Univ.-Prof. Dipl.-Phys. Dr. Ivo Hofacker
Research Group Bioinformatics and Computational Biology
Währinger Straße 29
Head
1090 Wien
Room : 5.30
Courses
Winter term 2026
-
270020 PR Bachelor Laboratory Course D - Theoretical Chemistry and Computational Biological Chemistry
-
270021 SE Writing of the Bachelor´s Thesis
-
301590 VU Fundamental Bioinformatics
-
311599 UE Laboratory Course: Bioinformatics
-
500501 SE Doctoral Research Seminar - Data and Knowledge
Summer term 2026
-
270020 PR Bachelor Laboratory Course D - Theoretical Chemistry and Computational Biological Chemistry
-
270021 SE Writing of the Bachelor´s Thesis
-
270054 VO Bioinformatics of Nucleic Acids
-
301578 VO Special Topics in Bioinformatics
-
500501 SE Doctoral Research Seminar - Data and Knowledge
-
530034 SE Journal Club Bio- and Cheminformatics
Winter term 2025
-
270020 PR Bachelor Laboratory Course D - Theoretical Chemistry and Computational Biological Chemistry
-
270021 SE Writing of the Bachelor´s Thesis
-
301590 VU Fundamental Bioinformatics
-
301599 UE Laboratory Course: Bioinformatics
-
500501 SE Doctoral Research Seminar - Data and Knowledge
Publications
Distinguishing self from non-self RNA by editing-specific inosine patterns. / Varada, Rajagopal; Leuchtenberger, Alina F.; Vesely, Cornelia et al.
In: Nucleic Acids Research, Vol. 54, No. 16, gkag845, 09.09.2026.
Publications: Contribution to journal › Article › Peer Reviewed
Rational design of mechanically active RNAs: de novo engineering of functional exoribonuclease-resistant RNAs. / Sidl, Leonhard (Corresponding author); Walter, Jule; Gutenbrunner, Katrin et al.
In: Nucleic Acids Research, Vol. 54, No. 9, gkag473, 22.05.2026.
Publications: Contribution to journal › Article › Peer Reviewed
MicroRNA-Mediated Obstruction of Stem-loop Alternative Splicing (MIMOSAS) regulates long-range alternative splicing in Drosophila. / Ruan, Kai; Liu, Jiaqi; Xia, Melanie et al.
In: Nucleic Acids Research, Vol. 54, No. 7, gkag356, 24.04.2026.
Publications: Contribution to journal › Article › Peer Reviewed
Experimental identification of preQ1-binding RNAs in the pathogenic bacterium Listeria monocytogenes. / Hanisch, Malou; Flemmich, Laurin; Mitteregger, Christoph et al.
In: RSC Chemical Biology, Vol. 6, No. 12, 14.10.2025, p. 1867-1878.
Publications: Contribution to journal › Article › Peer Reviewed
Computational complexity, algorithmic scope, and evolution. / Sidl, Leonhard; Faissner, Maximilian; Uhlir, Manuel et al.
In: Journal of Physics: Complexity, Vol. 6, No. 1, 015013, 01.03.2025.
Publications: Contribution to journal › Article › Peer Reviewed
Old Dog, New Tricks: Exact Seeding Strategy Improves RNA Design Performances. / Boury, Théo; Sidl, Leonhard; Hofacker, Ivo L. et al.
Research in Computational Molecular Biology - 29th International Conference, RECOMB 2025, Proceedings. ed. / Sriram Sankararaman. Springer Science and Business Media Deutschland GmbH, 2025. p. 134-152 (Lecture Notes in Computer Science, Vol. 15647 LNBI).
Publications: Contribution to book › Contribution to proceedings › Peer Reviewed
tRNA expression and modification landscapes, and their dynamics during zebrafish embryo development. / Rappol, Tom; Waldl, Maria; Chugunova, Anastasia et al.
In: Nucleic Acids Research, Vol. 52, No. 17, 23.09.2024, p. 10575-10594.
Publications: Contribution to journal › Article › Peer Reviewed
Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data. / Thiel, Bernhard C; Bussi, Giovanni; Poblete, Simón (Corresponding author) et al.
In: Nucleic Acids Research, Vol. 52, No. 16, 09.09.2024, p. e73.
Publications: Contribution to journal › Article › Peer Reviewed
Sequence Design for RNA-RNA Interactions. / Waldl, Maria; Yao, Hua Ting; Hofacker, Ivo L. (Corresponding author).
