37 citations · 123 across the 13 of their papers we have counts for
14 papers
RNAmountAlign: efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment
Amir H. Bayegan, Peter Clote
Alignment of structural RNAs is an important problem with a wide range of applications. Since function is often determined by molecular structure, RNA alignment programs should tak…
Small-world networks and RNA secondary structures
Defne Surujon, Yann Ponty, Peter Clote
Let Sn denote the network of all RNA secondary structures of length n, in which undirected edges exist between structures s, t such that t is obtained from s by the addition, remov…
On the scale-free nature of RNA secondary structure networks
Peter Clote
A network is scale-free if its connectivity density function is proportional to a power-law distribution. Scale-free networks may provide an explanation for the robustness observed…
Minimum length RNA folding trajectories
Amir H. Bayegan, Peter Clote
The Kinfold and KFOLD programs for RNA folding kinetics implement the Gillespie algorithm to generate stochastic folding trajectories from an initial structure s to a target struct…
RNA folding kinetics using Monte Carlo and Gillespie algorithms?
Peter Clote, Amir H. Bayegan
RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra p…
RNAiFold2T: Constraint Programming design of thermo-IRES switches
Juan Antonio Garcia-Martin, Ivan Dotu, Javier Fernandez-Chamorro +4
Motivation: RNA thermometers (RNATs) are cis-regulatory ele- ments that change secondary structure upon temperature shift. Often involved in the regulation of heat shock, cold shoc…