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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

Lorenz, R., Wolfinger, M. T., Tanzer, A., & Hofacker, I. L. (2016). Predicting RNA secondary structures from sequence and probing data. Methods, 103, 86-98. https://doi.org/10.1016/j.ymeth.2016.04.004

Tanzer, A., Ochsenreiter, R. W., Wolfinger, M., & Hofacker, I. (2016). Evolution of regulatory RNA elements in Zika viruses and other Flaviviridae. Paper presented at Virus Genomics and Evolution, Hinxton, Cambridge, United Kingdom.

Sedlyarov, V., Fallmann, J., Ebner, F. D., Huemer, J., Sneezum, L., Ivin, M., Kreiner, K., Tanzer, A., Vogl, C., Hofacker, I., & Kovarik, P. (2016). Tristetraprolin binding site atlas in the macrophage transcriptome reveals a switch for inflammation resolution. Molecular Systems Biology, 12(5), [868]. https://doi.org/10.15252/msb.20156628

Lorenz, R., Hofacker, I. L., & Stadler, P. F. (2016). RNA folding with hard and soft constraints. Algorithms for Molecular Biology, 11(1), [8]. https://doi.org/10.1186/s13015-016-0070-z

Farman, M. R., Hofacker, I., Amman, F., & Vecerek, B. (2016). Transcriptomics of Bordetella & Human Phagocytes Interplay. Paper presented at DK RNA Retreat 2016 Vienna, Wien, Austria.

Kucharik, M., Hofacker, I. L., Stadler, P. F., & Qin, J. (2016). Pseudoknots in RNA folding landscapes. Bioinformatics, 32(2), 187-194. https://doi.org/10.1093/bioinformatics/btv572

Fallmann, J., Sedlyarov, V., Tanzer, A., Kovarik, P., & Hofacker, I. L. (2016). AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements. Nucleic Acids Research, 44(D1), D90-D95. https://doi.org/10.1093/nar/gkv1238

Lorenz, R., Luntzer, D., Hofacker, I., Stadler, P., & Wolfinger, M. (2016). SHAPE directed RNA folding. Bioinformatics, 32(1), 145-147. https://doi.org/10.1093/bioinformatics/btv523

Badelt, S., Flamm, C., & Hofacker, I. L. (2016). Computational Design of a Circular RNA with Prionlike Behavior. Artificial Life, 22(2), 172-184. https://doi.org/10.1162/ARTL_a_00197

Hsiao, Y-T., Lee, W-P., Yang, W., Mueller, S., Flamm, C., Hofacker, I., & Kuegler, P. (2016). Practical Guidelines for Incorporating Knowledge-Based and Data-Driven Strategies into the Inference of Gene Regulatory Networks. I E E E - A C M Transactions on Computational Biology and Bioinformatics, 13(1), 64-75. https://doi.org/10.1109/TCBB.2015.2465954

Theis, C., Zirbel, C. L., Höner zu Siederdissen, C., Anthon, C., Hofacker, I. L., Nielsen, H., & Gorodkin, J. (2015). RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure. PLoS ONE, 10(10), [e0139900]. https://doi.org/10.1371/journal.pone.0139900

Kerpedjiev, P., Hammer, S., & Hofacker, I. L. (2015). Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams. Bioinformatics, 31(20), 3377-3379. https://doi.org/10.1093/bioinformatics/btv372

Hecker, N., Christensen-Dalsgaard, M., Seemann, S. E., Havgaard, J. H., Stadler, P. F., Hofacker, I. L., Nielsen, H., & Gorodkin, J. (2015). Optimizing RNA structures by sequence extensions using RNAcop. Nucleic Acids Research, 43(17), 8135-8145. https://doi.org/10.1093/nar/gkv813

Kerpedjiev, P., Hammer, S., & Hofacker, I. (2015). Simple, Shareable, Online RNA Secondary Structure Diagrams. Paper presented at BOSC 2015, Dublin, Ireland.

Petkovic, S., Badelt, S., Block, S., Flamm, C., Delcea, M., Hofacker, I., & Mueller, S. (2015). Sequence-controlled RNA self-processing: computational design, biochemical analysis, and visualization by AFM. RNA, 21(7), 1249-1260. https://doi.org/10.1261/rna.047670.114

Kerpedjiev, P., Siederdissen, C. H. Z., & Hofacker, I. L. (2015). Predicting RNA 3D structure using a coarse-grain helix-centered model. RNA, 21(6), 1110-1121. https://doi.org/10.1261/rna.047522.114

Lavender, C. A., Lorenz, R., Zhang, G., Tamayo, R., Hofacker, I. L., & Weeks, K. M. (2015). Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA. PLoS Computational Biology, 11(5), [e1004126]. https://doi.org/10.1371/journal.pcbi.1004126

Berkemer, S., Höner zu Siederdissen, C., Amman, F., Wintsche, A., Will, S., Hofacker, I., Prohaska, S. J., & Stadler, P. (2015). Processed Small RNAs in Archaea and BHB Elements. Genomics and Computational Biology, 1(1), e18. https://doi.org/10.18547/gcb.2015.vol1.iss1.e18

zu Siederdissen, C. H., Hofacker, I. L., & Stadler, P. F. (2015). Product Grammars for Alignment and Folding. I E E E - A C M Transactions on Computational Biology and Bioinformatics, 12(3), 507-519. https://doi.org/10.1109/TCBB.2014.2326155

Badelt, S., Hammer, S., Flamm, C., & Hofacker, I. L. (2015). Thermodynamic and kinetic folding of riboswitches. Methods in Enzymology, 553, 193-213. https://doi.org/10.1016/bs.mie.2014.10.060

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