Theoretical Biochemistry Group

Institute for Theoretical Chemistry

Font size: Increase font size Decrease font size Switch style sheet from default to highcontrast and back

Irene K. Beckmann

Irene_K_Beckmann

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

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: doi.org/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

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

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.

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.