Univ.-Prof. Dipl.-Phys. Dr. Ivo Hofacker
1090 Wien
Room : 5.30
Courses
Summer term 2026
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270020 PR Bachelor Laboratory Course D - Theoretical Chemistry and Computational Biological Chemistry
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270021 SE Writing of the Bachelor´s Thesis
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270054 VO Bioinformatics of Nucleic Acids
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301578 VO Special Topics in Bioinformatics
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500501 SE Doctoral Research Seminar - Data and Knowledge
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530034 SE Journal Club Bio- and Cheminformatics
Winter term 2025
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270020 PR Bachelor Laboratory Course D - Theoretical Chemistry and Computational Biological Chemistry
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270021 SE Writing of the Bachelor´s Thesis
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301590 VU Fundamental Bioinformatics
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301599 UE Laboratory Course: Bioinformatics
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500501 SE Doctoral Research Seminar - Data and Knowledge
Summer term 2025
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053049 SE Master Seminar
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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
-
301600 UE Bioinformatics-Practicum II
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500501 SE Doctoral Research Seminar - Data and Knowledge
Publications
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, 13.04.2026.
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
Phylogenetic and Chemical Probing Information as Soft Constraints in RNA Secondary Structure Prediction. / von Löhneysen, Sarah (Corresponding author); Spicher, Thomas; Varenyk, Yuliia et al.
In: Journal of computational biology : a journal of computational molecular cell biology, Vol. 31, No. 6, 01.06.2024, p. 549-563.
Publications: Contribution to journal › Article › Peer Reviewed
Projects
RNAdeco: decorating RNA for a purpose
Jantsch, M. F. (Project Coordinator), Ameres, S. (Project Lead) & Hofacker, I. (Project Lead)
1/03/20 → 29/02/28
Project: Research funding
Vorhersage von RNA-RNA Interakt
Hofacker, I. (Project Lead)
1/12/16 → 30/11/20
Project: Research funding
Transcri. Analyse von Bordetell
Hofacker, I. (Project Lead)
29/10/15 → 28/10/18
Project: Research funding
RNA Biology
Leodolter-Barta, A. (Project Lead), von Haeseler, A. (Co-Lead), Bläsi, U. (Project Lead), Görke, B. (Co-Lead), Hofacker, I. (Co-Lead), Moll, I. (Co-Lead), Ayatollahi, Z. (Admin) & Martins, A. (Admin)
1/12/06 → 30/06/21
Project: Research funding
Talks
Predicting the Effect of RNA Modifications on RNA Structure
Hofacker, I. (Speaker), Spicher, T. (Contributor), Varenyk, Y. (Contributor), Lorenz, R. (Contributor) & Wolfinger, M. T. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Progress and Challenges in RNA Secondary Structure Prediction
Hofacker, I. (Speaker)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Positional Impacts on tRNA Structure: Constraint-Based Prediction and Links to Modification Sites
Spicher, T. (Speaker), Varenyk, Y. (Contributor), Lorenz, R. (Contributor) & Hofacker, I. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Design of cotranscriptional folding paths
Badelt, S. (Speaker), Miksch , L. (Contributor) & Hofacker, I. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Detecting Pseudouridines in tRNAs: Addressing Computational Mapping Errors
Velandia-Huerto, C. A. (Speaker) & Hofacker, I. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Coarse Grained Sampling of 3D RNA Structures in Ernwin
Hofacker, I. (Speaker)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Structure and Design of RNase resistant RNA structures
Sidl, L. P. (Speaker) & Hofacker, I. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Free energy calculation of modified nucleotides by molecular dynamics simulations
Spicher, T. (Speaker), Lorenz, R. (Contributor) & Hofacker, I. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
The effect of modified nucleotides on RNA structure
Varenyk, Y. (Speaker), Lorenz, R. (Contributor), Spicher, T. (Contributor) & Hofacker, I. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
The effect of modified nucleotides on RNA structure
Varenyk, Y. (Speaker), Lorenz, R. (Contributor), Spicher, T. (Contributor) & Hofacker, I. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Computational Estimation of Energy Parameters
Spicher, T. (Speaker), Lorenz, R. (Contributor) & Hofacker, I. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Modeling RNA-RNA interaction formation on direct paths
Waldl, M. (Speaker), Hofacker, I. (Contributor) & Will, S. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
The effect of modified nucleotides on secondary structure prediction in tRNA
Varenyk, Y. (Speaker), Hofacker, I. (Contributor), Lorenz, R. (Contributor) & Spicher, T. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Predicting the effect of modified nucleotides on RNA structure
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Computational Estimation of Energy Parameters for modified Nucleotides
Spicher, T. (Speaker), Lorenz, R. (Contributor) & Hofacker, I. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Incongruent Evolution of RNA Sequence and Structure
Waldl, M. (Speaker), Will, S. (Contributor), Wolfinger, M. T. (Contributor), Hofacker, I. (Contributor) & Stadler, P. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Modified nucleotides in RNA secondary structure prediction
Varenyk, Y. (Speaker), Hofacker, I. (Contributor), Lorenz, R. (Contributor) & Spicher, T. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Experiments in Deep Learning for RNA Secondary Structure Prediction
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Features of RNA-RNA interaction kinetics
Waldl, M. (Speaker), Will, S. (Contributor) & Hofacker, I. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Simulations of cotranscriptional folding explain the impact of sequence mutations
Badelt, S. (Speaker), Lorenz, R. (Contributor) & Hofacker, I. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Experiments in Deep Learning for RNA Secondary Structure Prediction
Hofacker, I. (Keynote speaker)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
An RNA kinetics ansatz derived from an efficient prediction of RNA pathways
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Experiments in Deep Learning for RNA Secondary Structure Prediction
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Incongruent Evolution of RNA Sequence and Structure
Waldl, M. (Speaker), Will, S. (Contributor), Hofacker, I. (Contributor) & Stadler, P. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Modeling RNA-RNA interaction formation on direct paths