RNA Design: Methods and Protocols. ed. / Alexander Churkin; Danny Barash. Springer Nature, 2024. p. 1-16 (Methods in Molecular Biology, Vol. 2847).
Publications: Contribution to book › Chapter › Peer Reviewed
Comparative RNA Genomics. / Backofen, Rolf; Gorodkin, Jan; Hofacker, Ivo et al.
Comparative Genomics: Methods and Protocols . 2. ed. Humana, New York, NY, 2024. p. 347–393 (Methods in Molecular Biology, Vol. 2802).
Publications: Contribution to book › Chapter › Peer Reviewed
1
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10
out of
193
Projects
decorating RNA for a purpose
Jantsch, Michael F. (Project Coordinator),
Ameres, Stefan
(Project Lead),
Hofacker, Ivo
(Project Lead)
01/03/2020 29/02/2028
Active
RNA Biology
Leodolter-Barta, Andrea
(Project Lead),
von Haeseler, Arndt (Co-Lead),
Bläsi, Udo
(Project Lead),
Görke, Boris
(Co-Lead),
Hofacker, Ivo
(Co-Lead),
Moll, Isabella
(Co-Lead),
Ayatollahi, Zahra
(Admin),
Martins, Angela (Admin)
01/12/2006 30/06/2021
Finished
Talks
Progress and challenges in RNA secondary structure prediction
Ivo Hofacker
Talk or oral contribution
12.5.2026
The impact of post-transcriptional modifications on the tRNA secondary structure"
Thomas Spicher
,
Katrin Gutenbrunner
,
Ronny Lorenz
,
Ivo Hofacker
41st TBI Winterseminar in Bled
Conference,
Talk or oral contribution
8.2.2026
Predicting the Effect of RNA Modifications on RNA Structure
Ivo Hofacker
,
Thomas Spicher
,
Yuliia Varenyk
,
Ronny Lorenz
,
Michael Thomas Wolfinger
2025 RiboClub Annual Meeting
Conference,
Talk or oral contribution
21.9.2025
Progress and Challenges in RNA Secondary Structure Prediction
Ivo Hofacker
Talk or oral contribution
19.9.2025
Positional Impacts on tRNA Structure: Constraint-Based Prediction and Links to Modification Sites
Thomas Spicher
,
Yuliia Varenyk
,
Ronny Lorenz
,
Ivo Hofacker
SFB RNA Deco Annual RNA Retreat
Conference,
Talk or oral contribution
11.9.2025
Design of cotranscriptional folding paths
Stefan Badelt
,
Laurenz Miksch
,
Ivo Hofacker
40th TBI Winterseminar, Bled
Conference,
Talk or oral contribution
9.2.2025
Detecting Pseudouridines in tRNAs: Addressing Computational Mapping Errors
Cristian A. Velandia-Huerto
,
Ivo Hofacker
SFB RNA Deco Retreat Innsbruck
Seminar/Workshop,
Talk or oral contribution
6.2.2025
Coarse Grained Sampling of 3D RNA Structures in Ernwin
Ivo Hofacker
Computational Approaches to RNA Structure and Function
Seminar/Workshop,
Talk or oral contribution
21.7.2024
Structure and Design of RNase resistant RNA structures
Leonhard Paul Sidl
,
Ivo Hofacker
Vienna Doctoral School in Chemistry: Panel A: Retreat 2024
Seminar/Workshop,
Talk or oral contribution
19.2.2024
Free energy calculation of modified nucleotides by molecular dynamics simulations
Thomas Spicher
,
Ronny Lorenz
,
Ivo Hofacker
39th TBI Winterseminar in Bled
Seminar/Workshop,
Talk or oral contribution
11.2.2024
The effect of modified nucleotides on RNA structure
Yuliia Varenyk
,
Ronny Lorenz
,
Thomas Spicher
,
Ivo Hofacker
39th TBI Winterseminar in Bled
Seminar/Workshop,
Talk or oral contribution
11.2.2024
The effect of modified nucleotides on RNA structure
Yuliia Varenyk
,
Ronny Lorenz
,
Thomas Spicher
,
Ivo Hofacker
SFB 80 RNA-DECO: Decorating RNA for a purpose
Conference,
Talk or oral contribution
1.2.2024
Computational Estimation of Energy Parameters
Thomas Spicher
,
Ronny Lorenz
,
Ivo Hofacker
38th TBI Winterseminar in Bled
Seminar/Workshop,
Talk or oral contribution
12.2.2023
Modeling RNA-RNA interaction formation on direct paths
Maria Waldl
,
Ivo Hofacker
,
Sebastian Will
38th TBI Winterseminar in Bled
Seminar/Workshop,
