Stefan Badelt

The paper introduces fuzzyfold, a Rust-based software framework for stochastic RNA folding kinetics, enabling efficient simulation of long RNA molecules and flexible model integration.

The paper introduces DrTransformer, a deterministic algorithm for simulating cotranscriptional RNA folding, capable of handling RNAs longer than 200 nucleotides.

This paper evaluates deep learning models for RNA secondary structure prediction, highlighting their limitations and showing they cannot fully capture RNA structure properties.

The paper presents computational methods to simulate cotranscriptional RNA folding, applying them to the E. coli SRP RNA to infer metastable structures and their timing during transcription.