Ryszard Kierzek

Longer Is Not Always Better: Effects of Equilibration Length on Umbrella Sampling Estimations for RNA Hairpin Folding Stabilities

This study shows that longer equilibration times in umbrella sampling can alter free energy landscapes and reduce agreement with experimental data for RNA hairpin folding.

Nearest Neighbor Parameters for Estimating RNA Folding Stability with In Vivo-like Conditions

The paper develops a new RNA folding model using in vivo-like ionic conditions, improving tRNA structure prediction but showing minimal overall impact on secondary structure predictions.

Pan-cancer discovery of driver mutations in long noncoding RNAs reveals widespread functional rewiring of RNA regulatory elements

The paper identifies 121 lncRNA driver mutations across 19 cancer types using 12,631 genomes, showing mutations disrupt RNA-binding protein interactions to promote oncogenesis.

Nearest Neighbor Parameters for Estimating the Folding Stability of RNA Including Pseudouridine

This paper presents nearest neighbor parameters for estimating RNA folding stability with pseudouridine, derived from optical melting experiments, and demonstrates their application in modeling RNA secondary structures.

RNA Folding Nearest Neighbor Parameters Including the Modification 1-Methyl-Pseudouridine

This paper develops new RNA folding nearest neighbor parameters for sequences containing 1-methyl-pseudouridine, showing it stabilizes RNA folding and improves tRNA ensemble modeling.

Accurate in silico predictions of modified RNA interactions to a prototypical RNA-binding protein with {lambda}-dynamics

This paper uses {lambda}-dynamics to predict RNA binding preferences of human Pumilio, including modified RNAs, showing high accuracy compared to experimental data.

Short 2'-O-methyl/LNA oligomers as highly-selective inhibitors of miRNA production in vitro and in vivo

This paper develops 2'-OMe/LNA oligonucleotides to selectively inhibit specific miRNA precursors, demonstrating in vitro and in vivo target selectivity for miRNA family members.

Secondary Structure Prediction for RNA Sequences Including N6-methyladenosine

The paper introduces updated RNA secondary structure prediction tools and parameters for N6-methyladenosine, enabling analysis of modified RNA structures.

Secondary structure of subgenomic RNA M of SARS-CoV-2

This study determines the secondary structure of SARS-CoV-2 subgenomic RNA M through in vitro probing, revealing features important for its function and potential therapeutic applications.