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
21 - 40 out of 181


Gelhausen, R., Will, S., Hofacker, I. L., Backofen, R., & Raden, M. (2019). Constraint maximal inter-molecular helix lengths within RNA-RNA interaction prediction improves bacterial sRNA target prediction. In E. De Maria, A. Fred, & H. Gamboa (Eds.), PROCEEDINGS OF THE 12TH INTERNATIONAL JOINT CONFERENCE ON BIOMEDICAL ENGINEERING SYSTEMS AND TECHNOLOGIES, VOL 3 (BIOINFORMATICS): Part of 12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 20192019 (pp. 131-140). SciTePress. https://doi.org/10.5220/0007689701310140


Dienstbier, A., Pouchnik, D., Wildung, M., Amman, F., Hofacker, I. L., Parkhill, J., Holubova, J., Sebo, P., & Vecerek, B. (2018). Comparative genomics of Czech vaccine strains of Bordetella pertussis. Pathogens and Disease, 76(7), [fty071]. https://doi.org/10.1093/femspd/fty071






Backofen, R., Gorodkin, J., Hofacker, I. L., & Stadler, P. F. (2018). Comparative RNA genomics. In Methods in Molecular Biology (pp. 363-400). Humana Press, Inc.. Methods in Molecular Biology Vol. 1704 https://doi.org/10.1007/978-1-4939-7463-4_14



Alkan, F., Wenzel, A., Palasca, O., Kerpedjiev, P., Rudebeck, A. F., Stadler, P. F., Hofacker, I. L., & Gorodkin, J. (2017). RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets. Nucleic Acids Research, 45(8), [e60]. https://doi.org/10.1093/nar/gkw1325




Hoelzer, M., Kraehling, V., Amman, F., Barth, E., Bernhart, S. H., Carmelo, V. A. O., Collatz, M., Doose, G., Eggenhofer, F., Ewald, J., Fallmann, J., Feldhahn, L. M., Fricke, M., Gebauer, J., Gruber, A. J., Hufsky, F., Indrischek, H., Kanton, S., Linde, J., ... Marz, M. (2016). Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells. Scientific Reports, 6, [34589]. https://doi.org/10.1038/srep34589



21 - 40 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