Theoretical Biochemistry Group
Institute for Theoretical Chemistry
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I am working within the field of RNA structure prediction in 3D with special interest on:
RNA-RNA Interaction (PhD)
FWF-I-2874 is a shared project of the Bioinformatics Group at Albert-Ludwigs-University in Freiburg
(Germany) and the TBI at the University of Vienna that focuses on predicting RNA-RNA interactions.
Pseudoknots (Master)
Pseudoknots help to form stable structures or support reaction pathways. As the prediction of pseudoknot is a computational hard issue.
The aim was to identify pseudoknots in the 3D structure of noncoding RNA, to classify these pseudoknots according to their topological genus,
to analyse the frequency of different classes of pseudoknots and to describe their structural features.
Publications
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Waldl, M., Beckmann, I.K., Will, S., Hofacker, I.L. (2023) Modeling Kinetics of RNA RNA Interactions in Direct Paths bioRxiv DOI: 10.1101/2023.07.28.548983 |
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Waldl, M., Spicher, T., Lorenz, R., Beckmann, I.K., Hofacker, I.L., Von Lohneysen, S., Stadler, P. (2023) Local RNA Folding Revisited Journal of Bioinformatics and Computational Biology DOI: 10.1142/S0219720023500166 |
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Gosavi, D., Wower, I., Beckmann, 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. DOI: 10.1101/2021.05.13.444024 |
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Thiel, B.C., Beckmann, I.K., Kerpedjiev, P., Hofacker, I.L. (2019) 3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements. F1000Research, 8:287 [version 2; peer review: 2 approved] DOI: 10.12688/f1000research.18458.2 |
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Weissinger, E. M., Borchers, S., Silvani, A., Provasi, E., Radrizzani, M., Beckmann, I.K., Benati, C., Schmidtke, J., Kuehnau, W., Schweier, P., Luther, S., Fernandez-Munoz, I., Beutel, G., Ciceri, F., Bonini, C., Ganser, A., Hertenstein, B., Stadler, M. (2015) Long term follow up of patients after allogeneic stem cell transplantation and transfusion of HSV-TK transduced T-cells. Frontiers in Pharmacology, 6(April), 1–9., DOI: 10.3389/fphar.2015.00076 |
Talks
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Modeling RNA-RNA interaction formation on direct paths Waldl, M., Beckmann, I.K., Will, S., Hofacker, I.L. 7th Computational Approaches to RNA Structure and Function meeting, Benasque, Spain (2022) |
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Constrained folding simulations of RNA-RNA Interaction in 3D 35nd TBI Winterseminar in Bled, Slowenia (2020) |
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RNA-RNA Interaction in 3D - Local folding simulations 17th Herbstseminar Bioinformatik in Doubice, Czech Republic (2019) |
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Trajectories of CopA-CopT under the ”CPU microscope" 34nd TBI Winterseminar in Bled, Slowenia (2019) |
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Prediction of RNA-RNA Interaction in 3D with Focus on Kissing Hairpins 16th Herbstseminar Bioinformatik in Doubice, Czech Republic (2018) |
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Identification and Classification of Pseudoknots and their Impact on RNA 3D structure prediction 33nd TBI Winterseminar in Bled, Slowenia (2018) |
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Predicting Pseudoknots in RNA 3D structures 15th Herbstseminar Bioinformatik in Doubice, Czech Republic (2017) |
Posters
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Vienna Doctoral School in Chemistry - DoSChem, Bad Waltersdorf, Austria (2022) Modelling the kinetics of RNA-RNA interaction formation Waldl, M., Beckmann, I.K., Will, S., Hofacker, I.L. |
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23nd EMBL PhD Symposium: The Big Picture: Zooming into Life, Heidelberg, Germany (2021) Modelling the formation of RNA-RNA interaction in 3D Beckmann, I.K., Waldl, M., Will, S., Hofacker, I.L. |
RNA Biology forever - Vienna RNA Meeting 2021, Vienna, Austria (2021) Waldl, M., Beckmann, I.K., Will, S., Hofacker, I.L. |
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Doctoral School of Chemistry Panel A, Seitenstetten, Austria (2021) MODELING THE KINETICS OF RNA-RNA INTERACTION FORMATION Waldl, M., Beckmann, I.K., Will, S., Hofacker, I.L. |
22nd EMBL PhD Symposium: The Roaring 20s: A New Decade for Life Sciences, Heidelberg, Germany (2020) Waldl, M., Beckmann, I.K., Will, S., Hofacker, I.L. |
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14th Microsymposium on Small RNA Biology, Vienna, Austria (2019) Coarse-Grained RNA 3D Structure Prediction with auxiliary Experimental Data Beckmann, I.K., Thiel, B.C., Hofacker, I.L. |
Austrian Swiss RNA Meeting, Fuschlsee, Austria (2019) Waldl, M., Beckmann, I.K., Will, S., Hofacker, I.L. |
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Vienna RNA Spring Meeting, Retz, Austria (2018) Identification and Classification of Pseudoknots and their Impact on RNA 3D structure prediction Beckmann, I.K., Thiel, B., Hofacker, I.L. |