Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery. - Felipe Merino; Benjamin Bouvier; Vlad Cojocaru (PLoS Comput. Biol., 2015)

Optimizing the Multivalent Binding of the Bacterial Lectin LecA by Glycopeptide Dendrimers for Therapeutic Purposes. - Benjamin Bouvier (J. Chem. Inf. Model., 2016)

Paradiseo: from a modular framework for evolutionary computation to the automated design of metaheuristics: 22 years of Paradiseo. - Johann Dréo; Arnaud Liefooghe; Sébastien Vérel; Marc Schoenauer; Juan Julián Merelo Guervós; Alexandre Quemy; Benjamin Bouvier; Jan Gmys (GECCO Companion, 2021)

Protein-Protein Interface Topology as a Predictor of Secondary Structure and Molecular Function Using Convolutional Deep Learning. - Benjamin Bouvier (J. Chem. Inf. Model., 2021)

A Comparison of Two Decoupled Methods for Simultaneous Multiple Robots Path Planning. - Benjamin Bouvier; Julien Marzat (DARS, 2022)

Substituted Oligosaccharides as Protein Mimics: Deep Learning Free Energy Landscapes. - Benjamin Bouvier (J. Chem. Inf. Model., 2024)