Section: New Results

RNA design

In a paper published in Algorithmica [6], we have shown that our previous results  [30] hold for more sophisticated energy models where base-pairs are associated with arbitrary energy contributions. This result, which required a complete overhaul of our previous proofs (e.g. using arguments based on graph coloring), allows us to foresee an extension of (at least some of) our results to state-of-the-art models, such as the Turner energy model.

In collaboration with Danny Barash's group at Ben-Gurion university (Israel), we contributed a review of existing tools and techniques for RNA design, which was published in Briefings in Bioinformatics series [3].

Finally, in a paper [14] recently accepted for a presentation at the prestigious RECOMB'18 conference, we revisited the problem of generating at random an RNA sequence which is simultaneously compatible with a set of target secondary structures. This problem was previously addressed by our collaborators at the TBI Vienna/Univ. Leipzig, using an exponential-time algorithm. We established the #P-hardness of the problem, and its inapproximibility in general. However, the problem is still amenable to an efficient parametrization, and we proposes an FTP algorithm named RNARedPrint based on the tree decomposition for the random generation, to which we adapted a multidimensionnal Boltzmann sampling technique in order to gain (probabilistic) control over secondary features such as the GC%, the relative free-energy of the various structures...