Irene K. Beckmann

I am working within the field of RNA structure prediction in 3D with special interest on:

RNA-RNA Interaction

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.

RNA Pseudoknots

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

Beckmann, I.K., Waldl, M., Will, S., Hofacker, I.L. (2024)
3D feasibility of 2D RNA–RNA interaction paths by stepwise folding simulations
RNA
DOI: 10.1261/rna.079756.123

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

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

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

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

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

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)

Constrained folding simulations of RNA-RNA Interaction in 3D
35nd TBI Winterseminar in Bled, Slowenia (2020)

RNA-RNA Interaction in 3D - Local folding simulations
17th Herbstseminar Bioinformatik in Doubice, Czech Republic (2019)

Trajectories of CopA-CopT under the ”CPU microscope"
34nd TBI Winterseminar in Bled, Slowenia (2019)

Prediction of RNA-RNA Interaction in 3D with Focus on Kissing Hairpins
16th Herbstseminar Bioinformatik in Doubice, Czech Republic (2018)

Identification and Classification of Pseudoknots and their Impact on RNA 3D structure prediction
33nd TBI Winterseminar in Bled, Slowenia (2018)

Predicting Pseudoknots in RNA 3D structures
15th Herbstseminar Bioinformatik in Doubice, Czech Republic (2017)

Posters

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.

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)
Modelling RNA-RNA Interactions in 3D
Beckmann, I.K., Waldl, M., Will, S., Hofacker, I.L.

Modelling the kinetics of RNA-RNA Interaction formation
Waldl, M., Beckmann, I.K., Will, S., Hofacker, I.L.

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)
Conformation conditions of RNA-RNA interaction in 3D structure prediction
Beckmann, I.K., Waldl, M., Will, S., Hofacker, I.L.

Modeling the formation of RNA-RNA interactions
Waldl, M., Beckmann, I.K., Will, S., Hofacker, I.L.

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)
Prediction of RNA-RNA Interaction in 3D
Beckmann, I.K., Waldl, M., Will, S., Hofacker, I.L.

Fast Analysis of RNA-RNA Interaction Kinetics for Refining RNA TargetingScreens
Waldl, M., Beckmann, I.K., Will, S., Hofacker, I.L.

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.

Activities at the University of Vienna

since 2020
ID*A – Initiative Doktorandinnen* Austausch
self-organized mentoring, group coaching, training & expert talks

Theoretical Biochemistry Group

Institute for Theoretical Chemistry