Ronny Lorenz

Salt corrections for RNA secondary structures in the ViennaRNA package

The paper updates the ViennaRNA package to include salt corrections for RNA secondary structure prediction, improving accuracy under varying ion concentrations.

DrTransformer: Heuristic cotranscriptional RNA folding using the nearest neighbor energy model

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

Caveats to deep learning approaches to RNA secondary structure prediction

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

RNAxplorer: Harnessing the Power of Guiding Potentials for Sampling RNA Landscapes

RNAxplorer improves RNA structure sampling by using guiding potentials to explore underrepresented regions, producing more diverse and representative samples.

CUDA RNAfold

The paper modifies RNAfold to run on CUDA GPUs, enabling parallel computation of RNA secondary structures with up to 14 times speedup on GPUs compared to a GPGPU Tesla.

SHAPE directed RNA folding

The paper introduces a method for RNA structure prediction using SHAPE reactivities integrated with thermodynamics-based algorithms in the viennaRNA Package.

A guide to computational cotranscriptional folding featuring the SRP RNA

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.