modified nucleotides on RNA structure

Ivo Hofacker (Invited speaker)

26 Oct 2022

Activity: Talks and presentationsTalk or oral contributionScience to Science


Computational Estimation of Energy Parameters for modified Nucleotides

Thomas Spicher (Speaker), Ronny Lorenz (Contributor) & Ivo Hofacker (Contributor)

3 Oct 2022

Activity: Talks and presentationsTalk or oral contributionScience to Science


Incongruent Evolution of RNA Sequence and Structure

Maria Waldl (Speaker), Sebastian Will (Contributor), Michael Thomas Wolfinger (Contributor), Ivo Hofacker (Contributor) & Peter Stadler (Contributor)

3 Oct 2022

Activity: Talks and presentationsTalk or oral contributionScience to Science


Modified nucleotides in RNA secondary structure prediction

Yuliia Varenyk (Speaker), Ivo Hofacker (Contributor), Ronny Lorenz (Contributor) & Thomas Spicher (Contributor)

3 Oct 2022

Activity: Talks and presentationsTalk or oral contributionScience to Science


Experiments in Deep Learning for RNA Secondary Structure Prediction

Ivo Hofacker (Invited speaker)

18 Sep 2022

Activity: Talks and presentationsTalk or oral contributionScience to Science


Features of RNA-RNA interaction kinetics

Maria Waldl (Speaker), Sebastian Will (Contributor) & Ivo Hofacker (Contributor)

18 Sep 2022

Activity: Talks and presentationsTalk or oral contributionScience to Science


Simulations of cotranscriptional folding explain the impact of sequence mutations

Stefan Badelt (Speaker), Ronny Lorenz (Contributor) & Ivo Hofacker (Contributor)

18 Sep 2022

Activity: Talks and presentationsTalk or oral contributionScience to Science


Experiments in Deep Learning for RNA Secondary Structure Prediction

Ivo Hofacker (Keynote speaker)

6 Sep 2022

Activity: Talks and presentationsTalk or oral contributionScience to Science


An RNA kinetics ansatz derived from an efficient prediction of RNA pathways

Ivo Hofacker (Invited speaker)

7 Aug 2022

Activity: Talks and presentationsTalk or oral contributionScience to Science


Experiments in Deep Learning for RNA Secondary Structure Prediction

Ivo Hofacker (Invited speaker)

7 Aug 2022

Activity: Talks and presentationsTalk or oral contributionScience to Science


Incongruent Evolution of RNA Sequence and Structure

Maria Waldl (Speaker), Sebastian Will (Contributor), Ivo Hofacker (Contributor) & Peter Stadler (Contributor)

7 Aug 2022

Activity: Talks and presentationsTalk or oral contributionScience to Science


Modeling RNA-RNA interaction formation on direct paths

Maria Waldl (Speaker), Irene Katharina Beckmann-Schneider (Contributor), Sebastian Will (Contributor) & Ivo Hofacker (Contributor)

7 Aug 2022

Activity: Talks and presentationsTalk or oral contributionScience to Science


MODELING THE KINETICS OF RNA-RNA INTERACTION FORMATION

Maria Waldl (Speaker), Irene Katharina Beckmann-Schneider (Contributor), Sebastian Will (Contributor) & Ivo Hofacker (Contributor)

17 Nov 2021

Activity: Talks and presentationsTalk or oral contributionScience to Science


Prediction of co-transcriptional RNA folding for Modeling Riboswitches

Ivo Hofacker (Keynote speaker)

7 Oct 2019

Activity: Talks and presentationsTalk or oral contributionScience to Science


Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Structure

Maria Waldl (Speaker), Sebastian Will (Contributor), Michael Thomas Wolfinger (Contributor), Ivo Hofacker (Contributor) & Peter Stadler (Contributor)

30 Sep 2019

Activity: Talks and presentationsTalk or oral contributionScience to Science


Co-transcriptional RNA folding kinetics

Ivo Hofacker (Invited speaker)

9 Sep 2019

Activity: Talks and presentationsTalk or oral contributionScience to Science


Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Structure

Maria Waldl (Contributor), Sebastian Will (Contributor), Michael Thomas Wolfinger (Contributor), Ivo Hofacker (Speaker) & Peter Stadler (Contributor)

4 Sep 2019

Activity: Talks and presentationsTalk or oral contributionScience to Science


Human & Bordetella pertussis co-expression networks

Mariam Rukhama Farman (Speaker) & Ivo Hofacker (Contributor)

10 Feb 2019

Activity: Talks and presentationsTalk or oral contributionScience to Science


Computational Approaches to RNA Folding Kinetics

Ivo Hofacker (Invited speaker)

15 Jan 2019

Activity: Talks and presentationsTalk or oral contributionScience to Science


RNA secondary Structures

Ivo Hofacker (Invited speaker)

14 Jan 2019

Activity: Talks and presentationsTalk or oral contributionScience to Science


RNA-RNA Interaction Kinetics for Refining RNA Targeting Screens

Maria Waldl (Speaker), Sebastian Will (Contributor) & Ivo Hofacker (Contributor)