Waldl, M. (Speaker), Beckmann-Schneider, I. K. (Contributor), Will, S. (Contributor) & Hofacker, I. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
MODELING THE KINETICS OF RNA-RNA INTERACTION FORMATION
Waldl, M. (Speaker), Beckmann-Schneider, I. K. (Contributor), Will, S. (Contributor) & Hofacker, I. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Prediction of co-transcriptional RNA folding for Modeling Riboswitches
Hofacker, I. (Keynote speaker)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Structure
Waldl, M. (Speaker), Will, S. (Contributor), Wolfinger, M. T. (Contributor), Hofacker, I. (Contributor) & Stadler, P. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Co-transcriptional RNA folding kinetics
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Structure
Waldl, M. (Contributor), Will, S. (Contributor), Wolfinger, M. T. (Contributor), Hofacker, I. (Speaker) & Stadler, P. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Human & Bordetella pertussis co-expression networks
Farman, M. R. (Speaker) & Hofacker, I. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Computational Approaches to RNA Folding Kinetics
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
RNA secondary Structures
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
RNA-RNA Interaction Kinetics for Refining RNA Targeting Screens
Waldl, M. (Speaker), Will, S. (Contributor) & Hofacker, I. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
RNA-RNA Interaction Kinetics for Refining RNA Targeting Screens
Waldl, M. (Speaker), Will, S. (Contributor) & Hofacker, I. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Co-transcriptional Folding Kinetics and Riboswitch Modeling
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Identification and Classification of Pseudoknots and their Impact on RNA 3D structure prediction
Beckmann-Schneider, I. K. (Speaker), Thiel, B. (Contributor) & Hofacker, I. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
Predicting Pseudoknots in RNA 3D structures
Beckmann-Schneider, I. K. (Speaker) & Hofacker, I. (Contributor)
Activity: Talks and presentations › Talk or oral contribution › Science to Science
RNA 2D folding Dynamics and 3D Structure Prediction
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Coarse Grain 3D RNA Structure Prediction
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Computational Biology with RNA Structures, Interactions, and Dynamics
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Beyond RNA secondary structure
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
siRNA and Oligo Design
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
RNA folding kinetics and energy landscapes
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Energy directed RNA folding
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
In silico Annotation of noncoding RNAs and their Targets
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Beyond RNA secondary structure:G-quadruplexes and non-canonical pairs
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Predicting Targets and Effects of Bacterial small RNAs
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Predicting functional RNA structures
Hofacker, I. (Speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Folding with Fancy Constraints -Secondary Structures from Probing Data
Hofacker, I. (Speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
RNA Structures, Interactions, and Folding Kinetics
Hofacker, I. (Speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Folding Kinetics and Energy Landscapes for RNA Secondary Structures
Hofacker, I. (Speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
RNA in silico: Bioinformatik im postgenomischen Zeitalter
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
RNA Folding Kinetics and Dynamic Landscapes
Hofacker, I. (Speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Advances in RNA Bioinformatics. Prediction of RNA Structures, Interactions, and Folding Kinetics
Hofacker, I. (Speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
The art of RNA homology search
Hofacker, I. (Speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Prediction of bacterial small RNA targets
Hofacker, I. (Speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Micro RNA Discovery in Sequencing Data without a Genome
Hofacker, I. (Speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Beyond secondary structures: Predicting non-canonical pairs
Hofacker, I. (Speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
In silico annotation of noncoding RNAs and their targets
Hofacker, I. (Speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
RNA Folding Dynamics -- trajectories and landscapes
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
RNA Genefinding
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Energy Landscapes for RNA Folding: Time- dependent Landscapes and 2D Projections
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Bioinformatics for the Modern RNA World:From Gene Finding to Function
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Detection, annotation, and target search for noncoding RNAs
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
ncRNA Annotation and Target Prediction
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
RNA Bioinformatics: From structure prediction to RNA gene finding
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Introduction to non-coding RNA gene finding
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
From noncoding RNA Search to Annotation
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Prediction of ncRNA Interaction Targets
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
RNA Structure thermodynamics, basic folding
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Solving RNA bioinformatics problems using the Vienna RNA Package
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Stochastic Models, HMMs, SCFGs, and model training
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Computational Detection and Analysis of noncoding RNAs
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Prediction of RNA-RNA interaction
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Prediction of RNA-RNA interaction
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Computational Detection and Annotation of Non-Coding RNAs
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Basic Algorithms in RNA Bioinformatics
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Noncoding RNAs in Bacteria
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
RNA Bioinformatics -- An Overview
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
Prediction of RNA-RNA interaction
Hofacker, I. (Invited speaker)
Activity: Talks and presentations › Talk or oral contribution › Other
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