Michael T. Wolfinger

This study designs functional exoribonuclease-resistant RNAs using a mechanics-aware approach, achieving wild-type efficiency without sequence similarity to known xrRNAs.

The paper maps RNA secondary structure ensembles in living E. coli cells, identifying conserved structural elements and cold shock-responsive RNA thermometers.

KinPFN approximates RNA folding kinetics using prior-data fitted networks, achieving fast and accurate predictions with synthetic data training.

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 updates the phylogeny of Chikungunya virus and identifies lineage-specific RNA architecture in its untranslated regions.

The paper introduces bi-alignments to model incongruent evolution of RNA sequence and structure, showing they are a special case of 4-way alignments and finding such incongruence is not rare in the Rfam database.

The paper analyzes Musashi binding elements in Zika and related Flavivirus 3’UTRs using a thermodynamic model to show ZIKV MBEs are maximally accessible and linked to neurotropism.

The paper uses comparative genomics to analyze 3’UTR RNA structures in flaviviruses, identifying conserved xrRNAs and duplicated structures across different viral groups.

The paper identifies 27 new telomerase RNAs in Saccharomycetacea but finds that most Saccharomycotina genomes lack annotated telomerase RNA due to sequence variability.

The paper introduces an efficient method to model co-transcriptional RNA-ligand interaction dynamics, exemplified with a riboswitch from Mesoplasma florum.

This paper describes an in silico workflow for designing RNA switches that change structure in response to ligands, using a theophylline aptamer as an example.

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