1 Oct 2018

Activity: Talks and presentationsTalk or oral contributionScience to Science


RNA-RNA Interaction Kinetics for Refining RNA Targeting Screens

Maria Waldl (Speaker), Sebastian Will (Contributor) & Ivo Hofacker (Contributor)

25 Sep 2018

Activity: Talks and presentationsTalk or oral contributionScience to Science


Co-transcriptional Folding Kinetics and Riboswitch Modeling

Ivo Hofacker (Invited speaker)

15 Jul 2018

Activity: Talks and presentationsTalk or oral contributionScience to Science


Identification and Classification of Pseudoknots and their Impact on RNA 3D structure prediction

Irene Katharina Beckmann-Schneider (Speaker), Bernhard Thiel (Contributor) & Ivo Hofacker (Contributor)

11 Feb 2018

Activity: Talks and presentationsTalk or oral contributionScience to Science


Predicting Pseudoknots in RNA 3D structures

Irene Katharina Beckmann-Schneider (Speaker) & Ivo Hofacker (Contributor)

2 Oct 2017

Activity: Talks and presentationsTalk or oral contributionScience to Science


RNA 2D folding Dynamics and 3D Structure Prediction

Ivo Hofacker (Invited speaker)

26 May 2016

Activity: Talks and presentationsTalk or oral contributionOther


Coarse Grain 3D RNA Structure Prediction

Ivo Hofacker (Invited speaker)

14 Apr 2016

Activity: Talks and presentationsTalk or oral contributionOther


Computational Biology with RNA Structures, Interactions, and Dynamics

Ivo Hofacker (Invited speaker)

9 Jan 2016

Activity: Talks and presentationsTalk or oral contributionOther


Beyond RNA secondary structure

Ivo Hofacker (Invited speaker)

28 Jun 2014

Activity: Talks and presentationsTalk or oral contributionOther


siRNA and Oligo Design

Ivo Hofacker (Invited speaker)

25 Jun 2014

Activity: Talks and presentationsTalk or oral contributionOther


RNA folding kinetics and energy landscapes

Ivo Hofacker (Invited speaker)

24 Jun 2014

Activity: Talks and presentationsTalk or oral contributionOther


Energy directed RNA folding

Ivo Hofacker (Invited speaker)

23 Jun 2014

Activity: Talks and presentationsTalk or oral contributionOther


In silico Annotation of noncoding RNAs and their Targets

Ivo Hofacker (Invited speaker)

11 Apr 2014

Activity: Talks and presentationsTalk or oral contributionOther


Beyond RNA secondary structure:G-quadruplexes and non-canonical pairs

Ivo Hofacker (Invited speaker)

26 Jun 2013

Activity: Talks and presentationsTalk or oral contributionOther


Predicting Targets and Effects of Bacterial small RNAs

Ivo Hofacker (Invited speaker)

4 Jun 2013

Activity: Talks and presentationsTalk or oral contributionOther


Predicting functional RNA structures

Ivo Hofacker (Speaker)

11 Oct 2012

Activity: Talks and presentationsTalk or oral contributionOther


Folding with Fancy Constraints -Secondary Structures from Probing Data

Ivo Hofacker (Speaker)

24 Jul 2012

Activity: Talks and presentationsTalk or oral contributionOther


RNA Structures, Interactions, and Folding Kinetics

Ivo Hofacker (Speaker)

4 Jul 2012

Activity: Talks and presentationsTalk or oral contributionOther


Folding Kinetics and Energy Landscapes for RNA Secondary Structures

Ivo Hofacker (Speaker)

21 Jun 2012

Activity: Talks and presentationsTalk or oral contributionOther


RNA in silico: Bioinformatik im postgenomischen Zeitalter

Ivo Hofacker (Invited speaker)

9 May 2012

Activity: Talks and presentationsTalk or oral contributionOther


RNA Folding Kinetics and Dynamic Landscapes

Ivo Hofacker (Speaker)

20 Jan 2012

Activity: Talks and presentationsTalk or oral contributionOther


Advances in RNA Bioinformatics. Prediction of RNA Structures, Interactions, and Folding Kinetics

Ivo Hofacker (Speaker)

19 Nov 2011

Activity: Talks and presentationsTalk or oral contributionOther


The art of RNA homology search

Ivo Hofacker (Speaker)

15 Nov 2011

Activity: Talks and presentationsTalk or oral contributionOther


Prediction of bacterial small RNA targets

Ivo Hofacker (Speaker)

16 Jul 2011

Activity: Talks and presentationsTalk or oral contributionOther


Micro RNA Discovery in Sequencing Data without a Genome

Ivo Hofacker (Speaker)

15 Jul 2011

Activity: Talks and presentationsTalk or oral contributionOther


Beyond secondary structures: Predicting non-canonical pairs

Ivo Hofacker (Speaker)

