The design of an RNA sequence v that encodes an input target protein sequence w is a
crucial aspect of messenger RNA (mRNA) vaccine development. There are an exponential …

Formation of base pairs between the nucleotides of a ribonucleic acid (RNA) sequence
gives rise to a complex and often highly branched RNA structure. While numerous studies …

We propose a new deterministic methodology to predict the secondary structure of RNA
sequences. What information of stem is important for structure prediction, and is it enough …

Minimum free energy prediction of RNA secondary structures is based on the Nearest
Neighbor Thermodynamics Model. While such predictions are typically good, the accuracy …

Myriad viruses use positive-strand RNA molecules as their genomes. Far from being only a
repository of genetic material, viral RNA performs numerous other functions mediated by its …

The branching of an RNA molecule is an important structural characteristic yet difficult to
predict correctly, especially for longer sequences. Using plane trees as a combinatorial …

We propose a new deterministic methodology to predict RNA sequence and protein folding.
Is stem enough for structure prediction? The main idea is to consider all possible stem …

Estimation of distribution algorithms (EDAs) are successfully applied in the fields of
bioinformatics for tasks such as gene structure analysis, protein structure prediction, and …