Ivo L. Hofacker

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

The paper introduces a multiscale pipeline using SAXS data and computational models to determine RNA 3D structures from low-resolution to atomistic precision.

The paper develops tRAM-seq to study tRNA expression and modification during zebrafish embryo development, revealing a reprogramming of the tRNA pool around gastrulation.

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

The paper introduces a targeted RNA-RNA interaction kinetics model to analyze kinetic properties of RNA-RNA interactions and identifies key features that influence interaction formation.

The paper identifies microRNA-mediated interference with RNA stem-loop structures as a novel mechanism regulating alternative splicing across the transcriptome.

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.

This study optimizes the coding sequence of the human VDAC membrane protein to enhance cell-free expression by analyzing translation initiation factors and developing a scoring function for expression prediction.

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

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

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.