Publications & Research
Peer-reviewed work at the intersection of RNA biology, computational structural biology, and machine learning.
The research underpinning RNA Design's consulting practice is active and ongoing. Publications below represent peer-reviewed work from Michael T. Wolfinger's group at the University of Vienna.
Active Research Directions
Publications
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2026
Rational design of mechanically active RNAs: de novo engineering of functional exoribonuclease-resistant RNAs
This paper reports the rational, de novo engineering of functional exoribonuclease-resistant RNAs (xrRNAs), establishing sequence–structure design principles that link mechanical RNA topology to XRN1 resistance and expanding the toolkit for programmable synthetic RNA biology.
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2025
Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis
This paper reports the discovery of conserved RNA regulatory switches in living cells by integrating RNA secondary structure ensemble mapping with covariation analysis, revealing structural elements that control gene expression at the RNA level.
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2025
From structure to function: Computational insights into Musashi-RNA complexes in the context of viral pathogenesis
This paper reviews computational and structural insights into Musashi–RNA complexes, emphasising how Musashi proteins interact with viral RNAs to modulate replication and pathogenesis, and exploring implications for antiviral strategies and synthetic biology.
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2025
KinPFN: Bayesian approximation of RNA folding kinetics using prior-data fitted networks
This paper presents KinPFN, a deep-learning method based on prior-data fitted networks that approximates RNA folding-time distributions from only a few simulated examples, enabling orders-of-magnitude faster and accurate modelling of RNA folding kinetics and related biological processes.
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2025
Bayesian approximation of RNA folding times
This paper highlights the methodological foundations of KinPFN by detailing its synthetic prior design and in-context learning strategy, and demonstrates how these innovations enable rapid, accurate approximation of RNA folding-time distributions as a lightweight extension to existing kinetic simulators.
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2024
Pan-flavivirus analysis reveals sfRNA-independent, 3’UTR-biased siRNA production from an insect-specific flavivirus
This paper shows that mosquito-specific flaviviruses, such as Kamiti River virus, exploit their unusually long RNA tail to drive a distinct small-RNA immune reaction in mosquitoes, pointing to a novel way these viruses interact with insect hosts.