NUMEV MIPS Seminar: “RNA Design: Challenging but Exemplary in Its Combinatorial Nature”

The NUMEV Seminars are open to a wide audience of students and researchers from all disciplines who wish to learn more about the current research areas of the NUMEV-MIPS community (Mathematics, Computer Science, Physics, and Systems) or about opportunities to develop their skills and expertise.

RNA Design: Challenging but Exemplary in Its Combinatorial Nature

Yann Ponty
, Research Director at the CNRS – LIX, École Polytechnique, and Institut Polytechnique de Paris.

RNA design is a field of computational biology that aims to generate RNA sequences designed to perform a specific function. Design aims to achieve a wide variety of objectives, such as: encoding a given amino acid sequence; optimizing translation levels; avoiding degradation by nucleases; exposing specific recognition sites for interaction with partners; adopting alternative conformations depending on the presence or absence of metabolites. From a computational perspective, RNA design can generally be approached as a search/random generation of sequences that contain or avoid specific motifs, are compatible with one or more structures, or adopt a predefined structure as a unique energy-minimizing conformation (also known as inverse folding).  Most of the associated problems are difficult in the sense of complexity theory ((NP/#P)-hard), but are highly relevant in practice and undoubtedly deserve to be addressed from the perspective of the science of society.

In this presentation, I will provide an overview of the field and discuss the relevance of key computational challenges in the context of healthcare and synthetic biology. This work is based on numerous collaborations, including (but not limited to) Danny Barash, Théo Boury, Laurent Bulteau, Cédric Chauve, Alain Denise, Stefan Hammer, Alice Héliou, Jan Manuch, Bertrand Marchand, Ladislav Stacho, Wei Wang, Sebastian Will, and Hua-Ting Yao…