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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

Tanzer, A., Lorenz, R., & Hofacker, I. (2014). Detection of RNA G-Quadruplexes within and across genomes. In Book of Abstracts http://www.gcb2014.de/

Kucharik, M., Hofacker, I. L., Stadler, P. F., & Qin, J. (2014). Basin Hopping Graph: a computational framework to characterize RNA folding landscapes. Bioinformatics, 30(14), 2009-2017. https://doi.org/10.1093/bioinformatics/btu156

Marz, M., Beerenwinkel, N., Drosten, C., Fricke, M., Frishman, D., Hofacker, I. L., Hoffmann, D., Middendorf, M., Rattei, T., Stadler, P. F., & Toepfer, A. (2014). Challenges in RNA virus bioinformatics. Bioinformatics, 30(13), 1793-1799. https://doi.org/10.1093/bioinformatics/btu105

Hämmerle, H. K., Amman, F., Vecerek, B., Stuelke, J., Hofacker, I., & Bläsi, U. (2014). Impact of Hfq on the Bacillus subtilis Transcriptome. PLoS ONE, 9(6), [e98661]. https://doi.org/10.1371/journal.pone.0098661

Amman, F., Wolfinger, M. T., Lorenz, R., Hofacker, I. L., Stadler, P. F., & Findeiss, S. (2014). TSSAR: TSS annotation regime for dRNA-seq data. BMC Bioinformatics, 15(1), [89]. https://doi.org/10.1186/1471-2105-15-89

Badelt, S., Flamm, C., & Hofacker, I. (2014). Computational design of a circular RNA with prion-like behaviour. In Proceedings of the 14th International Conference on the Synthesis and Simulation of Living Systems (pp. 565-568). MIT Press. https://doi.org/10.7551/978-0-262-32621-6-ch091

Gorodkin, J., Hofacker, I., & Ruzzo, W. L. (2014). Concepts and Introduction to RNA Bioinformatics. Methods in Molecular Biology, 1097, 1-31. https://doi.org/10.1007/978-1-62703-709-9_1

Hofacker, I. (2014). Energy-Directed RNA Structure Prediction. Methods in Molecular Biology, 1097, 71-84. https://doi.org/10.1007/978-1-62703-709-9_4

Hofacker, I., & Lorenz, R. (2014). Predicting RNA Structure: Advances and Limitations. In C. Waldsich (Ed.), RNA Folding: Methods and Protocols (pp. 1-19). Humana Press, Inc.. Methods in Molecular Biology Vol. 1086 https://doi.org/10.1007/978-1-62703-667-2

Theis, C., Höner Zu Siederdissen, C., Hofacker, I. L., & Gorodkin, J. (2013). Automated identification of RNA 3D modules with discriminative power in RNA structural alignments. Nucleic Acids Research, 41(22), 9999-10009. https://doi.org/10.1093/nar/gkt795

Siederdissen, C. H. Z., Hammer, S., Abfalter, I., Hofacker, I. L., Flamm, C., & Stadler, P. F. (2013). Computational Design of RNAs with Complex Energy Landscapes. Biopolymers: original research on biological molecules and assemblies, 99(12), 1124-1136. https://doi.org/10.1002/bip.22337

Höner zu Siederdissen, C., Hofacker, I., & Stadler, P. (2013). How to Multiply Dynamic Programming Algorithms. Paper presented at BSB & X-Meeting 2013, Recife, Brazil. http://bsb2013.cin.ufpe.br/

Märtens, B., Amman, F., Manoharadas, S., Zeichen, L., Orell, A., Albers, S-V., Hofacker, I., & Bläsi, U. (2013). Alterations of the Transcriptome of Sulfolobus acidocaldarius by Exoribonuclease aCPSF2. PLoS ONE, 8(10), [76569]. https://doi.org/10.1371/journal.pone.0076569

Eggenhofer, F., Hofacker, I. L., & Höner zu Siederdissen, C. (2013). CMCompare webserver: comparing RNA families via covariance models. Nucleic Acids Research, 41(W1), W499-W503. https://doi.org/10.1093/nar/gkt329

Sabarinathan, R., Tafer, H., Seemann, S. E., Hofacker, I. L., Stadler, P. F., & Gorodkin, J. (2013). The RNAsnp web server: predicting SNP effects on local RNA secondary structure. Nucleic Acids Research, 41(W1), W475-W479. https://doi.org/10.1093/nar/gkt291

Mueller, S. A., Findeiss, S., Pernitzsch, S. R., Wissenbach, D. K., Stadler, P. F., Hofacker, I. L., von Bergen, M., & Kalkhof, S. (2013). Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics. Journal of Proteomics, 86, 27-42. https://doi.org/10.1016/j.jprot.2013.04.036

Amman, F., Bernhart, S. H., Doose, G., Hofacker, I. L., Qin, J., Stadler, P. F., & Will, S. (2013). The trouble with long-range base pairs in RNA folding. In J. C. Setubal, & N. F. Almeida (Eds.), Advances in Bioinformatics and Computational Biology: 8th Brazilian Symposium on Bioinformatics, BSB 2013, Recife, Brazil, November 3-7, 2013 (Vol. 8213 LNBI, pp. 1-11). Springer. Lecture Notes in Computer Science Vol. 8213 https://doi.org/10.1007/978-3-319-02624-4_1

Siederdissen, C. H. Z., Hofacker, I. L., & Stadler, P. F. (2013). How to Multiply Dynamic Programming Algorithms. In JC. Setubal, & NF. Almeida (Eds.), ADVANCES IN BIOINFORMATICS AND COMPUTATIONAL BIOLOGY (pp. 82-93). Springer-Verlag Berlin. Lecture Notes in Computer Science Vol. 8213

Sabarinathan, R., Tafer, H., Seemann, S. E., Hofacker, I., Stadler, P., & Gorodkin, J. (2013). RNAsnp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNPs. Human Mutation, 34(4), 546-556. https://doi.org/10.1002/humu.22273

Lorenz, R., Bernhart, S. H., Qin, J., Siederdissen, C. H. Z., Tanzer, A., Amman, F., Hofacker, I. L., & Stadler, P. F. (2013). 2D Meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction. I E E E - A C M Transactions on Computational Biology and Bioinformatics, 10(4), 832-844. https://doi.org/10.1109/TCBB.2013.7

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