26 May 2011

Activity: Talks and presentationsTalk or oral contributionOther


In silico annotation of noncoding RNAs and their targets

Ivo Hofacker (Speaker)

13 May 2011

Activity: Talks and presentationsTalk or oral contributionOther


RNA Folding Dynamics -- trajectories and landscapes

Ivo Hofacker (Invited speaker)

30 Apr 2010

Activity: Talks and presentationsTalk or oral contributionOther


RNA Genefinding

Ivo Hofacker (Invited speaker)

28 Apr 2010

Activity: Talks and presentationsTalk or oral contributionOther


Energy Landscapes for RNA Folding: Time- dependent Landscapes and 2D Projections

Ivo Hofacker (Invited speaker)

5 Aug 2009

Activity: Talks and presentationsTalk or oral contributionOther


Bioinformatics for the Modern RNA World:From Gene Finding to Function

Ivo Hofacker (Invited speaker)

9 Jul 2009

Activity: Talks and presentationsTalk or oral contributionOther


Detection, annotation, and target search for noncoding RNAs

Ivo Hofacker (Invited speaker)

26 Jan 2009

Activity: Talks and presentationsTalk or oral contributionOther


ncRNA Annotation and Target Prediction

Ivo Hofacker (Invited speaker)

13 Jan 2009

Activity: Talks and presentationsTalk or oral contributionOther


RNA Bioinformatics: From structure prediction to RNA gene finding

Ivo Hofacker (Invited speaker)

12 Nov 2008

Activity: Talks and presentationsTalk or oral contributionOther


Introduction to non-coding RNA gene finding

Ivo Hofacker (Invited speaker)

19 Jul 2008

Activity: Talks and presentationsTalk or oral contributionOther


From noncoding RNA Search to Annotation

Ivo Hofacker (Invited speaker)

28 Apr 2008

Activity: Talks and presentationsTalk or oral contributionOther


Prediction of ncRNA Interaction Targets

Ivo Hofacker (Invited speaker)

28 Apr 2008

Activity: Talks and presentationsTalk or oral contributionOther


RNA Structure thermodynamics, basic folding

Ivo Hofacker (Invited speaker)

14 Apr 2008

Activity: Talks and presentationsTalk or oral contributionOther


Solving RNA bioinformatics problems using the Vienna RNA Package

Ivo Hofacker (Invited speaker)

14 Apr 2008

Activity: Talks and presentationsTalk or oral contributionOther


Stochastic Models, HMMs, SCFGs, and model training

Ivo Hofacker (Invited speaker)

14 Apr 2008

Activity: Talks and presentationsTalk or oral contributionOther


Computational Detection and Analysis of noncoding RNAs

Ivo Hofacker (Invited speaker)

4 Feb 2008

Activity: Talks and presentationsTalk or oral contributionOther


Prediction of RNA-RNA interaction

Ivo Hofacker (Invited speaker)

29 Oct 2007

Activity: Talks and presentationsTalk or oral contributionOther


Prediction of RNA-RNA interaction

Ivo Hofacker (Invited speaker)

20 Oct 2007

Activity: Talks and presentationsTalk or oral contributionOther


Computational Detection and Annotation of Non-Coding RNAs

Ivo Hofacker (Invited speaker)

30 Sep 2007

Activity: Talks and presentationsTalk or oral contributionOther


Basic Algorithms in RNA Bioinformatics

Ivo Hofacker (Invited speaker)

17 Sep 2007

Activity: Talks and presentationsTalk or oral contributionOther


Noncoding RNAs in Bacteria

Ivo Hofacker (Invited speaker)

17 Sep 2007

Activity: Talks and presentationsTalk or oral contributionOther


RNA Bioinformatics -- An Overview

Ivo Hofacker (Invited speaker)

17 Sep 2007

Activity: Talks and presentationsTalk or oral contributionOther


Prediction of RNA-RNA interaction

Ivo Hofacker (Invited speaker)

21 May 2007

Activity: Talks and presentationsTalk or oral contributionOther


RNAdeco: decorating RNA for a purpose

Jantsch, M. F., Ameres, S. & Hofacker, I.

1/03/2029/02/28

Project: Research funding


Vorhersage von RNA-RNA Interakt

Hofacker, I.

1/12/1630/11/20

Project: Research funding


Transcri. Analyse von Bordetell

Hofacker, I.

29/10/1528/10/18

Project: Research funding


RNA-Funktionskontrolle

Hofacker, I.

24/03/1123/03/14

Project: Research funding


nicht kodierende RNAs

Hofacker, I.

1/12/1031/01/19

Project: Research funding


RNA Biology

Leodolter-Barta, A., von Haeseler, A., Bläsi, U., Görke, B., Hofacker, I., Moll, I., Ayatollahi, Z. & Martins, A.

1/12/0630/06/21

Project: Research funding


Department of Theoretical Chemistry

Deputy Head

Währinger Straße 17
1090 Wien
Room: 306/307

T: +43-1-4277-52738

ivo.hofacker@univie.ac.at