Publications

2026

A spectral framework for measuring diversity in multiple sequence alignments

Vaitea Opuu
PLoS Computational Biology paper

D-LIM: A neural network for interpretable gene–gene interactions

Shuhui Wang, Alexandre Allauzen, Philippe Nghe, Vaitea Opuu
PLoS Computational Biology paper

Ligand-based machine learning models to classify active compounds for prostaglandin EP2 receptor

Paul Dupuyds, Anita Rayar, Vaitea Opuu, Camille Lescanne, Shuhui Wang, J.P. Annereau, Philippe Nghe, Luis Briseño-Roa
Scientific Reports paper

2025

A guide for active learning in synergistic drug discovery

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

Exploring the space of self-reproducing ribozymes using generative models

Camille N. Lambert, Vaitea Opuu, Francesco Calvanese, Polina Pavlinova, Francesco Zamponi, Eric J. Hayden, Martin Weigt, Matteo Smerlak, Philippe Nghe
Nature Communications paper

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

2023

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 Méchulam, Emmanuelle Schmitt, Thomas Simonson
Protein Science paper

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, Lluís Quintana‐Murci, Tatsuhiko Ozawa, Sylvie van der Werf, Philippe Nghe, Nadia Naffakh, Andrew D. Griffiths, Catherine Isel
Proceedings of the National Academy of Sciences paper

2022

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

Vaitea Opuu, Nono S. C. Merleau, Vincent Messow, Matteo Smerlak
PLoS Computational Biology paper

2021

Computational Design of PDZ-Peptide Binding

Nicolas Panel, Francesco Della Villa, Vaitea Opuu, David Mignon, Thomas Simonson
Methods in molecular biology book chapter

Knowledge-Based Unfolded State Model for Protein Design

Vaitea Opuu, David Mignon, Thomas Simonson
Methods in molecular biology book chapter

2020

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

Vaitea Opuu, Giuliano Nigro, Thomas Gaillard, Emmanuelle Schmitt, Yves Méchulam, Thomas Simonson
PLoS Computational Biology paper

Physics-Based Computational Protein Design: An Update

David Mignon, Karen Druart, Eleni Michael, Vaitea Opuu, Savvas Polydorides, Francesco Della Villa, Thomas Gaillard, Nicolas Panel, Georgios Archontis, Thomas Simonson
The Journal of Physical Chemistry A 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, Melissa S. 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 Virginia Ruiz Cuevas, Mariam Sissoko, Nicolas Sompairac, Audrey Vallerix, Violaine Verrecchia, Marc Delarue, Raphaël 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, Élodie 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