Secondary structure plays an important role in determining the function of noncoding RNAs.
Hence, identifying RNA secondary structures is of great value to research. Computational …

RNA secondary structures have proven essential for understanding the regulatory functions
performed by RNA such as microRNAs, bacterial small RNAs, or riboswitches. This success …

Abstract The Vienna RNA Websuite is a comprehensive collection of tools for folding, design
and analysis of RNA sequences. It provides a web interface to the most commonly used …

Motivation: For several decades, free energy minimization methods have been the dominant
strategy for single sequence RNA secondary structure prediction. More recently, stochastic …

The ViennaRNA package is a widely used collection of programs for thermodynamic RNA
secondary structure prediction. Over the years, many additional tools have been developed …

The coarse graining method to be advocated in this paper consists of two main steps. First,
the propagation of an ensemble of molecular states is described as a Markov chain by a …

We have developed a hidden Markov model and optimization procedure for photon-based
single-molecule FRET data, which takes into account the trace-dependent background …

RNA aptamers are ribonucleic acids that bind to specific target molecules. An RNA aptamer
for a disease-related protein has great potential for development into a new drug. However …

Gene repression induced by the formation of transcriptional terminators represents a prime
example for the coupling of RNA synthesis, folding, and regulation. In this context, map** …

We introduce here a heuristic approach to kinetic RNA folding that constructs secondary
structures by stepwise combination of building blocks. These blocks correspond to …