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Univ.-Prof. Dipl.-Phys. Dr. Ivo Hofacker

T: +43-1-4277-52738

ivo.hofacker@univie.ac.at

http://www.tbi.univie.ac.at/

Summer term 2024

053521 VU Bioinformatics of sequences and structures

270020 PR Bachelor Laboratory Course D - Theoretical Chemistry and Computational Biological Chemistry

270021 SE Writing of the Bachelor´s Thesis

270034 PR Practical Course Bioinformatics of Nucleic Acids

270054 VO Bioinformatics of Nucleic Acids

301578 VO Special Topics in Bioinformatics

301600 UE Bioinformatics-Practicum II

500501 SE Doctoral Research Seminar - Data and Knowledge

Winter term 2023

053049 SE Master Seminar

053531 PR Software development project in bioinformatics

270020 PR Bachelor Laboratory Course D - Theoretical Chemistry and Computational Biological Chemistry

270021 SE Writing of the Bachelor´s Thesis

270236 PR Practical Course on Problems of Bioinformatics in Chemistry and Biology

270299 VO Basics of Informatics for Chemistry and Biology

301590 VU Fundamental Bioinformatics

301599 UE Laboratory Course: Bioinformatics

500501 SE Doctoral Research Seminar - Data and Knowledge

530009 SE Advanced Topics and Algorithms in Bio- and Cheminformatics

Summer term 2023

053521 VU Bioinformatics of sequences and structures

270020 PR Bachelor Laboratory Course D - Theoretical Chemistry and Computational Biological Chemistry

270021 SE Writing of the Bachelor´s Thesis

270034 PR Practical Course Bioinformatics of Nucleic Acids

270054 VO Bioinformatics of Nucleic Acids

301578 VO Special Topics in Bioinformatics

301600 UE Bioinformatics-Practicum II

500501 SE Doctoral Research Seminar - Data and Knowledge

Beckmann-Schneider, I. K., Waldl, M., Will, S., & Hofacker, I. L. (2024). 3D feasibility of 2D RNA-RNA interaction paths by stepwise folding simulations. RNA, 30(2), 113-123. https://doi.org/10.1261/rna.079756.123

Farman, M. R., Petrackova, D., Kumar, D., Drzmisek, J., Saha, A., Curnova, I., Capek, J., Hejnarova, V., Amman, F., Hofacker, I., & Vecerek, B. (2023). Avirulent phenotype promotes Bordetella pertussis adaptation to the intramacrophage environment. Emerging microbes & infections, 12(1), [e2146536]. https://doi.org/10.1080/22221751.2022.2146536

Yao, H. T., Lorenz, R., Hofacker, I. L., & Stadler, P. F. (2023). Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package. Algorithms for Molecular Biology, 18(1), [8]. https://doi.org/10.1186/s13015-023-00236-0

Varenyk, Y., Spicher, T., Hofacker, I. L., & Lorenz, R. (2023). Modified RNAs and predictions with the ViennaRNA Package. Bioinformatics, 39(11), [btad696]. https://doi.org/10.1093/bioinformatics/btad696

Waldl, M., Spicher, T., Lorenz, R., Beckmann, I. K., Hofacker, I. L., Von Löhneysen, S., & Stadler, P. F. (2023). Local RNA folding revisited. Journal of Bioinformatics and Computational Biology, 21(4), [2350016]. https://doi.org/10.1142/S0219720023500166

Mrozowich, T., Park, S. M., Waldl, M., Henrickson, A., Tersteeg, S., Nelson, C. R., De Klerk, A., Demeler, B., Hofacker, I. L., Wolfinger, M. T., & Patel, T. R. (2023). Investigating RNA-RNA interactions through computational and biophysical analysis. Nucleic Acids Research, 51(9), 4588-4601. https://doi.org/10.1093/nar/gkad223

Badelt, S., Lorenz, R., & Hofacker, I. L. (2023). DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model. Bioinformatics (Oxford, England), 39(1), [btad034]. https://doi.org/10.1093/bioinformatics/btad034

