AtomSurf: Surface Representation for Learning on Protein Structures.
V Mallet, S Attaiki, M Ovsjanikov

Semi-supervised learning and large-scale docking data accelerate RNA virtual screening.
JG Carvajal-Patino, V Mallet, D Becerra, LF Nino, C Oliver, J Waldispuhl
preprint code

Finding Antibodies in Cryo-EM densities with CrAI.
V Mallet, C Rapisarda, H Minoux, M Ovsjanikov

Approximate network motif mining via graph learning
C Oliver, D Chen, V Mallet, P Philippopoulos, K Borgwardt

Leveraging binding-site structure for drug discovery with point-cloud methods.
Vincent Mallet, Carlos G Oliver, Nicolas Moitessier, and Jerome Waldispuhl.


AlignScape, displaying sequence similarity using self-organizing maps.
Isaac Filella-Merce, Vincent Mallet, Eric Durand, Michael Nilges, Guillaume Bouvier, Riccardo Pellarin.
In Frontiers in Bioinformatics, 2024
paper code

InDeep: 3D fully convolutional neural networks to assist in silico drug design on protein-protein interactions.
Vincent Mallet, Luis Checa Ruano, Alexandra Moine Franel, Michael Nilges, Karen Druart, Guillaume Bouvier, and Olivier Sperandio.
In Bioinformatics, 2022
paper code

RNAglib: A python package for RNA 2.5D graphs.
Vincent Mallet, Carlos Oliver, Jonathan Broadbent, William L Hamilton, and Jérôme Waldispühl.
In Bioinformatics Application Notes, 2022
paper code webpage documentation pip

Reverse-complement equivariant networks for DNA sequences.
Vincent Mallet and Jean-Philippe Vert.
In Advances in Neural Information Processing Systems (NeurIPS), 2021
paper code pip

VeRNAl: A Tool for Mining Fuzzy Network Motifs in RNA.
Carlos Oliver, Vincent Mallet∗, Pericles Philippopoulos, William L Hamilton, and Jérôme Waldispühl.
In Bioinformatics, 2021
paper code

OptiMol: Optimization of binding affinities in chemical space for drug discovery. Jacques Boitreaud, Vincent Mallet∗, Carlos Oliver, and Jérome Waldispuhl.
In Journal of Chemical Information and Modeling, 2020
paper code

quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories. Vincent Mallet, Michael Nilges, and Guillaume Bouvier.
In Bioinformatics, 2020
paper code pip

Augmented base pairing networks encode RNA-small molecule binding preferences.
Carlos Oliver, Vincent Mallet, Roman Sarrazin Gendron, Vladimir Reinharz, William L Hamilton, Nicolas Moitessier, and Jérome Waldispuhl.
In Nucleic Acids Research (NAR), 2020
paper code webserver