RNA structure prediction
Predicting RNA secondary structure and the full Boltzmann ensemble, and mapping structure in living cells. This is the methodological core the other areas build on.
Borovská et al., Nature Biotechnology (2025)
ViennaRNA · RNAConSnake
University of Groningen · University of Vienna (TBI)
Active
RNA engineering
Rational, de novo design of RNAs with defined mechanical and functional properties, turning sequence and structure principles into programmable molecules.
Walter et al., Nucleic Acids Res. (2026)
ViennaRNA design routines
Leipzig University · University of Vienna (TBI)
Active
Functional RNAs
Identifying RNA elements that regulate gene expression, riboswitches and structured regulatory motifs, and the covariation signatures that reveal them.
Mrozovich et al., Nucleic Acids Res. (2023) · Borovská et al., Nature Biotechnology (2025)
RNAConSnake · covariation analysis
University of Lethbridge · University of Groningen
Active
Viral RNA biology
Structured RNA in RNA viruses: subgenomic flaviviral RNAs, protein RNA recognition in pathogenesis, and the discovery of novel viruses.
Besson et al., J. Virology (2024) · Wang et al., J. Gen. Virology (2024) · Darai et al., ScienceAsia (2025)
Structure & covariation toolchain
Radboud University Nijmegen · The University of Queensland · Chulalongkorn University
Continuing
RNA evolution
Reading evolutionary signal in RNA, covariation as evidence of conserved structure, and phylogenetic placement of newly discovered viral clades.
McBroome et al., Nature Microbiol. (2024) · Wang et al., J. Gen. Virology (2024)
Nextstrain resources · ViennaRNA covariation analysis
University of California Santa Cruz · The University of Queensland
Continuing
RNA folding kinetics
How RNA folds over time, not just where it lands. Approximating folding time distributions fast enough to be used routinely alongside structure prediction.
Scheuer et al., ICLR '25
KinPFN
University of Freiburg · University of Vienna (TBI)
Active
Computational methods
Method development where it accelerates a well defined RNA analysis problem, prior data fitted networks, in-context learning, and reproducible workflows.
Scheuer et al., ICLR '25 & AI for Nucleic Acids Workshop (2025)
KinPFN · RNAConSnake
University of Freiburg · University of Vienna (TBI)
Active
RNA protein recognition
Structure-guided analysis of how proteins recognise RNA, including modelling and refinement workflows applied to viral RNA protein complexes.
Darai et al., Bull. Chem. Soc. Jpn (2023) · Darai et al., ScienceAsia (2025)
Molecular modelling workflows
Chulalongkorn University · University of Vienna
Continuing
The evidence for each theme sits in the publication record.