Gosavi, D., Wower, I., Beckmann-Schneider, I. K., Hofacker, I. L., Wower, J., Wolfinger, M. T., & Sztuba-Solinska, J. (2022). Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus internal Ribosome Entry Site. RNA Biology, 19(1), 496-506. https://doi.org/10.1080/15476286.2022.2058818

Flamm, C., Wielach, J., Wolfinger, M. T., Badelt, S., Lorenz, R., & Hofacker, I. L. (2022). Caveats to Deep Learning Approaches to RNA Secondary Structure Prediction. Frontiers in bioinformatics, 2, [835422]. https://doi.org/10.3389/fbinf.2022.835422

Zayni, S., Damiati, S., Moreno-Flores, S., Amman, F., Hofacker, I., Jin, D., & Ehmoser, E-K. (2021). Enhancing the Cell-Free Expression of Native Membrane Proteins by In Silico Optimization of the Coding Sequence-An Experimental Study of the Human Voltage-Dependent Anion Channel. Membranes, 11(10), [741]. https://doi.org/10.3390/membranes11100741

Entzian, G., Hofacker, I. L., Ponty, Y., Lorenz, R., & Tanzer, A. (2021). RNAxplorer: harnessing the power of guiding potentials to sample RNA landscapes. Bioinformatics, 37(15), 2126-2133. https://doi.org/10.1093/bioinformatics/btab066

Wolfinger, M. T., Ochsenreiter, R. W., & Hofacker, I. (2021). Functional RNA Structures in the 3′ UTR of Mosquito-Borne Flaviviruses. In D. Frishman, & M. Marz (Eds.), Virus Bioinformatics Chapman and Hall/CRC. https://doi.org/10.1201/9781003097679

Mueller, T., Miladi, M., Hutter, F., Hofacker, I., Will, S., & Backofen, R. (2020). The locality dilemma of Sankoff-like RNA alignments. Bioinformatics, 36, I242-I250. https://doi.org/10.1093/BIOINFORMATICS/BTAA431

Petrackova, D., Farman, M. R., Amman, F., Linhartova, I., Dienstbier, A., Kumar, D., Drzmisek, J., Hofacker, I., Eugenia Rodriguez, M., & Vecerek, B. (2020). Transcriptional profiling of human macrophages during infection with Bordetella pertussis. RNA Biology, 17(5), 731-742. https://doi.org/10.1080/15476286.2020.1727694

Kim, D. N., Thiel, B. C., Mrozowich, T., Hennelly, S. P., Hofacker, I. L., Patel, T. R., & Sanbonmatsu, K. Y. (2020). Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution. Nature Communications, 11(1), [148]. https://doi.org/10.1038/s41467-019-13942-4

Waldl, M., Will, S., Wolfinger, M. T., Hofacker, I. L., & Stadler, P. F. (2020). Bi-alignments as models of incongruent evolution of RNA sequence and secondary structure. In P. Cazzaniga, D. Besozzi, I. Merelli, & L. Manzoni (Eds.), Computational Intelligence Methods for Bioinformatics and Biostatistics: 16th International Meeting, CIBB 2019, Revised Selected Papers (Vol. 12313, pp. 159-170). Springer. Lecture Notes in Computer Science Vol. 12313 https://doi.org/10.1007/978-3-030-63061-4_15

Lorenz, R., Flamm, C., Hofacker, I. L., & Stadler, P. F. (2020). Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding. In E. DeMaria, A. Fred, & H. Gamboa (Eds.), Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies: Volume 3: BIOINFORMATICS, 23-31, 2020 , Valletta, Malta (pp. 23-31). SciTePress. https://doi.org/10.5220/0008916600230031

Gelhausen, R., Will, S., Hofacker, I. L., Backofen, R., & Raden, M. (2019). INTARNAHELIX-composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction. Journal of Bioinformatics and Computational Biology (JBCB), 17(5), [1940009]. https://doi.org/10.1142/S0219720019400092