Talk or oral contribution
12.2.2023
The effect of modified nucleotides on secondary structure prediction in tRNA
Yuliia Varenyk
,
Ivo Hofacker
,
Ronny Lorenz
,
Thomas Spicher
38th TBI Winterseminar in Bled
Seminar/Workshop,
Talk or oral contribution
12.2.2023
Predicting the effect of modified nucleotides on RNA structure
Ivo Hofacker
Vienna RNA Conference - RNA modification and processing
Conference,
Talk or oral contribution
26.10.2022
Computational Estimation of Energy Parameters for modified Nucleotides
Thomas Spicher
,
Ronny Lorenz
,
Ivo Hofacker
18th Herbstseminar der Bioinformatik
Seminar/Workshop,
Talk or oral contribution
3.10.2022
Incongruent Evolution of RNA Sequence and Structure
Maria Waldl
,
Sebastian Will
,
Michael Thomas Wolfinger
,
Ivo Hofacker
,
Peter Stadler
18th Herbstseminar der Bioinformatik
Seminar/Workshop,
Talk or oral contribution
3.10.2022
Modified nucleotides in RNA secondary structure prediction
Yuliia Varenyk
,
Ivo Hofacker
,
Ronny Lorenz
,
Thomas Spicher
18th Herbstseminar der Bioinformatik
Seminar/Workshop,
Talk or oral contribution
3.10.2022
Experiments in Deep Learning for RNA Secondary Structure Prediction
Ivo Hofacker
Dagstuhl Seminar: Rational Design of RiboNucleic Acids
Seminar/Workshop,
Talk or oral contribution
18.9.2022
Features of RNA-RNA interaction kinetics
Maria Waldl
,
Sebastian Will
,
Ivo Hofacker
Dagstuhl Seminar: Rational Design of RiboNucleic Acids
Seminar/Workshop,
Talk or oral contribution
18.9.2022
Simulations of cotranscriptional folding explain the impact of sequence mutations
Stefan Badelt
,
Ronny Lorenz
,
Ivo Hofacker
Dagstuhl Seminar: Rational Design of RiboNucleic Acids
Seminar/Workshop,
Talk or oral contribution
18.9.2022
Experiments in Deep Learning for RNA Secondary Structure Prediction
Ivo Hofacker
German Conference on Bioinformatics (GCB 2022)
Conference,
Talk or oral contribution
6.9.2022
An RNA kinetics ansatz derived from an efficient prediction of RNA pathways
Ivo Hofacker
7th Computational Approaches to RNA Structure and Function meeting
Conference,
Talk or oral contribution
7.8.2022
Experiments in Deep Learning for RNA Secondary Structure Prediction
Ivo Hofacker
7th Computational Approaches to RNA Structure and Function meeting
Conference,
Talk or oral contribution
7.8.2022
Incongruent Evolution of RNA Sequence and Structure
Maria Waldl
,
Sebastian Will
,
Ivo Hofacker
,
Peter Stadler
7th Computational Approaches to RNA Structure and Function meeting
Conference,
Talk or oral contribution
7.8.2022
Modeling RNA-RNA interaction formation on direct paths
Maria Waldl
,
Irene Katharina Beckmann-Schneider
,
Sebastian Will
,
Ivo Hofacker
7th Computational Approaches to RNA Structure and Function meeting
Conference,
Talk or oral contribution
7.8.2022
MODELING THE KINETICS OF RNA-RNA INTERACTION FORMATION
Maria Waldl
,
Irene Katharina Beckmann-Schneider
,
Sebastian Will
,
Ivo Hofacker
Doctoral School of Chemistry Panel A
Lecture series, colloquium,
Talk or oral contribution
17.11.2021
Prediction of co-transcriptional RNA folding for Modeling Riboswitches
Ivo Hofacker
5th Annual Meeting on RNA: from basic research to industrial applications
Conference,
Talk or oral contribution
7.10.2019
Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Structure
Maria Waldl
,
Sebastian Will
,
Michael Thomas Wolfinger
,
Ivo Hofacker
,
Peter Stadler
17. Herbstseminar der Bioinformatik
Seminar/Workshop,
Talk or oral contribution
30.9.2019
Co-transcriptional RNA folding kinetics
Ivo Hofacker
RNA Informatics 2019
Conference,
Talk or oral contribution
9.9.2019
Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Structure
