Publications

2025

Hybrid Generative Model: Bridging Machine Learning and Biophysics to Expand RNA Functional Diversity

Vaitea Opuu
bioRxiv preprint

A Guide for Active Learning in Synergistic Drug Discovery

Shuhui Wang, Alexandre Allauzen, Philippe Nghe, Vaitea Opuu
Scientific Reports article

2024

Global regulators enable bacterial adaptation to a phenotypic trade-off

Matthew Deyell, Vaitea Opuu, Andrew D Griffiths, Sander J Tans, Philippe Nghe
iScience paper

Expanding the space of self-reproducing ribozymes using probabilistic generative models

Camille N Lambert, Vaitea Opuu, Francesco Calvanese, Francesco Zamponi, Eric Hayden, Martin Weigt, Matteo Smerlak, Philippe Nghe
bioRxiv preprint

Hypothesis-driven interpretable neural network for interactions between genes

Shuhui Wang, Alexandre Allauzen, Philippe Nghe, Vaitea Opuu
bioRxiv preprint

2023

High-throughput droplet-based analysis of influenza A virus genetic reassortment by single-virus RNA sequencing

Kuang-Yu Chen, Jayaprakash Karuppusamy, Mary B O’Neill, Vaitea Opuu, Mathieu Bahin, Sophie Foulon, Pablo Ibanez, Lluis Quintana-Murci, Tatsuhiko Ozawa, Sylvie van der Werf, Philippe Nghe, Nadia Naffakh, Andrew Griffiths, Catherine Isel
Proceedings of the National Academy of Sciences paper

Enzyme redesign and genetic code expansion

Vaitea Opuu, Thomas Simonson
Protein Engineering, Design and Selection paper

Redesigning methionyl‐tRNA synthetase for β‐methionine activity with adaptive landscape flattening and experiments

Vaitea Opuu, Giuliano Nigro, Christine Lazennec‐Schurdevin, Yves Mechulam, Emmanuelle Schmitt, Thomas Simonson
Protein Science paper

2022

RAFFT: Efficient prediction of RNA folding pathways using the fast Fourier transform

Vaitea Opuu, Nono SC Merleau, Vincent Messow, Matteo Smerlak
PLOS Computational Biology paper

Investigating graph neural network for RNA structural embedding

Vaitea Opuu, Hélène Bret
Machine Learning for Structural Biology Workshop, NeurIPS 2022 conference

Knowledge-Based Unfolded State Model for Protein Design

Vaitea Opuu, David Mignon, Thomas Simonson
Computational Peptide Science chapter

2021

Computational Design of PDZ-Peptide Binding

Nicolas Panel, Francesco Villa, Vaitea Opuu, David Mignon, Thomas Simonson
PDZ Mediated Interactions: Methods and Protocols chapter

2020

Physics-Based Computational Protein Design: An Update

David Mignon, Karen Druart, Eleni Michael, Vaitea Opuu, Savvas Polydorides, Francesco Villa, Thomas Gaillard, Nicolas Panel, Georgios Archontis, Thomas Simonson
The Journal of Physical Chemistry A paper

Adaptive landscape flattening allows the design of both enzyme: Substrate binding and catalytic power

Vaitea Opuu, Giuliano Nigro, Thomas Gaillard, Emmanuelle Schmitt, Yves Mechulam, Thomas Simonson
PLoS computational biology paper

A physics-based energy function allows the computational redesign of a PDZ domain

Vaitea Opuu, Young Joo Sun, Titus Hou, Nicolas Panel, Ernesto J Fuentes, Thomas Simonson
Scientific Reports paper

2018

Meet-U: educating through research immersion

Nika Abdollahi, Alexandre Albani, Eric Anthony, Agnes Baud, Mélissa Cardon, Robert Clerc, Dariusz Czernecki, Romain Conte, Laurent David, Agathe Delaune, Samia Djerroud, Pauline Fourgoux, Nadège Guiglielmoni, Jeanne Laurentie, Nathalie Lehmann, Camille Lochard, Rémi Montagne, Vasiliki Myrodia, Vaitea Opuu, Elise Parey, Lélia Polit, Sylvain Privé, Chloé Quignot, Maria Ruiz-Cuevas, Mariam Sissoko, Nicolas Sompairac, Audrey Vallerix, Violaine Verrecchia, Marc Delarue, Raphael Guérois, Yann Ponty, Sophie Sacquin-Mora, Alessandra Carbone, Christine Froidevaux, Stéphane Le Crom, Olivier Lespinet, Martin Weigt, Samer Abboud, Juliana Bernardes, Guillaume Bouvier, Chloé Dequeker, Arnaud Ferré, Patrick Fuchs, Gaëlle Lelandais, Pierre Poulain, Hugues Richard, Hugo Schweke, Elodie Laine, Anne Lopes
PLoS computational biology paper

2017

Computational design of fully overlapping coding schemes for protein pairs and triplets

Vaitea Opuu, Martin Silvert, Thomas Simonson
Scientific reports paper