NUMEV MIPS Seminar “RNA Design: Difficult but Exemplary Combinatorial”

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: Difficult but exemplary combinatorial

Yann Ponty
Research Director CNRS – LIX, Ecole Polytechnique, Institut Polytechnique de Paris.

RNA design is a discipline of computational biology that aims to produce RNA sequences targeting a predefined function. The design has a wide variety of objectives, for example: encoding a given amino acid sequence; optimizing translation levels; escaping 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 random search/generation of sequences that present/avoid motifs, are compatible with one or more structures, or adopt a predefined structure as a single energy-minimizing conformation (aka reverse 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 a societal science perspective.

In this presentation, I will provide an overview of the field and the relevance of key computational problems in the context of health and synthetic biology. This work is based on multiple 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, Hua-Ting Yao...