Maria Waldl
,
Sebastian Will
,
Michael Thomas Wolfinger
,
Ivo Hofacker
,
Peter Stadler
CIBB 2019
Conference,
Talk or oral contribution
4.9.2019
Human & Bordetella pertussis co-expression networks
Mariam Rukhama Farman
,
Ivo Hofacker
34th TBI Winterseminar in Bled
Seminar/Workshop,
Talk or oral contribution
10.2.2019
Computational Approaches to RNA Folding Kinetics
Ivo Hofacker
Algorithms in Structural Bioinformatics (AlgoSB)
Summer/Winter school,
Talk or oral contribution
15.1.2019
RNA secondary Structures
Ivo Hofacker
Algorithms in Structural Bioinformatics (AlgoSB)
Summer/Winter school,
Talk or oral contribution
14.1.2019
RNA-RNA Interaction Kinetics for Refining RNA Targeting Screens
Maria Waldl
,
Sebastian Will
,
Ivo Hofacker
16. Herbstseminar der Bioinformatik
Conference,
Talk or oral contribution
1.10.2018
RNA-RNA Interaction Kinetics for Refining RNA Targeting Screens
Maria Waldl
,
Sebastian Will
,
Ivo Hofacker
German Conference on Bioinformatics (GCB 2018)
Conference,
Talk or oral contribution
25.9.2018
Co-transcriptional Folding Kinetics and Riboswitch Modeling
Ivo Hofacker
Computational Analysis of RNA Structure and Function
Seminar/Workshop,
Talk or oral contribution
15.7.2018
Identification and Classification of Pseudoknots and their Impact on RNA 3D structure prediction
Irene Katharina Beckmann-Schneider
,
Bernhard Thiel
,
Ivo Hofacker
33rd TBI Winterseminar in Bled
Seminar/Workshop,
Talk or oral contribution
11.2.2018
Predicting Pseudoknots in RNA 3D structures
Irene Katharina Beckmann-Schneider
,
Ivo Hofacker
15. Herbstseminar der Bioinformatik
Seminar/Workshop,
Talk or oral contribution
2.10.2017
RNA 2D folding Dynamics and 3D Structure Prediction
Ivo Hofacker
Workshop "RNA: Structure, Dynamics, and Function"
Seminar/Workshop,
Talk or oral contribution
26.5.2016
Coarse Grain 3D RNA Structure Prediction
Ivo Hofacker
Retreat of the DK RNA Biology and SFB RNA-REG
Conference,
Talk or oral contribution
14.4.2016
Computational Biology with RNA Structures, Interactions, and Dynamics
Ivo Hofacker
51st Winter Seminar
Seminar/Workshop,
Talk or oral contribution
9.1.2016
Beyond RNA secondary structure
Ivo Hofacker
cphRNA 2014: Summer School in RNA Bioinformatics
Conference,
Talk or oral contribution
28.6.2014
siRNA and Oligo Design
Ivo Hofacker
cphRNA 2014: Summer School in RNA Bioinformatics
Conference,
Talk or oral contribution
25.6.2014
RNA folding kinetics and energy landscapes
Ivo Hofacker
cphRNA 2014: Summer School in RNA Bioinformatics
Conference,
Talk or oral contribution
24.6.2014
Energy directed RNA folding
Ivo Hofacker
cphRNA 2014: Summer School in RNA Bioinformatics
Conference,
Talk or oral contribution
23.6.2014
In silico Annotation of noncoding RNAs and their Targets
Ivo Hofacker
Retreat of the DK RNA Biology and SFB RNA-REG
Conference,
Talk or oral contribution
11.4.2014
Beyond RNA secondary structure:G-quadruplexes and non-canonical pairs
Ivo Hofacker
Bioinformatics 2013 / BIT13
Conference,
Talk or oral contribution
26.6.2013
Predicting Targets and Effects of Bacterial small RNAs
Ivo Hofacker
Regulating with RNA in Bacteria
Conference,
Talk or oral contribution
4.6.2013
Folding with Fancy Constraints -Secondary Structures from Probing Data
Ivo Hofacker
Talk or oral contribution
24.7.2012
Folding Kinetics and Energy Landscapes for RNA Secondary Structures
Ivo Hofacker
Talk or oral contribution
21.6.2012
RNA in silico: Bioinformatik im postgenomischen Zeitalter
Ivo Hofacker
Talk or oral contribution
9.5.2012
Advances in RNA Bioinformatics. Prediction of RNA Structures, Interactions, and Folding Kinetics
Ivo Hofacker