Schneider, A. D. B., Ochsenreiter, R., Hostager, R., Hofacker, I. L., Janies, D., & Wolfinger, M. T. (2019). Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture. Viruses, 11(9), [798]. https://doi.org/10.3390/v11090798

Deforges, J., Reis, R. S., Jacquet, P., Sheppard, S., Gadekar, V. P., Hart-Smith, G., Tanzer, A., Hofacker, I. L., Iseli, C., Xenarios, I., & Poirier, Y. (2019). Control of Cognate Sense mRNA Translation by cis-Natural Antisense RNAs. Plant Physiology, 180(1), 305-322. https://doi.org/10.1104/pp.19.00043

Computational Estimation of Energy Parameters

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

12 Feb 2023

Activity: Talks and presentations › Talk or oral contribution › Science 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 presentations › Talk or oral contribution › Science 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 presentations › Talk or oral contribution › Science to Science

Predicting the effect of modified nucleotides on RNA structure

Ivo Hofacker (Invited speaker)

26 Oct 2022

Activity: Talks and presentations › Talk or oral contribution › Science 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 presentations › Talk or oral contribution › Science 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 presentations › Talk or oral contribution › Science 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 presentations › Talk or oral contribution › Science to Science

Experiments in Deep Learning for RNA Secondary Structure Prediction

Ivo Hofacker (Invited speaker)

18 Sep 2022

Activity: Talks and presentations › Talk or oral contribution › Science to Science

Features of RNA-RNA interaction kinetics

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

18 Sep 2022

Activity: Talks and presentations › Talk or oral contribution › Science 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 presentations › Talk or oral contribution › Science to Science

Experiments in Deep Learning for RNA Secondary Structure Prediction

Ivo Hofacker (Keynote speaker)

6 Sep 2022

Activity: Talks and presentations › Talk or oral contribution › Science to Science

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

Ivo Hofacker (Invited speaker)

7 Aug 2022

Activity: Talks and presentations › Talk or oral contribution › Science to Science

Experiments in Deep Learning for RNA Secondary Structure Prediction

Ivo Hofacker (Invited speaker)

7 Aug 2022

Activity: Talks and presentations › Talk or oral contribution › Science 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 presentations › Talk or oral contribution › Science 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 presentations › Talk or oral contribution › Science 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 presentations › Talk or oral contribution › Science to Science

Prediction of co-transcriptional RNA folding for Modeling Riboswitches

Ivo Hofacker (Keynote speaker)

7 Oct 2019

Activity: Talks and presentations › Talk or oral contribution › Science 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 presentations › Talk or oral contribution › Science to Science

Co-transcriptional RNA folding kinetics

Ivo Hofacker (Invited speaker)

9 Sep 2019

Activity: Talks and presentations › Talk or oral contribution › Science 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 presentations › Talk or oral contribution › Science to Science

Human & Bordetella pertussis co-expression networks

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

10 Feb 2019

Activity: Talks and presentations › Talk or oral contribution › Science to Science

Computational Approaches to RNA Folding Kinetics

Ivo Hofacker (Invited speaker)

15 Jan 2019

Activity: Talks and presentations › Talk or oral contribution › Science to Science

RNA secondary Structures

Ivo Hofacker (Invited speaker)

14 Jan 2019

Activity: Talks and presentations › Talk or oral contribution › Science 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 presentations › Talk or oral contribution › Science 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 presentations › Talk or oral contribution › Science to Science

Co-transcriptional Folding Kinetics and Riboswitch Modeling

Ivo Hofacker (Invited speaker)

15 Jul 2018

Activity: Talks and presentations › Talk or oral contribution › Science 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 presentations › Talk or oral contribution › Science to Science

Predicting Pseudoknots in RNA 3D structures

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

2 Oct 2017

Activity: Talks and presentations › Talk or oral contribution › Science to Science