Author

David H. Mathews

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Open access Sep 2026

Markov models of SHAPE data improve secondary structure prediction

It is shown that discretized SHAPE data display context dependence within loop regions and within stem regions and Markov models are used to formally capture such dependencies and demonstrates that finer modeling of SHAPE data has the potential to push the limits of data-guided secondary structure prediction.

Yi-Fan Yang, David H. Mathews, Sharon Aviran · bioRxiv · 0 citations

Open access Sep 2026

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

A new model in Advanced Dulbecco's Modified Eagle Medium, which mimics mammalian extracellular ionic composition, is developed, which provides RNA folding parameters for helical base stacks and loop motifs and improves the biological relevance of RNA secondary structure predictions and establishes a foundation for stud...

Olivia M. Hiltke, E. Kierzek, Martina Prochota et al. · bioRxiv · 0 citations