Talk or oral contribution
19.11.2011
Micro RNA Discovery in Sequencing Data without a Genome
Ivo Hofacker
Talk or oral contribution
15.7.2011
Beyond secondary structures: Predicting non-canonical pairs
Ivo Hofacker
Talk or oral contribution
26.5.2011
In silico annotation of noncoding RNAs and their targets
Ivo Hofacker
Talk or oral contribution
13.5.2011
RNA Folding Dynamics -- trajectories and landscapes
Ivo Hofacker
EMBO Practical Course on Computational RNA Biology 2010
Conference,
Talk or oral contribution
30.4.2010
RNA Genefinding
Ivo Hofacker
EMBO Practical Course on Computational RNA Biology 2010
Conference,
Talk or oral contribution
28.4.2010
Energy Landscapes for RNA Folding: Time- dependent Landscapes and 2D Projections
Ivo Hofacker
Computational methods for RNA analysis
Seminar/Workshop,
Talk or oral contribution
5.8.2009
Bioinformatics for the Modern RNA World:From Gene Finding to Function
Ivo Hofacker
Talk or oral contribution
9.7.2009
Detection, annotation, and target search for noncoding RNAs
Ivo Hofacker
KU Bioinformatics Workshop 2009
Seminar/Workshop,
Talk or oral contribution
26.1.2009
ncRNA Annotation and Target Prediction
Ivo Hofacker
EMBO Workshop New Functions of Regulatory RNAs in Pro- and Eucaryotes
Seminar/Workshop,
Talk or oral contribution
13.1.2009
RNA Bioinformatics: From structure prediction to RNA gene finding
Ivo Hofacker
Talk or oral contribution
12.11.2008
Introduction to non-coding RNA gene finding
Ivo Hofacker
ISMB 2008
Conference,
Talk or oral contribution
19.7.2008
From noncoding RNA Search to Annotation
Ivo Hofacker
Non-Coding RNAs: Computational Challenges and Applications
Conference,
Talk or oral contribution
28.4.2008
Prediction of ncRNA Interaction Targets
Ivo Hofacker
Non-Coding RNAs: Computational Challenges and Applications
Conference,
Talk or oral contribution
28.4.2008
RNA Structure thermodynamics, basic folding
Ivo Hofacker
EMBO Practical Course on Computational RNA Biology 2008
Summer/Winter school,
Talk or oral contribution
14.4.2008
Solving RNA bioinformatics problems using the Vienna RNA Package
Ivo Hofacker
EMBO Practical Course on Computational RNA Biology 2008
Summer/Winter school,
Talk or oral contribution
14.4.2008
Stochastic Models, HMMs, SCFGs, and model training
Ivo Hofacker
EMBO Practical Course on Computational RNA Biology 2008
Summer/Winter school,
Talk or oral contribution
14.4.2008
Computational Detection and Analysis of noncoding RNAs
Ivo Hofacker
Talk or oral contribution
4.2.2008
Prediction of RNA-RNA interaction
Ivo Hofacker
IMA Workshop, RNA in Biology, Bioengineering and Nanotechnology
Seminar/Workshop,
Talk or oral contribution
29.10.2007
Prediction of RNA-RNA interaction
Ivo Hofacker
Workshop Medical Applications of ncRNA at the 3rd World Congress on
Regenerative Medicine
Seminar/Workshop,
Talk or oral contribution
20.10.2007
Computational Detection and Annotation of Non-Coding RNAs
Ivo Hofacker
Ernst Klenk Symposium in Molecular Medicine
Conference,
Talk or oral contribution
30.9.2007
Basic Algorithms in RNA Bioinformatics
Ivo Hofacker
Mini course on non-coding RNAs and RNA informatics 2007
Summer/Winter school,
Talk or oral contribution
17.9.2007
Noncoding RNAs in Bacteria
Ivo Hofacker
Mini course on non-coding RNAs and RNA informatics 2007
Summer/Winter school,
Talk or oral contribution
17.9.2007
RNA Bioinformatics -- An Overview
Ivo Hofacker
Mini course on non-coding RNAs and RNA informatics 2007
Summer/Winter school,
Talk or oral contribution
17.9.2007
Prediction of RNA-RNA interaction
Ivo Hofacker
Microsymposium on Small RNAs
Conference,
Talk or oral contribution
21.5.2007