Publications

Publications

A Comprehensive Library for RNA Structure-Function Modeling Luis Wyss, Vincent Mallet, Wissam Karroucha*, Karsten Borgwardt, Carlos Oliver ICLR Workshop AI4NA preprint

AtomSurf: Surface Representation for Learning on Protein Structures.
Vincent Mallet∗, Souhaib Attaiki∗, Yangyang Miao∗, Bruno Correia, and Maks Ovsjanikov.
In ICLR 2025
paper

Structure-based rna drug discovery with deep-learning assisted virtual screening.
Juan Guillermo Carvajal Patiño∗, Vincent Mallet∗, David Becerra, Luis Fernando Niño, Carlos Oliver, and Jérôme Waldispühl.
In Nature Communications, 2025
paper code

Indeepnet: a web platform for predicting functional binding sites in proteins using indeep.
Fabien Mareuil, Rachel Torchet, Luis Checa Ruano, Vincent Mallet, Michael Nilges, Guillaume Bouvier, and Olivier Sperandio.
In Nucleic Acids Research 2025
paper

Finding Antibodies in Cryo-EM densities with CrAI.
Vincent Mallet, Chiara Rapisarda, Hervé Minoux, Maks Ovsjanikov
In Bioinformatics, 2025
paper

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

Preprints

Approximate network motif mining via graph learning
Carlos Oliver, Dexiong Chen, Vincent Mallet, Pericles Philippopoulos, Karsten Borgwardt
preprint

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